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The cloud forest species Meriania macrophylla (Benth.) Triana has pseudocampanulate flowers with bulbous stamen appendages, typical for the passerine pollination syndrome found in the Melastomataceae tribe Merianieae. The species is further characterized by strong stamen dimorphism (heteranthery), a condition otherwise associated with pollen‐rewarding bee‐pollinated species (both in Melastomataceae and beyond). In passerine‐pollinated Merianieae, however, flowers usually only show weak stamen dimorphism. Here, we conducted field and laboratory investigations to determine the pollinators of M. macrophylla and assess the potential role of strong heteranthery in this species. Our field observations in Costa Rica confirmed syndrome predictions and indeed proved pollination by passerine birds in M. macrophylla. The large bulbous set of stamens functions as a food‐body reward to the pollinating birds, and as trigger for pollen release (bellows mechanism) as typical for the passerine syndrome in Merianieae. In contrast to other passerine‐pollinated Merianieae, the second set of stamens has seemingly lost its rewarding and pollination function, however. Our results demonstrate the utility of the pollination syndrome concept even in light of potentially misleading traits such as strong heteranthery., We tested the concept of pollination syndromes by investigating the tropical tree species Meriania macrophylla. In a previous study, this species had been predicted as passerine pollinated based on bulbous stamen appendages serving as nutritive food‐body reward for passerines. We confirm this prediction through field investigations and show that pollination syndromes are a useful concept if system specific floral functional traits are considered.

Aluminum (Al) toxicity on acid soils adversely affects maize yields, which can be overcome by combining soil amendments with genetic tolerance. In maize, ZmMATE1 confers Al tolerance via Al-activated citrate release, whereby citrate forms non-toxic complexes with Al3+ in the rhizosphere. Here, we investigated Al tolerance mechanisms in maize germplasm originated from Kenya based on quantitative trait loci (QTL) mapping. Five QTLs and four epistatic interactions explained ~51% of the phenotypic variation for Al tolerance. The lack of Al tolerance QTL on chromosome 6 and the much lower expression of ZmMATE1 in both Kenyan lines than in Cateto Al237, which donates the superior allele of ZmMATE1, strongly indicate that this gene does not play a significant role in Al tolerance in neither parent. In turn, maize homologs to genes previously implicated in Al tolerance in other species, ZmNrat1, ZmMATE3, ZmWRKY and ZmART1, co-localized with Al tolerance QTL and were more highly expressed in the parent that donate favorable QTL alleles. However, these candidate genes will require further studies for functional validation on maize Al tolerance. The existence of Al tolerance mechanisms independent from ZmMATE1 suggests it is possible to develop highly Al tolerant cultivars by pyramiding complementary Al tolerance genes in maize.

Buriti (Mauritia flexuosa L.f), a palm tree native to South America and widely distributed in Brazil, displays significant ecological, economic and biotechnological importance. However, the disorderly extractivism and environmental degradation of its endemic areas are leading to reductions in, and/or extinction of the buriti palm tree, causing ecological imbalance with significant economic losses for rural communities and genetic diversity. Consequently, populational genetic diversity studies have become relevant as a strategy for conserving the species. Therefore, this study evaluated the genetic structure of 10 populations from the Lençóis Maranhenses region, in the state of Maranhão, Brazil, using microsatellite markers. Results indicated that eight pairs displayed a high level of polymorphism in the populations evaluated (98.5 %). The genetic diversity estimations allowed for identifying 220 alleles (average of 9.5 alleles/loci), and the heterozygosity averages observed (Ho) were lower than the heterozygosity expected (He) in the population (0.16 and 0.64) and loci levels (0.15 and 0.65), respectively. The Shannon Index (I) mean value of 1.36 indicated high diversity and genotypic richness in the populations evaluated, while the population index (FST) indicated a low value (0.05) and the fixation index pertaining to individuals indicated a high value (FIS = 0.79) exhibiting a moderate population distribution structure, and pointing to greater diversity between individuals. Based on these results, populations denominated as PA and PB presented a high genetic similarity (0.219), while populations denominated as PF and PJ exhibited more distant genetic characteristics (0.519). These results can be correlated based on prioritization of conservation of this non?domesticated species, influenced by environmental characteristics, suggesting that the genetic diversity found should be conserved in a germplasm bank, and subsequently exploited in breeding programs. Made available in DSpace on 2021-09-21T18:00:26Z (GMT). No. of bitstreams: 1 Genetic-structure.pdf: 1206206 bytes, checksum: 9a45c1a449e30e27d10e18360709b413 (MD5) Previous issue date: 2022

A embriogênese somática indireta (ESI) em Coffea canephora e Coffea eugenioides tem sida estabelecida e comparada durante a formação de calos e regeneração de embriões somáticos, evidenciando que essas espécies exibem a mesma resposta in vitro. No entanto, diferenças intraespecíficas em relação às respostas da ESI também foram relatadas. A ESI é influenciada por aspectos genéticos e fisiológicos. Nossos objetivos foram: (a) induzir a ESI em C. canephora e C. eugenioides; (b) identificar e quantificar os níveis endógenos do ácido indol-3-acético (IAA), zeatina (Z) e ácido giberélico GA 3 e GA 4 durante a indução de calo; e (c) determinar o número de cópias gênicas de AUX/IAA33 e YUC4 que estão envolvidos na via biosintética da auxina, e de WOX4 e LEC1 que estão envolvidos na via morfogênica. Utilizando cromatografia líquida acoplada à espectrometria de massas (LC-MS), a identificação e quantificação de IAA, GA 3 , GA 4 e Z foram realizadas em ambos os Coffea. Através da hibridação in situ por fluorescência (FISH), foi verificado o número de cópias dos genes AUX/IAA33, YUC4, WOX4 e LEC1. A ESI foi estabelecida para C. canephora e C. eugenioides, os quais exibiram a mesma resposta in vitro. No entanto, os dois Coffea diferiram em relação aos níveis dos hormônios endógenos, com exceção de IAA aos 90 dias. Essas espécies possuem duas cópias gênicas de AUX/IAA33, YUC4, WOX4 e LEC1, corroborando para sua diploidia. Portanto, nossos resultados mostram que C. canephora e C. eugenioides diferem no aspecto fisiológico, mas não no aspecto genético aqui investigado. Desse modo, nossos dados contribuem para a base do entendimento da resposta in vitro e para o aprimoramento dos procedimentos de propagação. Palavras-chave: Café. Cultura de Tecidos Vegetais. Regeneração in vitro. Embrião Somático. Genética. Fisiologia Vegetal Coffea canephora and Coffea eugenioides indirect somatic embryogenesis (ISE) has been established and compared during callus formation and somatic embryo regeneration, showing that these species exhibit the same response in vitro. However, intraspecific differences regarding ISE responses have also been reported. ISE is influenced by genetic and physiological aspects. We aimed to: (a) induce ISE in C. canephora and C. eugenioides; (b) identify and quantify the endogenous levels of indole-3-acetic acid (IAA), zeatin (Z) and gibberellic acid GA 3 and GA 4 during the callus induction; and (c) determine the number of gene copies of AUX/IAA33 and YUC4 that are involved in the auxin biosynthetic pathway, and of WOX4 and LEC1 that are involved in the morphogenic pathway. Using liquid chromatography coupled to mass spectrometry (LC-MS), the identification and quantification of IAA, GA 3 , GA 4 and Z was performed in both Coffea. From the fluorescence in situ hybridization, the copy number of the AUX/IAA33, YUC4, WOX4 and LEC1 genes was verified. ISE was established for C. canephora and C. eugenioides, which exhibited the same in vitro response. However, the two Coffea differed in relation to endogenous hormone levels, with the exception of IAA at 90 days. These species possess two gene copies of AUX/IAA33, YUC4, WOX4 and LEC1, corroborating to their diploidy. Therefore, our results show that C. canephora and C. eugenioides differ in the physiological aspect, but not in the genetic aspect investigated here. Thus, our data contribute as a basis to understand the in vitro response and for the improvement of the in vitro propagation procedures. Keywords: Coffee. Plant Tissue Culture. In vitro regeneration. Somatic Embryo. Genetic. Plant Physiology.

Fundação de Amparo à Pesquisa do Estado de Minas Gerais O plastídeo emergiu por endossimbiose. Essa organela possui um genoma circular (plastoma) de 100 a 220 kb com estrutura quadripartida e abrigando cerca de 130 genes. Os genes plastidiais estão principalmente envolvidos em dois processos, fotossíntese e expressão gênica. A não propagação de genes de plastídios através do pólen, resulta na redução da variação evolutiva desses genes, favorecendo seu uso como marcadores moleculares em estudos filogenéticos em classificações taxonômicos superiores. Por outro lado, existe uma grande variação nos espaços intergênicos e íntrons, que podem ser usados na filogenética em classificações taxonômicas mais baixas e estudos de genética populacional. A genômica dos plastídios nos permite visualizar a evolução das espécies por meio de rearranjos nos plastomas, divergência e degeneração gênica, seleção positiva e locais de edição de RNA. Portanto, o objetivo deste estudo foi o sequenciamento de três plastomas da subfamília Opuntioideae: Brasiliopuntia brasiliensis, Opuntia monacantha e Opuntia ficus-indica. Essas espécies são amplamente cultivadas e usadas para alimentação, forragem animal e fins ornamentais. Além disso, apresentam aplicações farmacológicas, pois possuem compostos bioativos interessantes. Aqui, caracterizamos em detalhes as estruturas dos plastídios, a evolução dos genes plastidiais, o mapeamento de marcadores moleculares e as relações filogenéticas com base nas sequências dos plastídios. Estruturalmente, Opuntioideae mostra rearranjos únicos dentro de Cactaceae, como expansão das regiões invertidas. As análises de evolução molecular dos genes codificadores de proteínas mostram uma alta divergência de genes envolvidos nas funções essenciais dos plastídios. Além disso, mais da metade desses genes de plastídios carregam assinaturas de seleção positiva. Vários sítios compartilhados de edição de RNA foram previstos para ocorrer nos genes plastidiais das três espécies em estudo. Além disso, centenas de marcadores moleculares foram mapeados nos plastomas aqui sequenciados, que são sequências informativas úteis para melhorar as classificações taxonômicas e estratégias de conservação dessas espécies. Além disso, a filogenia baseada em genes concatenados resultou em uma árvore bem sustentada; com Opuntioideae formando um clado monofilético que é um grupo irmão de Cactoideae. Por fim, este estudo elucida os padrões evolutivos da subfamília Opuntioideae (Cactaceae), e contribui com muitos dados úteis a serem explorados e aplicados para acessar e compreender a diversidade genética dessas espécies de Opuntioideae e traçar estratégias adequadas de uso racional e conservação. Palavras-chave: Evolução do plastoma. Divergência gênica. Rearranjos. Seleção positiva. Edição de RNA. Marcadores moleculares. The plastid emerged through endosymbiosis. This organelle has a circular genome (plastome) of 100 to 220 kb with a quadripartite structure and harboring around 130 genes. The plastid genes are mainly involved in two processes, photosynthesis and gene expression. The non- propagation of plastid genes trough pollen, results at reduced evolutionary variation of these genes, favoring their use as molecular markers in phylogenetic studies at higher taxonomic ranks. On the other hand, there is a high variation in intergenic spaces and introns, which can be used in phylogenetic at lower taxonomic ranks and population genetic studies. Plastid genomics allow us to visualize the evolution of species through plastome rearrangements, gene divergence and degeneration, positive selection, and RNA editing sites. Therefore, the aim of this study was the sequencing of three plastomes of the subfamily Opuntioideae: Brasiliopuntia brasiliensis, Opuntia monacantha, and Opuntia ficus-indica. These species are widely cultivated and used for food, animal fodder, and ornamental purposes. Besides, they have pharmacological applications, as they present interesting bioactive compounds. Here, we characterize in detail the plastome structures, evolution of plastid genes, mapping of molecular markers, and phylogenetic relationships based on plastid sequences. Structurally, Opuntioideae shows unique rearrangements within Cactaceae, such as expansion of the inverted regions. Molecular evolution analyses of the protein-coding genes show a high divergence of genes involved in essential plastid functions. Furthermore, more than half of these plastid genes bear signatures of positive selection. Several shared RNA editing sites were predicted to occur in the plastid genes of the three species in study. Besides, hundreds of molecular markers were mapped in the plastomes sequenced here, which are informative sequences useful to improve taxonomic classifications and conservation strategies of these species. Moreover, the phylogeny based on concatenated genes resulted in a well-supported tree; with Opuntioideae forming a monophyletic clade that is a sister group of Cactoideae. Finally, this study shades light on the evolutionary patterns of the subfamily Opuntioideae (Cactaceae), and contributes with plenty of useful data to be explored and applied to access and understand the genetic diversity of these Opuntioideae species and trace adequate strategies of rational use and conservation. Keywords: Plastome evolution. Gene divergence. Rearrangements. Positive selection. RNA editing. Molecular markers.

This study presents the status of ex situ and in situ conservation for the crop wild relatives of rice, potato, sweet potato, and finger millet in Brazil, and the subsequent germplasm collection expeditions. This research is part of a global initiative entitled ?Adapting Agriculture to Climate Change: Collecting, Protecting, and Preparing Crop Wild Relatives? supported by the Global Crop Diversity Trust. Species of the primary, secondary, and tertiary gene pools with occurrences reported in Brazil were included: Oryza alta Swallen, O. grandiglumis (Döll) Prod., O. latifolia Desv., O. glumaepatula Steud., Eleusine tristachya (Lam.) Lam., E. indica (L.) Gaertn., Solanum commersonii Dunal, S. chacoense Bitter, Ipomoea grandifolia (Dammer) O?Donell, I. ramosissima (Poir.) Choisy, I. tiliacea (Willd.) Choisy, I. triloba L., and I. cynanchifolia Meisn. The status of the ex situ and in situ conservation of each taxon was assessed using the gap analysis methodology, and the results were used to plan 16 germplasm collection expeditions. Seeds of the collected material were evaluated for viability, and the protocols for seed germination and cryopreservation were tested. The final conservation score, resulting from the gap analysis and including the average of the ex situ and in situ scores, resulted in a classification of medium priority of conservation for all the species, with the exception of I. grandifolia (high priority). The total accessions collected (174) almost doubled the total accessions of these crop wild relatives incorporated in Embrapa?s ex situ conservation system prior to 2015. In addition, accessions for practically absent species were collected for the ex situ conservation system, such as Ipomoea species, Eleusine indica, and Solanum chacoense. The methods used for dormancy breaking and low temperature conservation for the Oryza, Eleusine, and Ipomoea species were promising for the incorporation of accessions in the respective gene banks. The results show the importance of efforts to collect and conserve ex situ crop wild relatives in Brazil based on previous gap analysis. The complementarity with the in situ strategy also appears to be very promising in the country. Made available in DSpace on 2021-04-07T12:34:02Z (GMT). No. of bitstreams: 1 agronomy-11-00638-v2.pdf: 2212936 bytes, checksum: 8c5b2d70dc1c6550dd47601dff681696 (MD5) Previous issue date: 2021

Made available in DSpace on 2021-06-25T11:03:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-02-01 Using microsatellite loci, we assessed the mating system and genetic diversity of the dioecious tropical tree Genipa americana in a natural population (NP) and a progeny test (PT). For NP, we also estimated the paternity correlation within and among fruits and mean pollen dispersal distance. As expected for dioecious species, all offspring originated from outcrossing (t = 1). Mating among relatives (1-ts) and paternity correlation (rp) were variable among progenies (1-ts = 0.03-0.19; rp = 0.04-0.40), but greater in NP than in PT. Fixation index (F) was generally significant and lower in adults than in offspring, indicating selection against inbred individuals. Paternity correlation was higher within (0.40) than among (0.26) fruits, indicating a lower effective number of pollen donors (Nep) within (2.5) than among (3.8) fruits. Due to the higher rp in NP, the effective size within progenies (Ne) was lower (2.69) than PT (3.27). The pollen dispersal pattern was strongly leptokurtic, suggesting long-distance pollen dispersal (mean of 179 m). The results show that both populations can be used for seed collection in environmental reforestation programmes; however, considering that PT is structured in maternal progenies, NP is more suitable for seed collection due to the lower probability of mating among related trees. Universidade Federal Do Alagoas Campus de Engenharias e Ciências Agrárias Instituto Florestal de São Paulo, C.P. 1322 Universidade Estadual Paulista Instituto de Biotecnologia Unesp Embrapa Tabuleiros Costeiros Cia Energética de São Paulo Usina Porto Primavera Universidade Estadual Paulista Faculdade de Engenharia Unesp Universidade Estadual Paulista Instituto de Biotecnologia Unesp Universidade Estadual Paulista Faculdade de Engenharia Unesp

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from twoex-situcollections and a feral population. The UgandanC.canephoradiversity was then positioned relative to the species’ global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda’s nativeC.canephoradiversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute toex situconservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementaryin-situconservation ofCoffea canephorain native forests in northwestern Uganda.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico Em geral, o genoma plastidial (plastoma) de plantas terrestres contém cde 100-130 genes, organizados em uma molécula de DNA de 120-160 kb. O sequenciamento do plastoma é importante para estudos genéticos, filogenéticos e evolutivos. Os genes plastidiais são úteis para análises filogenéticas entre famílias e ordens, enquanto regiões como íntrons e regiões intergênicas são fontes de marcadores para uso em filogenias entre espécies/gêneros e em estudos de diversidade genética. Análise do plastoma permite a detecção de inversões e perdas gênicas, a seleção atuante nos genes plastidiais, e a predição de sítios de edição de RNA. No entanto, os plastomas de várias famílias de angiospermas permanecem pouco estudados. Assim, o objetivo deste estudo foi sequenciar pela primeira vez o plastoma completo de uma espécie das famílias Tropaeolaceae (Tropaeolum pentaphyllum) e Bixaceae (Bixa orellana) e contribuir para o melhor entendimento da evolução plastidial no gênero Passiflora, por meio do sequenciamento do plastoma de espécies do subgênero Passiflora e uma espécie do subgênero Deidamioides (Passiflora cirrhiflora). Este trabalho apresenta uma caracterização detalhada da estrutura dos plastomas, do conteúdo e da divergência gênica, de marcadores, dos sítios de edição de RNA e da filogenia de cada táxon aqui sequenciado. B. orellana apresentou algumas características específicas como seleção positiva atuando no gene psaI e 11 sítios de edição de RNA específicos. Paralelamente, T. pentaphyllum mostrou extensões especfícias nos genes matK e rpoA, e a predição de dois sítios de edição de RNA específicos. As espécies do subgênero Passiflora mostraram sequências altamente divergentes dos genes clpP e accD, e um polimorfismo significativo relacionado ao ganho e perda de sítios de edição de RNA. Por outro lado, P. cirrhiflora e outras espécies do subgênero Deidamioides apresentaram grande conservação de sítios de edição. No geral, as análises filogenéticas realizadas aqui mostraram árvores bem suportadas, porém algumas incongruências permaneceram para ser elucidadas com uma maior amostragem de taxóns. Neste estudo foi gerada uma grande quantidade de dados genômicos que poderá ser utilizados em várias análises relacionadas à genética, evolução, biotecnologia e conservação das espécies aqui estudadas e de outros taxóns relacionados. Palavras-chave: DNA de organela. Marcadores moleculares. Evolução do genoma plastidial. Normally, the plastid genome (plastome) of land plants contains 100-130 genes, which are organized in a DNA molecule of 120-160 kb. The plastome sequencing molecule has been important for studies related to genetic, evolution, and phylogenetic analyses. Plastid genes are useful to unveil phylogenetic relationships between families and botanical orders, while fast- evolving regions (i.e., introns and intergenic spacers) are a great source of molecular markers to use in phylogenetic analyses of low taxa and genetic diversity analysis. Also, the analysis of complete plastomes allows us to uncover unusual features such as large inversions, gene losses, the active selection acting on plastid genes, and the prediction of RNA editing sites. However, plastomes of several angiosperms families have remained poorly studied. Thus, the objective of this study was the sequencing of the first complete plastomes of the families Tropaeolaceae (Tropaeolum pentaphyllum) and Bixaceae (Bixa orellana); and contribute to a better understanding of the plastome evolution in the genus Passiflora (Passifloraceae) via plastome sequecing of six species of the subgenus Passiflora and Passiflora cirrhiflora of the subgenus Deidamioides. This work reports a detailed characterization of the plastomes, including the analysis of several parameters: structure of the plastomes, gene content, genetic divergence, molecular markers, RNA editing sites, and phylogenetic aspects. B. orellana showed some specific features if compared with other Malvales, such as positive selection acting on psaI gene and 11 specific RNA editing sites. Similarly, T. pentapphyllum showed specific extensions of the matK and rpoA genes, and two specific RNA editing sites. The species of the subgenus Passiflora showed highly divergent genes (i.e. clpP and accD) and a significant polymorphism of gains and losses of RNA editing sites. In contrast, P. cirrhiflora and other species of the subgenus Deidamioides showed a conserved set of RNA editing sites. In general, the phylogenetic analyses performed here showed well-supported trees, but some inconsistencies remained to be elucidated by using a larger number of sampled taxons. A large amount of genomic data was provided by this study, which is useful in various analyzes related to genetics, evolution, biotechnology, and conservation of the species studied here and other related taxa. Keywords: Organelle DNA. Molecular markers. Plastome evolution.

Submitted by Marcos Vinicius Dantas de Queiroz (dantas.queiroz@unesp.br) on 2021-01-08T21:25:32Z No. of bitstreams: 1 tese_final_MVDQ_merged.pdf: 11628034 bytes, checksum: c96b957a612e0f2929e068450cf4d1b6 (MD5) Rejected by Ana Paula Santulo Custódio de Medeiros null (asantulo@rc.unesp.br), reason: Prezado Marcos O documento enviado para a coleção Campus Unesp Rio Claro foi recusado pelos seguintes motivos: - Página de rosto: ao final da página falta constar a cidade de defesa. O correto é: Rio Claro - SP e na linha debaixo apenas o ano – 2020. - Ata de defesa: excluir do trabalho e adicionar a Folha de Aprovação, que deve ser solicitada à Seção de Pós-Graduação. - CAPES: A Portaria nº 206, de 04/09/2018 Dispõe sobre obrigatoriedade de citação da CAPES nos agradecimentos da seguinte forma: Art. 3º Deverão ser usadas as seguintes expressões, no idioma do trabalho (Não alterar, acrescentar ou excluir qualquer informação. 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Atenciosamente, Biblioteca Campus Rio Claro Repositório Institucional UNESP https://repositorio.unesp.br on 2021-01-11T12:39:53Z (GMT) Submitted by Marcos Vinicius Dantas de Queiroz (dantas.queiroz@unesp.br) on 2021-01-12T01:24:01Z No. of bitstreams: 1 tese_final_MVDQ_merged.pdf: 11640896 bytes, checksum: 4462f9d5181238ea2c728973459f4fbf (MD5) Approved for entry into archive by Ana Paula Santulo Custódio de Medeiros null (asantulo@rc.unesp.br) on 2021-01-13T12:38:37Z (GMT) No. of bitstreams: 1 dantas-queiroz_mv_dr_rcla_par.pdf: 1530865 bytes, checksum: 541b264a4bb93b8011efb1f7cec71a9a (MD5) Made available in DSpace on 2021-01-13T12:38:37Z (GMT). No. of bitstreams: 1 dantas-queiroz_mv_dr_rcla_par.pdf: 1530865 bytes, checksum: 541b264a4bb93b8011efb1f7cec71a9a (MD5) Previous issue date: 2020-12-14 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) No Capítulo I, começamos a investigar o padrão genético de V. oligantha, selecionando algumas de suas populações para testar a compatibilidade de marcadores microssatélites já desenvolvidos para Bromeliaceae. Satisfatoriamente, conseguimos amplificar 24 loci, sendo 20 deles polimórficos. Assim sendo, selecionamos os dez loci mais polimórficos e genotipamos 229 indivíduos pertencentes a 14 populações para utilizarmos em nossas análises subsequentes. O Capítulo II trata da filogeografia de V. oligantha. Aos microssatélites nucleares obtidos, incluímos 95 indivíduos sequenciados usando dois marcadores plastidiais. Com esses dados em mãos, datamos a origem e a diversificação intraespecífica de V. oligantha, além de estimarmos a diversidade genética, a estrutura populacional e taxas de migração entre populações. Também modelamos a distribuição ancestral de V. oligantha utilizando Modelagem de Nicho Ecológico, inferindo possíveis corredores ancestrais entre as populações atualmente fragmentadas. Conseguimos notar uma alta estruturação genética, característica usual de organismos de ambientes naturalmente fragmentados; entretanto, a estruturação parece estar de acordo com o padrão biogeográfico, sugerindo assim como os processos microevolutivos envolvidos na diversificação de linhagens puderam resultar nos padrões de endemismo observados hoje no Espinhaço. Por fim, a modelagem de nicho ecológico confirma nossa suspeita de que, no Último Glacial Máximo (LGM), V. oligantha tinha uma adequabilidade muito maior, ocupando áreas mais baixas, conectando populações antes isoladas, conforme demonstramos nas análises de corredores. Para verificarmos mais a fundo o efeito das mudanças climáticas passadas na demografia e na diversificação das espécies das montanhas quartzíticas brasileiras (BQM), nós partimos para uma abordagem de filogeografia comparada, o pano de fundo do Capítulo III. Lá, buscamos na literatura organismos endêmicos destas montanhas e que tivessem dados genéticos depositados no Genbank. Também utilizamos os dados da própria V. oligantha e geramos mais sequências de duas espécies típicas das BQM mineiras e baianas: Euphorbia attastoma (Euphorbiaceae) e Neoregelia bahiana (Bromeliaceae). Ao final, além dessas três espécies, analisamos os dados das plantas Lychnophora ericoides e Richterago discoidea (Asteraceae), Tibouchina papyrus (Melastomataceae) e Vellozia auriculata (Velloziaceae) e também dois anuros, Bokermmanohyla saxicola (Hylidae) e Pleurodema alium (Leptodactylidae). Com estas nove espécies, verificamos a dinâmica populacional da comunidade, encontrando que grande parte delas passou por uma expansão síncrona durante o LGM, um sinal da força das mudanças climáticas na demografia nessas espécies endêmicas. Por outro lado, os dois anuros não seguiram este padrão, onde P. alium permaneceu constante enquanto B. saxicola teve um bottleneck durante o LGM. O padrão demográfico encontrado também se reflete na modelagem da adequabilidade de cada espécie para o presente e o LGM, com exceção de B. saxicola, que apresentou uma adequabilidade maior do que aquela estimada pelos nossos dados genéticos. Outra análise que fizemos foi comparar a diversificação interespecífica de espécies co-distribuídas do Espinhaço com os padrões biogeográficos para a região, onde encontramos um padrão congruente, mas ao adicionarmos espécies não exclusivas dali o cenário congruente se desfez. Dessa forma, os padrões de endemismo no Espinhaço parecem ser idiossincráticos, onde os processos microevolutivos ocorrentes ali modelaram os padrões biogeográficos existentes hoje. In Chapter I, we investigated the genetic patterns of V. oligantha, selecting some of its populations to test the compatibility of previously developed microsatellites. Satisfactorily, we amplified 24 loci, although 20 of them were polymorphic. Thus, we selected the top ten most polymorphic loci and genotyped 229 individuals belonging to 14 populations. Chapter II is about the phylogeography of V. oligantha. With the nuclear microsatellites, we added 95 sequenced individuals, using two plastidial markers. With both datasets, we dated the origin and intraspecific diversification of V. oligantha, estimated its genetic diversity, population structure, and migration rates among populations. We also modeled the ancient distribution of V. oligantha using Ecological Niche Modelling, using it to inferring possible ancient corridors between the extant fragmented populations. We found a high genetic structure, a usual trait of species with a natural fragmented distribution; however, the structure seems to follow the biogeographic pattern, suggesting how the microevolutionary processes could shape the current patterns of endemism of the Espinhaço Range. Finally, the niche modeling confirmed our suspicion that, in the Last Glacial Maximum (LGM), the suitability of V. oligantha was wider than the current one, where it occupied lowlands, connecting isolated populations, as we showed with the corridor analysis. To deeply investigate the role of ancient climatic changes in the demography and diversification of species from the Brazilian Quartzitic Mountains (BQM), we used a comparative phylogeographic approach, the background of Chapter III. We conducted a literature survey seeking for endemic organisms of the BQM with available genetic data. Besides the data of V. oligantha, we also yielded sequences for more two species: Euphorbia attastoma (Euphorbiaceae) and Neoregelia bahiana (Bromeliaceae). Besides these three plant species, we incorporated genetic data of Lychnophora ericoides and Richterago discoidea (Asteraceae), Tibouchina papyrus (Melastomataceae), and Vellozia auriculata (Velloziaceae) and two anuran species, Bokermmanohyla saxicola (Hylidae) and Pleurodema alium (Leptodactylidae). Thus, with these nine species, we investigated their population dynamics, finding that most of them had a synchronous population expansion over the LGM, a result that supports the strength of climatic oscillations on the demography of these endemic species. Besides, we also compared the lineage diversification with the biogeographic patterns found in the Espinhaço Range, where a congruent diversification pattern was found. However, when we compared species non-endemic of the Espinhaço, this congruent pattern is blurred, suggesting that microevolutionary processes of the Espinhaço-endemic species are idiosyncratic. CAPES: 001

Os genomas das plantas são ricos em sequências repetitivas, inicialmente reconhecidas como "DNA lixo". Porém, atualmente tem sido demonstrado que elas desempenham papéis importantes em diferentes processos, como rearranjos cromossômicos, expressão e função gênica, além de influenciar nas diferenças de conteúdo de DNA nuclear entre as espécies. Neste cenário, a identificação, comparação e mapeamento de sequências repetitivas geram evidencias acerca da organização cariotípica das plantas. O presente estudo comparou cariótipos de três acessos de Zea mays, por meio de citogenética molecular, buscando responder se a variação do tamanho do genoma nuclear entre eles é promovida por quantidades diferenciais de sequências repetitivas e/ou por rearranjos cromossômicos estruturais. Além disso, identificamos e caracterizamos a distribuição de duas sequências de retrotransposons-LTR no cariótipo de Psidium guajava. No primeiro estudo, o conteúdo de DNA nuclear dos acessos de Z. mays revelou uma variação intraespecífica notável de 2C = 2,00 pg a 2C = 6,10 pg. A partir da análise comparativa dos cariótipos, uma deleção terminal heterozigótica no cromossomo 3 foi apontada como a causa do menor valor 2C, assim como foi observada uma translocação no braço curto do cromossomo 1. O maior valor 2C foi associado à distribuição mais abundante de retrotransposons-LTR da família Grande no cariótipo. Além disso, heteromorfismos foram encontrados em relação ao número e à posição da sequência de repetição em tandem de 180 pb. No segundo trabalho, identificamos e caracterizamos dois retrotransposons Copia LTR do ponto de vista genômico e cromossômico em P. guajava, uma árvore frutífera economicamente importante. A análise citogenômica evidenciou que essas duas sequências de Copia, identificadas como RLC_Pg_1 e RLC_Pg_2, estão relacionadas às linhagens RLC_egBianca_1 e RLC_egAle_2 de Eucalyptus grandis, respectivamente. Nosso trabalho fornece novos insights para esclarecer o papel dos elementos móveis na diversificação do cariótipo de P. guajava e Z. mays.Palavras-chave: Citogenética. Goiaba. Cariótipo. Milho. Genoma de planta. Sequências repetitivas. Plant genomes are rich in repetitive sequences, which were initially recognized as "junk DNA". However, currently it has been demonstrated that they play important roles different processes, such as chromosomal rearrangements, gene expression and function, in addition to influencing in differences of nuclear DNA content between species. In this scenario, the identification, comparison and mapping of repetitive sequences generate evidence about the karyotype organization of plants. The present study compared karyotypes of three Zea mays accessions, by molecular cytogenetic seeking to answer if the nuclear genome size variation among them is promoted by differential amounts of repetitive sequences and/or by structural chromosomal rearrangements. Furthermore, we identify and characterize the distribution of two LTR- retrotransposons sequence in Psidium guajava karyotype. In the first study, the measurement of the nuclear DNA content of Z. mays accessions revealed a remarkable intraspecific variation from 2C = 2.00 pg to 2C = 6.10 pg. From comparative karyotypes analysis, a heterozygous terminal deletion in chromosome 3 was pointed out as a cause of lower 2C value, as well as a translocation in the short arm of chromosome 1 was observed. Differently, higher 2C value was associated with the more abundant distribution of LTR-retrotransposons from the family Grande in the karyotype. Moreover, heteromorphisms were found regarding the number and position of the 180-bp tandem repeat sequence. In the second paper, we identified and characterized two Copia LTR-retrotransposons from a genomic and chromosomal point of view in P. guajava, an economically important fruit tree. The cytogenomic analysis evidenced that these two Copia sequences, identified as RLC_Pg_1 and RLC_Pg_2, are related to the lineages RLC_egBianca_1 and RLC_egAle_2 from Eucalyptus grandis, respectively. Our work provides new insights to enlighten the role of mobile elements in diversification the P. guajava and Z. mays karyotype. Keywords: Cytogenetics. Guava. Karyotype. Maize. Plant genome. Repetitive sequences.

The selection of superior genotypes of soybean entails a simultaneous evaluation of a number of favorable traits that provide a comparatively superior yield. Disregarding the population effect in the statistical model may compromise the estimate of variance components and the prediction of genetic values. The present study was undertaken to investigate the importance of including population effect in the statistical model and to determine the effectiveness of the index based on factor analysis and ideotype design via best linear unbiased prediction (FAI-BLUP) in the selection of erect, early, and high-yielding soybean progenies. To attain these objectives, 204 soybean progenies originating from three populations were examined for various traits of agronomic interest. The inclusion of the population effect in the statistical model was relevant in the genetic evaluation of soybean progenies. To quantify the effectiveness of the FAI-BLUP index, genetic gains were predicted and compared with those obtained by the Smith-Hazel and Additive Genetic indices. The FAI-BLUP index was effective in the selection of progenies with balanced, desirable genetic gains for all traits simultaneously. Therefore, the FAI-BLUP index is an adequate tool for the simultaneous selection of important traits in soybean breeding. The selection of superior genotypes of soybean entails a simultaneous evaluation of a number of favorable traits that provide a comparatively superior yield. Disregarding the population effect in the statistical model may compromise the estimate of variance components and the prediction of genetic values. The present study was undertaken to investigate the importance of including population effect in the statistical model and to determine the effectiveness of the index based on factor analysis and ideotype design via best linear unbiased prediction (FAI-BLUP) in the selection of erect, early, and high-yielding soybean progenies. To attain these objectives, 204 soybean progenies originating from three populations were examined for various traits of agronomic interest. The inclusion of the population effect in the statistical model was relevant in the genetic evaluation of soybean progenies. To quantify the effectiveness of the FAI-BLUP index, genetic gains were predicted and compared with those obtained by the Smith-Hazel and Additive Genetic indices. The FAI-BLUP index was effective in the selection of progenies with balanced, desirable genetic gains for all traits simultaneously. Therefore, the FAI-BLUP index is an adequate tool for the simultaneous selection of important traits in soybean breeding.

Trait selection is occasionally necessary to save money and time, as well as accelerate breeding program processes. This study aimed to propose two criteria to select traits based on a Procrustes analysis that are poorly explored in genetic breeding: Criterion 1 (backward algorithm) and Criterion 2 (exhaustive algorithm). Then, these two criteria were further compared with Jolliffe’s criterion, which has often been used to select traits in genetic diversity studies. Sixteen agronomic traits were considered, and 40 Conilon coffee (Coffea canephora) accessions were evaluated. This study showed that the flexibility in selecting traits by researcher preference, graphical visualization, and Procrustes statistic through criteria 1 and 2 is a fast and reliable alternative for decision-making. These decisions are based on the removal and addition of traits for phenotyping in studies of Conilon coffee diversity that can be applied to other crops. Other relevant aspects of selection traits criteria were also discussed.

162 p. Oil Palm (OP) is the crop with the highest oil yield per hectare and as a result, its use has spread rapidly in tropical regions of Asia, Africa and America. The main OP plantations consist of Elaeis guineensis (Eg) species, known to produce high amounts of oil. However, in American regions this species is being affected by the ¿Pudrición de Cogollo¿ disease leading to dead palms. Therefore, OP companies started crossing this species with E. oleifera (Eo) palms which is resistant to this disease. The obtained interspecific hybrids show interesting characteristic inherited from both parents; resistance to different diseases, interesting oil quality characteristics, competitive oil production and decreased height which prolongs its useful life. However, little work has been done in the improvement of these hybrids. This thesis tries to address this gap applying different molecular approaches. First, an extensive study of an amplicon of the ¿Shell-thickness¿ (Sh) gene has been conducted on 568 Eg, Eo and hybrid genotypes. Then, with the aim to discover promising new Candidate Genes (CG) that could be exploited in further molecular assisted selection systems (MAS) a large phenotypic study of 25 production and quality traits have been performed within 198 hybrid genotypes fllowed by two Association Mapping (AM) assays. These latter have been based on targeted CG and random Restriction site associated RNA sequencing(RARSeq) approaches. Neiker teknalia Lafabril Energy & Palma Sampoerna Agro

Jatropha curcas L. is a perennial plant with great potential for biodiesel production. Thus, the aim of this study was to select J. curcas genotypes for bioenergy purpose considering multitrait, multiharvest and effective population size. To this end, a data set with 70 J. curcas families, obtained through controlled crosses, evaluated in a randomized block design, with six replications, three plants per plot, spaced at 4 × 2 m was used. The following traits were evaluated: plant height in the 2014 and 2015 crop seasons; canopy projection in the row (2015 crop season); canopy projection between rows (2015 crop season); and grain yield (2015, 2016, and 2017 harvests). The mixed model methodology was used to estimate the variance components and to predict the genetic values. Superior genotypes were selected through Multitrait index based on factor analysis and genotype-ideotype distance (FAI-BLUP index), considering the effective population size. According to this index, 98% of all additive genetic variability were summarized in three factors. By adopting the selection intensity that allows maintaining the effective population size equal to 30 (i.e., selection of 214 individuals), the predicted gains were 15.56, 21.75, 4.16, and 5.37% for the traits grain yield in the 2015 and 2016 harvests, canopy projection in the row, and canopy projection between rows in the 2015 crop season, respectively. Thus, the results suggest that the FAI-BLUP index can be successfully used in J. curcas breeding. Made available in DSpace on 2020-11-19T09:17:19Z (GMT). No. of bitstreams: 1 Selection-of-Jatropha-genotypes-2020.pdf: 520397 bytes, checksum: 50c850df9586a5598dbe24bd37571e8b (MD5) Previous issue date: 2020

Genotyping-by-sequencing (GBS) datasets typically feature high rates of missingness and heterozygote undercalling, prompting the use of data imputation. We compared the accuracy of four imputation methods?NPUTE, Beagle, knearest neighbors imputation (KNNI), and fast inbreed line library imputation (FILLIN)?using GBS data of maize (Zea mays L.) inbred lines, genotyped using different multiplexing levels. Two strategies for SNP-calling and genotype imputation were evaluated. First, only lines genotyped through 96-plex were used for single nucleotide polymorphism (SNP) discovery, whereas both 96- and 384-plex were simultaneously used in the second strategy. In the first genotype imputation strategy, only the 96-plex lines were imputed, then the remaining lines were appended (96-plex-imputed plus 384-plex) and then imputed. In the second imputation strategy, we jointly imputed both datasets. We also investigated the impacts of including heterozygous genotypes and distinct rates of missing genotypes per locus. The different SNP-calling strategies and percentage of missing data did not substantially affect the imputation accuracy. However, the different imputation strategies showed a substantial effect. Generally, imputations were less accurate for heterozygotes. The scenario 96-plex-imputed plus 384-plex showed accuracies similar to the 96-plex scenario. Beagle and NPUTE produced the highest accuracies. Our results indicate that combining SNP-calling and imputation strategies can enhance genotyping in a cost-effective manner, resulting in higher imputation accuracies. Made available in DSpace on 2020-11-12T14:20:26Z (GMT). No. of bitstreams: 1 Single-nucleotide-polymorphism.pdf: 853268 bytes, checksum: 8621c2cd9ee8ae5d40282ce704ca311d (MD5) Previous issue date: 2020

There is a worldwide concern about a possible narrowing of the genetic base of most crops, as e.g. that of rice (Oryza sativa L.), as a result of the modern breeding practices. Thus, the purpose of this study was to investigate this phenomenon in the germplasm of elite paddy rice in southern Brazil, including frequently used accessions in crosses. The panel consisted of 91 accessions. Data of morphological traits, SNP markers and mineral content of husked and polished grain were analyzed by hierarchical clustering and principal component analysis. The SNP markers and hierarchical clustering proved most appropriate to assess the genetic variability. A narrowing of the genetic base of rice was confirmed, although a certain level of genetic variability was still found in the germplasm of elite paddy rice in south Brazilian rice, particularly for grain mineral content. Made available in DSpace on 2021-01-22T09:04:28Z (GMT). No. of bitstreams: 1 Artigo-Busanello-et-al-2020.pdf: 1994579 bytes, checksum: 7df191a977188fc578f6ec9820499c9d (MD5) Previous issue date: 2020

The onset of flowering is decisive to the reproductive success of plants. The objectives of this study were to characterize the phenotypic variation in heading date and estimate its heritability in segregating populations of oat (Avena sativa L.). F2 and F3 generations of two large populations, derived from crosses ‘URS Taura × Leggett’ and ‘FL0206B-S-B-S1 × UFRGS 078030-1’, were evaluated. A wide phenotypic variation in the number of days to heading was observed in both populations. Heritability coefficients of 0.68 and 0.46 were estimated for the ‘URS Taura × Leggett’ and ‘FL0206B-S-B-S1 × UFRGS 078030-1’ populations. Our results demonstrate that genetic differences derived from parents in response to photoperiod and temperature explain most of the phenotypic variation in heading date of oat populations. Understanding genetic and environmental effects on flowering expression is essential to increase the response to selection for well-adapted and high-yielding oat cultivars.

The objective of this study was to estimate the direct and indirect effects of agricultural, morphological, physiological, and root traits of popcorn lines, under two conditions of water supply: full irrigation (FI) and drought stress (DS). A complete randomized block design with three replications was used to evaluate the following traits: expanded popcorn volume per hectare (EPV), 100-grain weight (100GW), mean ear length, mean ear diameter, number of grains per row (NGR), prolificacy (PRO), anthesis to silking interval, tassel length, number of tassel branches, plant height, shoot dry matter, green index (SPAD), and canopy temperature depression (CTD), root angle (RA), tap root volume (TRV), and crown root volume (CRV). Analyses of variance and path analysis, and subsequent partitioning of direct and indirect effects were performed. For the traits EPV, PRO, CTD, RA, CRV and TRV, the genotype x environment interaction was significant. Drought stress had significant effects on EPV (&minus, 7.15%), 100GW (&minus, 23.52%), SPAD (&minus, 29.31%), CTD (87.15%), RA (24.54%), and CRV (44.89%). The traits NGR and SPAD were found to be decisive for the expression of EPV. The exploitation of these traits by indirect selection is expected to induce increments in EPV in environments under DS and FI.

The objective of this study was to evaluate gene expression related to water deficit tolerance in maize lines. For this, lines previously classified as tolerant (91-T and 32-T) and non-tolerant (24-NT and 57-NT) to water deficit were used. The seeds of the four lines were evaluated for emergence and emergence speed index, and the seedlings were evaluated for root and shoot length under two conditions of water availability (70 and 10% substrate water retention capacity). In transcript analysis, the expression of several genes associated with water deficit tolerance, ZmDBP3, ZmALDH9, ZmAN13, and ZmDREB2A, was evaluated by qRT-PCR for the 91-T and 57-NT lines. It can be concluded that soil water deficiency did not reduce root development. However, the shoot length was significantly lower under dry conditions. Through transcript analysis, the genes ZmDBP3 and ZmAN13 were identified as potential markers for the early selection of maize lines tolerant to water deficit.

Selection of more productive carrot genotypes is fundamental for crop breeding programs aiming to increase productivity and reduce cost production. Thus, the aim of this work was to evaluate gains from direct selection and to measure its effects on other agronomic traits of interest in carrots. Thirty six carrot genotypes were evaluated in two experiments: the first, sown in the second half of November 2016 and the second one in the first week of March 2017. The experimental plots covered a useful area of 1.5 m2, in transversal rows and 0.10-m double spacing between single rows x 0.20-m between double rows in a randomized block design with 3 replicates. At 90 days, the incidence of leaf blight was evaluated using a note scale and 100 days after sowing, roots were harvested measuring the number and mass of total, commercial and non-commercial roots of each plot. The direct selection of commercial root mass allowed to estimate indirect and expressive gains for most evaluated traits, allowing to select seven genotypes (populations 758, 751, 737, 736, 735, 744 and 742) which can be released as cultivar or for the formation of a broader genetic-based population. RESUMO A seleção de genótipos de cenoura mais produtivos é fundamental para os programas de melhoramento dessa cultura visando aumento na produção com redução dos custos. Assim, objetivou-se com esse trabalho avaliar o ganho com a seleção direta e medir seus efeitos em outras características agronômicas de interesse em cenoura. Para isso, 36 genótipos de cenoura foram avaliados em dois experimentos, sendo o primeiro semeado na segunda quinzena de novembro de 2016 e o segundo na primeira semana de março de 2017. As parcelas experimentais possuíram área útil de 1,5 m2, em fileiras transversais e espaçamento duplo 0,10 m (entre linhas simples) x 0,20 m (entre linhas duplas) no delineamento de blocos casualizados com três repetições. Aos 90 dias avaliou-se a incidência de queima das folhas por escala de notas e aos 100 dias após a semeadura, realizou-se a colheita das raízes, mensurando o número e massa das raízes, total, comercial e refugo de cada parcela. A seleção direta no caráter massa de raízes comerciais possibilitou estimar ganhos indiretos e expressivos para a maioria dos caracteres avaliados, permitindo assim, selecionar sete genótipos (populações 758, 751, 737, 736, 735, 744 e 742) os quais podem ser validados para lançamento ou para formação de uma população de base genética mais ampla.

Vegetation indices and canopy temperature are the most usual remote sensing approaches to assess cereal performance. Understanding the relationships of these parameters and yield may help design more efficient strategies to monitor crop performance. We present an evaluation of vegetation indices (derived from RGB images and multispectral data) and water status traits (through the canopy temperature, stomatal conductance and carbon isotopic composition) measured during the reproductive stage for genotype phenotyping in a study of four wheat genotypes growing under different water and nitrogen regimes in north Algeria. Differences among the cultivars were reported through the vegetation indices, but not with the water status traits. Both approximations correlated significantly with grain yield (GY), reporting stronger correlations under support irrigation and N-fertilization than the rainfed or the no N-fertilization conditions. For N-fertilized trials (irrigated or rainfed) water status parameters were the main factors predicting relative GY performance, while in the absence of N-fertilization, the green canopy area (assessed through GGA) was the main factor negatively correlated with GY. Regression models for GY estimation were generated using data from three consecutive growing seasons. The results highlighted the usefulness of vegetation indices derived from RGB images predicting GY.

Desequilíbrio de ligação (DL) e blocos de haplótipos têm sido um conhecimento preliminar e poderoso para estudos genômicos em humanos, animais e plantas. Nós objetivamos descrever as medidas de DL, D' e r 2 , e caracterizar os padrões de blocos de haplótipos em populações de milho-pipoca de origem tropical (sintético e população de melhoramento) e temperada (população biparental). As três populações foram genotipadas por genotipagem por sequenciamento (GBS), 190 ou 192 indivíduos de cada população. Após o controle de qualidade dos dados, o conjunto final de marcadores remanescentes para análise variou de 75.000 a 76.055 SNPs. D' e r 2 foram avaliados por cromossomo, e os blocos de haplótipos foram caracterizados por número e tamanho de blocos, e número de SNP. DL e blocos de haplótipos foram também avaliados em 12 genes contendo polimorfismos relacionados à biossíntese de zeína, amido, celulose e ácidos graxos. Nossos resultados mostraram que o sintético é a população com maior LD, seguida pela população biparental. Observamos valores médios baixos de r 2 nas populações. Há um decréscimo de LD inicialmente mais alto para os SNPs separados por 51-100 kb (3 a 7% para D' e 28 a 66% para r 2 , em média) e então uma diminuição gradual para o valor mínimo de LD para SNPs separados por 451- 500 kb. O número e a extensão dos blocos de haplótipos e o número de SNPs por bloco de haplótipos foram proporcionais à média de r 2 . No entanto, não se espera uma vantagem significativa do estudo de associação baseado em haplótipos e na seleção genômica ao longo das gerações, devido ao número reduzido de SNPs nos blocos de haplótipos (2 a 3). A abordagem intragênica de LD revelou que as populações tropicais (sintético e população de melhoramento) desenvolvidas pelo programa de melhoramento genético, com base no volume de expansão, têm maior LD e presença de blocos de haplótipos. No entanto, não podemos inferir que os maiores valores de r 2 observados em 11 dos 12 genes são devidos a seleção para qualidade em populações. Palavras-chave: Desequilíbrio de Fase Gamética. Haplótipos. População Biparental. Sintético. População de Melhoramento. Linkage disequilibrium (LD) and haplotype blocks have been a preliminary and powerful knowledge for genomic investigates in humans, animals and plants. We aimed to describe the LD measures, D’ and r 2 , and to characterize haplotype block patterns in popcorn populations (synthetic and breeding population) from tropical and temperate origins (biparental population). Three populations were genotyped by genotyping-by-sequencing (GBS), 190 or 192 individual from each population. After the data quality control the final marker set remaining for analysis ranged from 75,000 to 76,055 SNPs. D’ and r 2 were assessed per chromosome, and haplotype blocks were characterized by number and size of block, and SNP number. LD and haplotype blocks were also evaluated within 12 genes containing polymorphisms related to the biosynthesis of zein, starch, cellulose and fatty acids. Our results showed that the synthetic is the population with higher LD, followed by the biparental population. The lower average D' value in the breeding population reflects its recombination history. We observed low average r 2 values in the populations. There is an initially higher LD decrease for SNPs separated by 51- 100 kb (3 to 7% for D' and 28 to 66% for r 2 , on average) and then a gradual decrease to the minimum LD value for SNPs separated by 451-500 kb. The number and length of the haplotype blocks and the number of SNPs per haplotype block were proportional to the average r 2 . However, it is not expected a significant advantage of haplotype-based association study and along generations genomic selection, due to the reduced number of SNPs in the haplotype blocks (2 to 3). The LD intragenic approach revealed that tropical populations (synthetic and breeding population) developed by breeding program, based on expansion volume, have higher LD and presence of haplotype blocks. However, we cannot infer that the higher r 2 values observed in 11 of the 12 genes are due to selection for quality in populations. Keywords: Gametic Phase Disequilibrium. Haplotypes. Biparental Population. Synthetic. Breeding Population.

This study aimed to evaluate the genetic and cytological diversity and stability of 35 cherry tree accessions collected in Rio Grande do Sul. We used 15 RAPD (Random Amplified Polymorphic DNA) molecular markers and performed cytological analysis and number count of anthers. Analyses of genetic diversity allowed the separation of accessions into four groups, resulting in an average of 8.93 bands per primer amplified, 7.89 polymorphic bands, 88.08% of polymorphism and 86% of genetic similarity. Cytological analyses of gametic cells allowed for the characterization of accessions as diploids with n=11. In these, the average of meiotic cells considered normal was 82.12%; average pollen viability was 92.44% and in vitro germination was 40.26%; the average number of anthers was 161.85 anthers/flowers. Therefore, the accessions evaluated showed high genetic similarity and cytological stability and can be used in commercial plantations or hybridizations.

There is a demand for barley cultivars that are suitable for the malt industry as well as genotypes that are stable and better adapted for irrigation in the Cerrado. This study aimed to estimate the genetic parameters by assessing 69 barley genotypes from different countries, from 2012 to 2014, under irrigation in the Cerrado. Six agronomic characteristics were assessed: grain yield, plumpness kernel, thousand seeds weight, plant height, degree of plant lodging and days to heading. Analysis of variance, cluster test and phenotypic, genotypic and environmental correlations were performed. Significant effects were observed for genotypes, years and the G x E interaction. High values of broad-sense heritability (> 86%) were found for all the characteristics, which enabled direct selection. The Colombian accession MCU363PI402112 stood out for its agronomic characteristics. Genotype selection based on the phenotypic evaluations was possible due to their good experimental accuracy and precision. Precocious genotypes with high grain yields and homogeneous grain sizes were selected. Due to the environmental influence on the grain yield, additional studies concerning the components of yield in this environment are necessary to facilitate the selection of more productive genotypes.

This study aimed to estimate the genetic parameters, genetic correlations, genetic dissimilarity, and predicted gains with the selection of interspecific apomictic Paspalum plicatulum × Paspalum guenoarum hybrids in relation to seed yield traits. Nineteen genotypes that showed increased forage yield in previous studies were planted in a randomized complete block design with ten blocks. Traits evaluated in this study were: number of tillers/plant, number of reproductive tillers/plant, number of racemes/inflorescence, number of seeds/inflorescence, weight of a thousand seeds, and seed yield. Data were analyzed using a mixed model approach. The genotypes evaluated in our study showed improvement potential in relation to high heritability (H a 2 > 0.50 ), high precision (Acgen> 90%), and genetic dissimilarity (forming three groups) for seed yield traits. Seed yield showed high correlation to reproductive tillers that can be used as indirect selection tools for genetic improvement of seed yield.

[ES] La revolución que supone la secuenciación de próxima generación está permitiendo la resecuenciación del genoma completo (WGRS) de cientos o incluso miles de ejemplares de cultivos básicos y especies modelo. Con el lanzamiento de su genoma de referencia, progresivamente se están emprendiendo proyectos WGRS también para otras especies de plantas en una amplia variedad de estudios. En berenjena común (Solanum melongena L.), aunque se ha publicado un primer borrador de la secuencia del genoma de referencia, hasta el momento no se han realizado estudios de resecuenciación. En este capítulo presentamos los primeros resultados de la resecuenciación de ocho accesiones, siete de berenjena común y una del pariente silvestre S. incanum L., que corresponden a los progenitores de un cruce multiparental de generación avanzada (MAGIC) población que se encuentra actualmente en desarrollo utilizando la secuencia del genoma de la berenjena recién desarrollada que se presenta en el Cap. 7 de este libro. Se identificaron más de diez millones de polimorfismos entre las accesiones, el 90% de ellos en el S. incanum silvestre relacionado, lo que confirma la erosión genética de la berenjena común cultivada. Entre los progenitores de la población MAGIC, el patrón de distribución de polimorfismos comunes a lo largo de los cromosomas ha revelado posibles huellas de introgresión ancestral de cruces interespecíficos. El conjunto de polimorfismos se ha anotado extensamente y actualmente se está utilizando para análisis adicionales con el fin de genotipar eficientemente la población MAGIC en curso y diseccionar rasgos agronómicos y morfológicos importantes. La información proporcionada en este primer estudio de resecuenciación en berenjena será extremadamente útil para ayudar al fitomejoramiento a desarrollar nuevas variedades mejoradas y resistentes para enfrentar futuras amenazas y desafíos., [EN] The next-generation sequencing revolution is allowing the whole-genome resequencing (WGRS) of hundreds or even thousands of accessions for staple crops and model species. With the release of their reference genome, progressively also other plants, species are undertaking WGRS projects for a broad variety of studies. In common eggplant (Solanum melongena L.), although a first draft of the reference genome sequence has been published, no resequencing studies have been performed so far. In this chapter, we present the first results of the resequencing of eight accessions, seven of common eggplant and one of the wild relative S. incanum L., that correspond to the parents of a multi-parent advanced generation inter-cross (MAGIC) population that is currently under develop- ment using the newly developed eggplant genome sequence presented in Chap. 7 of this book. Over ten million polymorphisms were identified among the accessions, 90% of them in the wild related S. incanum, confirming the genetic erosion of the cultivated common eggplant. Among the MAGIC population parents, the common polymorphism distribu- tion pattern along the chromosomes has revealed possible footprints of ancestral intro- gression from interspecific crosses. The set of polymorphisms has been extensively anno- tated and currently is being used for further analyses in order to efficiently genotype the ongoing MAGIC population and to dissect important agronomic and morphological traits. The information provided in this first resequencing study in eggplant will be extremely helpful to assist plant breeding to develop new improved and resilient varieties to face future threats and challenges., This work has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de Economía, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER).

ilustraciones, fotografías, gráficas, tablas Potato is the third most important food around the world and is a basic for the food security and nutrition. The most devastating disease that affects this crop is late blight caused by Phytophthora infestans. Despite the progress made to understand the genetic mechanisms that underlie the quantitative resistance, still remain aspects to be known and clarified. The main objective of this research was to identify genetic regions associated with quantitative resistance to late blight in potato. The methodology employed for the analysis was Genome Wide Association Studies based on the identification of single nucleotide polymorphisms (SNPs). An association panel constituted by 150 genotypes that belong to Solanum tuberosum Group Phureja was assessed for its resistance to P. infestans in three environments. Two techniques were conducted for genotyping, one was GBS using two enzymes and the other was 2b Restriction site–associated DNA (2b-RAD). A matrix of 87,656 SNP was employed together with the phenotypic evaluation using the variable area under disease progress curve. The resistance trait of the genotypes was associated with SNPs distributed across the whole potato genome. The association analyses were conducted using a mixed model approach. The genotypic characterization of the Group Phureja did not show the presence of highly differentiated subgroups, from which the absence of population structure is inferred. However, a deviation from the Hardy-Weinberg equilibrium condition was found, due to an excess of heterozygous in the sample. In addition, differences were observed in the levels of infection of P. infestans between the leaves and the stems of the evaluated genotypes, which contributes to the dissection of organ-specific resistance to this pathogen. Finally, the association analysis reported 16 organ-specific QTL that confer resistance to late blight. These QTL explained from 13.7% to 50.9% of the phenotypic variance. These findings demonstrate the quantitative complexity of late blight resistance in potato. Likewise, it is necessary to continue exploring the genetic diversity within Group Phureja and its potential as a source of resistance within of the potato breeding program. La papa es el tercer alimento más importante del mundo y es considerado como un alimento básico para la seguridad alimentaria y la nutrición. La enfermedad más devastadora que afecta el cultivo de papa es la gota o tizón tardío causada por Phytophthora infestans. A pesar de los avances realizados para comprender los mecanismos genéticos que subyacen a la resistencia cuantitativa a esta enfermedad, aún muchos aspectos deben ser conocidos y clarificados. El objetivo principal de esta investigación fue identificar regiones genéticas asociadas con la resistencia cuantitativa a la gota en papa. La metodología empleada fue Asociación Amplia del Genoma basada en la identificación de polimorfismos de un solo nucleótido (SNP). Un panel de asociación constituido por 150 genotipos pertenecientes al Grupo Phureja de Solanum tuberosumse evaluó por su resistencia a P. infestansen tres ambientes diferentes. Dos técnicas se realizaron para el genotipaje una fue Genotipaje por Secuenciación (GBS) utilizando dos enzimas de restricción y la otra fue Sitio asociado a la restricción de ADN(2b-RAD) con fragmentos producidos por endonucleasas tipo IIB. Se utilizó una matriz de 87,656 SNP junto con la evaluación fenotípica de la enfermedad, la que se realizó a nivel de tallo y hojas. Para esto se cuantificó como parámetro el área bajo la curva del progreso de la enfermedad. El rasgo de resistencia de los genotipos se asoció con los SNP distribuidos en todo el genoma de la papa. Los análisis de asociación se llevarona cabo utilizando un enfoque de modelo mixto. Los resultados de la caracterización genotípica del Grupo Phureja, no mostraron la presencia de subgrupos altamente diferenciados, de donde se infiere la falta de estructura poblacional. Sin embargo, se encontró una desviación a la condición de Equilibrio Hardy-Weinberg, debido a un exceso de heterocigotos en la muestra. Con la caracterización fenotípica se observaron diferencias en los niveles de infección de P. infestansentre las hojas y los tallos de los genotipos evaluados, lo que contribuye a la disección de la resistencia órgano-específica a este patógeno. Finalmente, el análisis de asociación reportó 16 QTL órgano-específicos que están involucrados en la resistencia a gota. Estos QTL explicaron del 13.7% al 50.9% de la varianza fenotípica. Estos hallazgos demuestran la complejidad cuantitativa de la resistencia a gota en papa. De otro lado, es necesario continuar explorando la diversidad genética dentro de este Grupo y su potencial como fuente de resistencia dentro del programa de mejoramiento de papa. (Texto tomado de la fuente). Incluye anexos Doctorado Doctor en Ciencias Agrarias Genetics and plant breeding Ciencias Agronómicas

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[ES] La revolución que supone la secuenciación de próxima generación está permitiendo la resecuenciación del genoma completo (WGRS) de cientos o incluso miles de ejemplares de cultivos básicos y especies modelo. Con el lanzamiento de su genoma de referencia, progresivamente se están emprendiendo proyectos WGRS también para otras especies de plantas en una amplia variedad de estudios. En berenjena común (Solanum melongena L.), aunque se ha publicado un primer borrador de la secuencia del genoma de referencia, hasta el momento no se han realizado estudios de resecuenciación. En este capítulo presentamos los primeros resultados de la resecuenciación de ocho accesiones, siete de berenjena común y una del pariente silvestre S. incanum L., que corresponden a los progenitores de un cruce multiparental de generación avanzada (MAGIC) población que se encuentra actualmente en desarrollo utilizando la secuencia del genoma de la berenjena recién desarrollada que se presenta en el Cap. 7 de este libro. Se identificaron más de diez millones de polimorfismos entre las accesiones, el 90% de ellos en el S. incanum silvestre relacionado, lo que confirma la erosión genética de la berenjena común cultivada. Entre los progenitores de la población MAGIC, el patrón de distribución de polimorfismos comunes a lo largo de los cromosomas ha revelado posibles huellas de introgresión ancestral de cruces interespecíficos. El conjunto de polimorfismos se ha anotado extensamente y actualmente se está utilizando para análisis adicionales con el fin de genotipar eficientemente la población MAGIC en curso y diseccionar rasgos agronómicos y morfológicos importantes. La información proporcionada en este primer estudio de resecuenciación en berenjena será extremadamente útil para ayudar al fitomejoramiento a desarrollar nuevas variedades mejoradas y resistentes para enfrentar futuras amenazas y desafíos. [EN] The next-generation sequencing revolution is allowing the whole-genome resequencing (WGRS) of hundreds or even thousands of accessions for staple crops and model species. With the release of their reference genome, progressively also other plants, species are undertaking WGRS projects for a broad variety of studies. In common eggplant (Solanum melongena L.), although a first draft of the reference genome sequence has been published, no resequencing studies have been performed so far. In this chapter, we present the first results of the resequencing of eight accessions, seven of common eggplant and one of the wild relative S. incanum L., that correspond to the parents of a multi-parent advanced generation inter-cross (MAGIC) population that is currently under develop- ment using the newly developed eggplant genome sequence presented in Chap. 7 of this book. Over ten million polymorphisms were identified among the accessions, 90% of them in the wild related S. incanum, confirming the genetic erosion of the cultivated common eggplant. Among the MAGIC population parents, the common polymorphism distribu- tion pattern along the chromosomes has revealed possible footprints of ancestral intro- gression from interspecific crosses. The set of polymorphisms has been extensively anno- tated and currently is being used for further analyses in order to efficiently genotype the ongoing MAGIC population and to dissect important agronomic and morphological traits. The information provided in this first resequencing study in eggplant will be extremely helpful to assist plant breeding to develop new improved and resilient varieties to face future threats and challenges. This work has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and from Spanish Ministerio de Economía, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER).

Tese de Doutoramento, Ciências Agrárias, especialidade em Biotecnologia, 07 de dezembro de 2018, Universidade dos Açores. Os fungos micorrízicos arbusculares (FMA), simbiontes obrigatórios pertencentes ao filo Glomeromicota, formam relações mutualistas com cerca de 90% das espécies de plantas terrestres. Estes fungos fornecem água e minerais à planta e em troca a planta fornece produtos da fotossíntese. As comunidades de FMA presentes na rizosfera da planta endémica Picconia azorica, de duas ilhas do arquipélago dos Açores, foram estudadas com recurso a métodos morfológicos e moleculares. Os esporos de FMA isolados do solo foram morfologicamente classificados em 46 morfotipos. A caraterização molecular dos esporos foi efetuada por sequenciação de um fragmento de rADN com cerca de 1,5 kb (SSU-ITS-LSU) e resultou na obtenção de 125 sequências. Após análise filogenética estas sequências foram alocadas a 18 filotipos, as quais mostraram pertencer às famílias Acaulosporaceae, Archaeosporaceae, Claroideoglomeraceae, Gigasporaceae e Glomeraceae. Oito destas sequências não agruparam com nenhuma sequência previamente conhecida, o que sugere que correspondem a espécies que ainda não foram molecularmente identificadas ou que constituem novas espécies para a ciência. A análise da ecologia revelou que existem diferenças na comunidade de FMA entre as ilhas Terceira e São Miguel. A comunidade de FMA no solo da ilha Terceira é dominada por elementos das famílias Acaulosporaceae e Glomeraceae, enquanto, que em São Miguel é dominada pelas famílias Glomeraceae e Gigasporaceae. A análise microscópica das raízes de P. azorica revelou que as amostras se encontravam altamente colonizadas (89 – 99%) pelas diferentes estruturas do fungo (hifas, arbúsculos e vesículas), permitindo assim considerar a planta como sendo micotrófica e altamente dependente de FMA. A identificação dos fungos presentes nas raízes de P. azorica foi efetuada com base no fragmento de 1.5 kb do rADN e com recuso ao método de restrição terminal de fragmentos polimórficos (T-RFLP) conhecidos, no programa TRAMPR. A análise identificou 22 filotipos pertencentes às famílias Acaulosporaceae, Claroideoglomeraceae, Diversisporaceae, Gigasporaceae e Glomeraceae. Verificou-se que a espécie Acaulospora brasiliensis estava presente nas raízes de todas as plantas analisadas e que a família Glomeraceae foi a família mais representada com a identificação de 13 filotipos. Esta análise revelou ainda que em ambas as ilhas na colonização das raízes dominavam espécies da família Glomeraceae, sendo que nas raízes da ilha Terceira a presença de Acaulosporaceae foi mais frequente, enquanto, que nenhum membro da família Claroideoglomeraceae foi identificado em amostras de raízes de São Miguel. Os resultados destes estudos sugerem que as comunidades de FMA nas florestas nativas dos Açores são determinadas por fatores históricos e geográficos, bem como pelas propriedades químicas do solo e pelas condições ambientais. Para o estudo da capacidade de colonização de plantas micropropagadas pelas espécies Acaulospora laevis e Acaulospora koskei foram isolados e sequenciados segmentos de quatro genes de P. azorica homólogos a outros previamente relacionados à simbiose e foi analisada a expressão destes genes por qRT-PCR durante os estágios iniciais da simbiose com FMA. Nestes ensaios a indução da expressão por Ac. laevis revelou ser superior à obtida com Ac. koskei. A influência do FMA Funneliformis mosseae sobre o desenvolvimento de plantas de P. azorica micropropagadas foi estudada. Ao fim de 8 meses de tratamento as plantas inoculadas com o FMA revelaram-se maiores e mais robustas que as plantas não inoculadas. Esta é a primeira vez em que se estuda a condição de FMA presentes na rizosfera de P. azorica nas florestas nativas Açorianas. A P. azorica demonstrou elevada dependência pelos FMA o que revela sintonia com o facto de estes FMA terem revelado potencial para serem aplicados como promotores do sucesso na utilização de plantas micropropagadas em programas de conservação e restauração de florestas nativas no arquipélago dos Açores. ABSTRACT: Arbuscular mycorrhizal fungi (AMF) are obligate symbionts, belonging to the phylum Glomeromycota that form mutualistic symbioses with about 90% of land plant species. They provide the host plant with mineral nutrients and water, in exchange for photosynthetic products. The communities of AMF present in the rhizosphere of endemic tree Picconia azorica from two Azorean islands, Terceira and São Miguel, were assessed by morphological and molecular methods. AMF spores isolated from the soil were morphologically classified in 46 distinguishable morphotypes. Molecular characterisation of a c. 1.5 kb rDNA fragment, comprising SSU-ITS-LSU, resulted in 125 AMF sequences. Phylogenetic analyses assigned the sequences to 18 phylotypes, belonging to the families Acaulosporaceae, Archaeosporaceae, Claroideoglomeraceae, Gigasporaceae and Glomeraceae. Also, 8 phylotypes did not cluster with sequences of any described species implying that they are either species that have not yet been identified or are new to science. Ecological analyses revealed differences in AMF community composition between islands. In Terceira, the rhizospheric soil was dominated by species belonging to Acaulosporaceae and Glomeraceae, while São Miguel was dominated by Glomeraceae and Gigasporaceae. Microscopic survey of P. azorica root samples showed that all studied samples were highly colonised (89 – 99%) by AMF structures (hyphae, arbuscules and vesicles) which allowed us to classify the endemic plant as mycotrophic and highly dependent on AMF. The identity and diversity of AMF colonising the roots of P. azorica were assessed by terminal restriction fragment length polymorphism (T-RFLP) of the c. 1.5 Kb rDNA fragment. Database terminal restriction fragment length polymorphism (T-RFLP) approach in conjunction with TRAMPR package was used to identify the AMF community present in the roots. By that were identified 22 phylotypes belonging to Acaulosporaceae, Claroideoglomeraceae, Diversisporaceae, Gigasporaceae and Glomeraceae. Acaulospora brasiliensis was present in all studied roots of all sampled plants and Glomeraceae showed to be the more diverse family with 13 phylotypes identified. It was also observed differences in AMF community composition between islands. Although in both islands root colonization was dominated by species belonging to Glomeraceae, in Terceira the presence of Acaulosporaceae was more frequent, while no Claroideoglomeraceae were identified in São Miguel root samples. All results suggest that AMF communities in native forest of Azores are determined by geographic and historical factors as well as soil chemical properties and environmental conditions. The ability of Acaulospora laevis and Acaulospora koskei to colonised micropropagated plants of P. azorica was tested by isolating and sequencing of partial sequences of four P. azorica symbiosis-related genes and analyses of gene expression by qRT-PCR during early stages of AMF symbiosis. This revealed that both AMF species varied in their capacity to induce the early stages of the plant symbiotic response, in which Ac. laevis showed superior to Ac. koskei. The influence of Funneliformis mosseae on the growth of micropropagated P. azorica was investigated. After eight months of growth, inoculated plants showed to be bigger and more robust than non-inoculated plants. This is the first time that AMF status in the rhizosphere of P. azorica in native forest of the Azores was investigated. P. azorica showed to be highly dependent on AMF which is in line with the showed potential of AMF application as promoters of plant establishment in conservation and restoration of native forests of the Azores archipelago. Fundo Regional de Ciência e Tecnologia - FRCT (M2.1.2/F/041/2011)

Genetic variability can be generated through in vitro culture via somaclonal variation. This tool can be potentially useful in a breeding program involving apomictic buffelgrass genotypes. The aim of this work was to evaluate inter simple sequence repeats (ISSR) as molecular markers to detect genetic variation in in vitro buffelgrass regenerated plants. Six plants regenerated from in vitro anther culture, via somatic embryogenesis were used, as well as the anther donor genotype (RN 51) as control. Of a total of 26 ISSR primers tested, 22 amplified, detecting 12% polymorphism with a divergence between 5 and 24% from RN 51. Amplification products were observed with the primers containing di-, tri- or tetra-nucleotide sequences, with or without additional nucleotides at the 3′ end. The most informative primers were those containing the repetitive sequences GACAn, AGn or GAn. Moreover, the regenerants transplanted at field conditions differed in morphological characteristics among them and with respect to RN 51. This study confirms that ISSR are useful to identify genetic variability in in vitro regenerated buffelgrass plants. El cultivo in vitro permite generar variabilidad genética mediante variación somaclonal. Este fenómeno puede ser potencialmente útil en un programa de mejora en genotipos apomícticos de buffelgrass. El objetivo del presente estudio fue evaluar inter secuencias simples repetidas (ISSR) como marcadores moleculares en la detección de variación genética en plantas regeneradas in vitro de buffelgrass. Se utilizaron seis plantas regeneradas mediante el cultivo in vitro de anteras, vía embriogénesis somática, y el genotipo dador de anteras (NR 51) como control. De un total de 26 cebadores ISSR probados, 22 de ellos amplificaron, detectando un 12% de polimorfismo con una divergencia del 5 al 24% con respecto al material NR 51. Se observaron productos de amplificación con los cebadores que contienen secuencias di-, tri- o tetra-nucleótidos, con o sin nucleótidos adicionales en el extremo 3′. Los cebadores más informativos fueron aquellos que contenían secuencias repetitivas GACAn, AGn o GAn. Conjuntamente, las plantas trasplantadas a campo manifestaron características morfológicas diferentes entre ellas y con respecto al NR 51. El presente estudio confirma que el empleo de ISSR permite identificar variabilidad genética en plantas regeneradas in vitro de buffelgrass. Fil: Carloni, Edgardo. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: López Colomba, Eliana. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: Ribotta, Andrea. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: Quiroga, Mariana. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: Tommasino, Exequiel. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: Griffa, Sabrina. Instituto Nacional de Tecnología Agropecuaria (Argentina) Fil: Grunberg, Karina. Buenos Aires (Argentina). Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET).

Introducción General, Aspectos metodológicos, Objetivos, Discusión general y Conclusiones escritos en español, Tesis Univ. Granada. Departamento de Fisiología Vegetal. Leída el 13 de junio de 2008

Tesis Univ. Granada. Departamento de Genética, Este trabajo estuvo financiado por los proyectos EVOFLOR (CGL2006-04883), del Ministerio de Educación y Ciencias, y MONTES-CONSOLIDER Consolider-Ingenio (CSD2008-00040), beca del Programa Nacional de Formación de Personal Investigador del Ministerio de Educación y Ciencia (BES-2007-142206).

Genetic divergence between populations can lead to reproductive isolation. Hybrid incompatibilities (HI) represent intermediate points along a continuum toward speciation. In plants, genetic variation in disease resistance (R) genes underlies several cases of HI. The progeny of a cross between Arabidopsis (Arabidopsis thaliana) accessions Landsberg erecta (Ler, Poland) and Kashmir2 (Kas2, central Asia) exhibits immune-related HI. This incompatibility is due to a genetic interaction between a cluster of eight TNL (TOLL/INTERLEUKIN1 RECEPTOR-NUCLEOTIDE BINDING-LEU RICH REPEAT) RPP1 (RECOGNITION OF PERONOSPORA PARASITICA1)-like genes (R1-R8) from Ler and central Asian alleles of a Strubbelig-family receptor-like kinase (SRF3) from Kas2. In characterizing mutants altered in Ler/Kas2 HI, we mapped multiple mutations to the RPP1-like Ler locus. Analysis of these suppressor of Ler/Kas2 incompatibility (sulki) mutants reveals complex, additive and epistatic interactions underlying RPP1-like Ler locus activity. The effects of these mutations were measured on basal defense, global gene expression, primary metabolism, and disease resistance to a local Hyaloperonospora arabidopsidis isolate (Hpa Gw) collected from Gorzow (Gw), where the Landsberg accession originated. Gene expression sectors and metabolic hallmarks identified for HI are both dependent and independent of RPP1-like Ler members. We establish that mutations suppressing immune-related Ler/Kas2 HI do not compromise resistance to Hpa Gw. QTL mapping analysis of Hpa Gw resistance point to RPP7 as the causal locus. This work provides insight into the complex genetic architecture of the RPP1-like Ler locus and immune-related HI in Arabidopsis and into the contributions of RPP1-like genes to HI and defense.

Tese de Doutoramento, Biologia, 28 de maio de 2018, Universidade dos Açores. Lactuca watsoniana Trel., é uma herbácea perene, endémica do Arquipélago dos Açores. Localmente denominada de “Alfacinha”, pode ser encontrada em quatro das nove ilhas do Arquipélago dos Açores (Faial, Pico, Terceira e São Miguel), estando possivelmente extinta da ilha de São Jorge. O tamanho total estimado das populações é de 500 a 2000 indivíduos, mas observações recentes no campo indicam que poderão ser menos de 500 indivíduos. Considerada como taxon prioritário na Directiva Habitats (Annex B-II) bem como na Convenção de Berna em termos de conservação e está listada como ameaçada (EN B2ab (i, ii, iii); C2a(i)) na Lista Vermelha da IUCN 2017. Atualmente, a Lactuca watsoniana encontra-se restrita a zonas húmidas, ravinas profundas e estreitas, crateras zonas declivosas, prados naturais de Festuca, matos de Erica e florestas de Juniperus entre 600-800 m. Está ameaçada por perda e degradação de habitat, resultante de expansão dos pastos, invasão por espécies exóticas, introdução de herbívoros e distúrbio de áreas sensíveis por turistas e locais. Neste trabalho investigaram-se os seguintes tópicos: i) propagação vegetativa por sementes; ii) genética de populações; e iii) filogenética e filogeografia. Foi estabelecido um protocolo eficaz e exequível para propagação por via seminal, germinando as sementes com 0.1 mg l-1 GA3, ethephon, e um filtro de luz vermelha e um regime de temperatura alterna de 15/10°C, com um fotoperíodo de 12 horas. Este protocolo permitiu a produção de centenas de plântulas viáveis que foram replantadas na população de origem. Dada a necessidade de proceder ao reforço das populações naturais em algumas ilhas, pretendeu-se definir se existiam riscos de contaminação genética resultante da troca de material entre as diferentes ilhas, para isso estudou-se a estrutura e variabilidade genética das populações, usando 8 microssatélites nucleares, desenvolvidos especificamente para a L. watsoniana. Os resultados mostraram uma clara separação entre as várias ilhas dos Açores, estando a maior variação genética dentro das populações (55.0%), mas com níveis relativamente altos de variação entre os clusters (27.3%). Evidenciando um grau de diferenciação entre as populações elevado e fluxo genético com valores inferiores a 1, bem como a existência de isolamento e barreiras geográficas. De modo a clarificar a posição taxonómica da L. watsoniana, nomeadamente em relação a espécies próximas da Europa, Norte da América e de outros Arquipélagos da Macaronésia (Canárias), recorremos a marcadores moleculares nucleares (ITS) e quatro do cloroplasto. Na análise das sequências combinadas de ITS e do cloroplasto (Parsimónia, Máxima verosimilhança e Inferência Baeysiana) o taxon dos Açores, mostrou a existência de um padrão filogeográfico através do arquipélago, com a presença de 5 haplótipos distintos para a L. watsoniana, quatro endémicos em apenas uma ilha (Faial, Pico, Terceira e São Miguel) e um haplótipo com informação genética partilhada do Faial e Pico, bem como uma relação filogenética, bem suportada, com as Lactuca Norte Americanas. ABSTRACT: Lactuca watsoniana Trel., is a perennial herb, endemic to the Azores archipelago. Locally called "Alfacinha", the species is restricted to only four of the nine islands of the archipelago (São Miguel, Terceira, Pico and Faial) and is possibly extinct in São Jorge Island. Estimates of its total population size are 500 to 2,000 individuals, but recent field observations indicate that it can be fewer than 500 individuals. It is therefore considered a priority species for conservation and was listed as endangered on the IUCN Red List 2017. Furthermore, it was included in Annex II of the EC Habitats Directive and is protected under the Berne Convention. Lactuca watsoniana is currently restricted to the steep slopes of craters and ravines in temperate juniper rain forest between 600-800 m of altitude. The species is threatened by habitat loss and degradation resulting from changes in land use, namely expansion of pasture, invasion by exotic species, consumption by introduced herbivores and disturbance of sensitive areas by tourists and locals. In this thesis, we investigated the following topics: i) seed propagation; ii) population genetics; and iii) phylogenetics and phylogeography. We established and efficient and feasible seed propagation protocol by germinating the seeds germinate seeds with 0.1 mg l-1 GA3, ethephon, a red-light filter and a temperature regime of 15/10°C, and 12 hours’ photoperiod. This protocol allowed producing hundreds of viable seedlings that were reintroduced in the source population. Given the need to reinforce natural populations in some of the islands, we aimed to find out if any outbreeding risks existed, resulting from material exchanges between the different islands. For that, we studied the genetic structure and variability of the populations, using eight nuclear microsatellites, developed specifically, for Lactuca watsoniana. Our findings showed a clear separation among the islands, with the largest proportion of genetic variation found within populations (55.0%) but with relatively high levels of genetic variation both among clusters (27.3%). Furthermore, a high variability between the populations, a gene flow value below one, and the presence of geographical isolation and barriers were estimated. In order to clarify the taxonomic position of L. watsoniana, namely the phylogeographic and phylogenetic relationship with the morphologically similar species from Europe, North America and the geographically close taxa from the Canary Islands, we used one nuclear region (ITS) and four chloroplast markers. Parsimony, Maximum likelyhood and Bayesian Inference analyses were conducted and revealed a strongly supported monophyletic Lactuca clade, and a clear separation of Macaronesian endemic Lactuca in sister clades. Lactuca watsoniana, endemic to Azores, showed a phylogeographic pattern across the archipelago, with the presence of five different haplotypes for L. watsoniana: four single island endemics (Faial, Pico, Terceira e São Miguel) and one occurring on both Faial and Pico and a strongly supported phylogenetic relationship with North America Lactuca. Fundo Regional da Ciência pelo financiamento da Bolsa de Doutoramento (M3.1.2/F/032/2011 e FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE.

Conselho Nacional de Desenvolvimento Científico e Tecnológico O genoma plastidial (plastoma), em geral, é uma molécula circular apresentando cerca de 150 kb e 120 genes, os quais atuam, principalmente, na fotossíntese e na expressão gênica. A trajetória evolutiva dos plastomas abrange rearranjos estruturais, degeneração de genes, transferência de genes para o núcleo, seleção positiva e ganhos e de perdas de edições de RNA. Tais eventos são do interesse de diversas áreas da ciência vegetal, como filogenia, evolução, pesquisa básica e biotecnologia. Somado a isto, plastomas têm um conjunto de genes conservados útil na resolução de filogenias entre taxa distantes, sendo que o uso de plastomas inteiros em abordagens filogenômicas tem sido aplicado na resolução de relações intragenéricas. Em adição, sequências plastidiais de rápida evolução, como espaços intergênicos e introns, são fontes de marcadores moleculares aplicados em filogeografia e estudos genéticos. Por fim, plastomas são promissoras plataformas para aplicações biotecnológicas por meio da transformação plastidial. Muitos plastomas têm sido sequenciados com o avanço da tecnologia de sequenciamento nos últimos anos. Porém, plastomas de diversas espécies permanecem desconhecidos. Em vista disso, este estudo propôs-se a fornecer as sequências dos plastomas de cinco espécies oleaginosas utilizadas em diferentes demandas industriais: Linum ustitatissimum (Linaceae), Crambe abyssinica (Brassicaceae), Acrocomia aculeata, Astrocaryum murumuru, and A. aculeatum (Arecaceae). Neste estudo, uma detalhada caracterização destes plastomas relativo a marcadores moleculares, filogenia e evolução foi realizada. Análises de evolução molecular de genes plastidiais em Arecaceae mostram que genes altamente divergentes parecem ser traços evolutivos distintos de determinadas espécies, e que mais da metade dos genes carregam assinaturas de seleção positiva. Ademais, rearranjos únicos foram identificados em plastomas de Arecaceae e Linaceae. Ganhos e perdas de edições de RNA foram encontrados em todas as espécies sequenciadas, sugerindo uma relativamente alta taxa evolutiva deste processo nos plastídios. Adicionalmente, centenas de marcadores moleculares plastidiais foram mapeados, constituindo informação útil para estudos genéticos visando estabelecer estratégias de melhoramento genético, domesticação e conservação dos recursos naturais. Também são apresentadas filogenias com alta resolução e suporte, baseadas em genes concatenados e plastomas inteiros. Em síntese, este estudo lança luz acerca da trajetória evolutiva dos plastomas e suscita discussões sobre a relação entre adaptação ao ambiente e expressão de genes plastidiais. The plastid genome (plastome) is usually a circular molecule of about 150 kb and bears about 120 genes involved mainly in photosynthesis and gene expression. Its evolutionary trajectory includes structural rearrangements, gene degenerations, gene transfer to nucleus, positive selection, and events of gain and loss of RNA editing sites. These features are subject of interest in several areas of plant science such as phylogeny, evolution, basic research, and biotechnology. Additionally, plastomes bear a set of conserved genes useful for phylogenetic studies of deep relationships, so phylogenomic approaches based on whole plastomes have been also applied to resolve intrageneric relationships. Fast-evolving regions of plastid DNA such as intergenic spacers and introns, are source of molecular markers used routinely in phylogeographic and genetic studies. Finally, plastomes are a promising platform for biotechnological applications via plastid transformation. Over the last few years with the improvement of sequencing technology, many plastomes have been sequenced. Nevertheless, plastomes of several species belonging to different families remain unknown. Therefore, the purpose of this study was the sequencing of five plastomes of oleaginous species useful for different industry demands as follows: Linum ustitatissimum (Linaceae), Crambe abyssinica (Brassicaceae), Acrocomia aculeata, Astrocaryum murumuru, and A. aculeatum (Arecaceae). Here, it is presented a detailed characterization regarding molecular markers, phylogenetic inferences, and evolution. Molecular evolution analyses of protein- coding genes in Arecaceae show that highly divergent genes seem to evolve in a species- specific manner and more than half of the genes bear signatures of positive selection. Additionally, within Arecaceae and Linaceae were identified unique plastome rearrangements. It was also found events of gain and loss of RNA editing sites in all sequenced species, indicating a relatively high evolutionary rate of the RNA editing machinery. Hundreds molecular markers were identified in the plastomes sequenced here, providing information useful for several genetic studies aiming to stablish strategies for genetic breeding, domestication, and conservation of natural resources. Moreover, the phylogenies presented in this study, based on concatenated plastid genes or whole plastomes resulted in well-supported and well-resolved trees. Finally, this study sheds light on the evolutionary trajectory of plastomes, which give rise to questions about the relationships between environment adaptation and plastid gene expression.

Paspalum notatum é uma das mais importantes espécies das pastagens nativas do Sul do Brasil, que é a principal fonte forrageira para a pecuária. Os ecótipos nativos são tetraploides e de reprodução apomítica, o que impede o registro e a proteção de cultivares. Porém, uma variedade cultivada, Paspalum notatum var. saurae (cultivar Pensacola) é diplóide e sexual. O objetivo deste trabalho foi de poliploidizar artificialmente plantas de cv Pensacola, para serem utilizadas como genitores femininos em cruzamentos com genitores masculinos tetraploides e apomíticos. Plântulas e sementes foram tratadas por imersão com soluções de colchicina por tempo de exposição variável. Três plantas confirmaram número cromossômico tetraploide. As plantas polyploides obtidas serão avaliadas quanto ao modo de reprodução; se confirmarem ser sexuais, serão utilizadas nos esquemas de cruzamentos com plantas apomíticas nativas para obtenção de novos híbridos intraespecíficos. Paspalum notatum is one of the most important native grassland species of southern Brazil, and the main forage source for livestock. The native ecotypes are tetraploid and have apomictic reproduction, which prevents the registration and protection of plant varieties. However, the cultivated variety Paspalum notatum var. saurae (cultivar Pensacola) is diploid and sexual. The objective of this study was to artificially produce polyploid cv. Pensacola plants, to be used as female parents in crosses with male tetraploid and apomictic parents. Seedlings and seeds were immersed in colchicine solutions for different periods. A tetraploid chromosome number was confirmed in three plants. The reproduction mode of the resulting polyploid plants will be assessed; if confirmed to be sexual, they can be used in crosses with native apomictic plants to breed new intraspecific hybrids.

No norte do estado de Minas Gerais, existe um ecótono formado pela união de três formações vegetais, a Mata Atlântica, o Cerrado e a Caatinga. Esta região está ameaçada pela extração excessiva de madeira e destruição de habitat. Várias espécies de árvores tropicais nativas desta área de ecótono estão em perigo de extinção devido à sobre-exploração e perda de habitat. Cedrela fissilis é uma espécie de árvore nativa do Brasil e distribuída em florestas sazonais e matas ciliares no norte de Minas Gerais. Neste estudo, analisou-se a localização genealógica de uma população do Norte de Minas (PAN) em relação com as duas linhagens conhecidos (leste e oeste) de C.fissilis e, o estudo da estrutura genética e estimativas do sistema reprodutivo. Para obter tecido germinativo de sementes, adequado para extração de DNA, foram testados três métodos de desinfecção, quatro meios de cultura e um substrato comercial para plantas. Os resultados mostraram que a aplicação de técnicas in vitro com desinfecção aumentou germinação por um fator de 3 a 5 vezes, com respeito a não utilização de técnicas in vitro e a dupla desinfecção aumentou o fator de germinação 1,7 no que diz respeito à desinfecção simples. Encontramos altos valores de diversidade genética que diferenciaram a PAN das linhagens Leste e Oeste; assim, pode ser considerado como uma nova fonte de variabilidade dentro de C. fissilis. Os resultados confirmaram C. fissilis como espécie de reprodução cruzada com pequena proporção de autofecundação. PAN apresentou acasalamento entre parentes e população estruturada entre progênies como consequência de desvios do acasalamento ao acaso. Concluímos que as restrições no fluxo genético entre árvores reprodutivas levaram aos altos níveis de diferenciação genéticas observadas na população de PAN. In northern Minas Gerais state, there is an ecotone formed by the junction of three vegetation formations, Atlantic dry forest, Cerrado, and Caatinga. This region is threatened by over-logging and habitat destruction. Several tropical tree species native to this ecotone are endangered by extinction, subject to overexploitation and habitat loss. Cedrela fissilis is a tropical tree species native to Brazil and distributed in seasonal forests and gallery forests of northern Minas Gerais. In this study, we analyzed the genealogical placement of a population from northern Minas Gerais (PAN) related to the two known lineages (East and West) of C. fissilis and carry out genetic structure and mating system analyses of its offspring. To obtain tissue from seedling suitable for DNA extraction we tested three disinfection methods, four culture media and a commercial substrate for plants. The results showed that the application of in- vitro techniques jointly with disinfection increased the germination by a factor from 3 to 5 with respect to the non-use of in-vitro techniques, and the double disinfection increased the germination by a factor of 1.7 respect of the simple disinfection. We found high values of genetic diversity that differentiate from both the East and West lineages; thus, PAN can be considered as a new source of variability within C. fissilis. The results confirmed that C. fissilis is as an outcrossed species with some proportion of selfing. PAN presented mating among relatives, and population structure among offspring as a consequence of deviations from random mating. We concluded that restrictions to gene-flow among reproductive trees lead to the high levels of genetic differentiation observed in PAN.

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