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Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in coloration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common color pattern in African cichlids, vertical bars, and potential interactions between the two color patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both color patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.

Significant variability is available in the F2 population of brinjal. Top crosses of brinjal Biliudda badane × mullu badane produced from F1 generation were in augmented design at ZARS Shimogga in Kharif 2017. They have several characteristics of plant breeding significance with sufficient scope for added improvement to growing conditions. The F2 study showed significant variation for nine quantitative traits. Close estimates between GCV and PCV values indicated lesser influence of environmental factors on the expression of traits under study. In this investigation, the proportion of genetic contribution of high GCV, PCV coupled with high broad sense heritability and genetic advance to the overall phenotypic expression of the studied traits like number of fruits per plant, number primary branches, number of flowers per plant was high, indicating predominant control of additive genes, and these traits could be improved upon by selection without progeny testing. High magnitude of heritability for most of the characters suggested the progress of improvement in yield and its components. Differences in mean values of parents for various characters indicated involvement of diverse parents in the crosses studied. The F2 plants exceeded either of the parents for most of the characters, which seems to be due to transgressive segregation.

Bacterial wilt caused by Ralstonia solanacearum is the main bacterial disease in potato. Solanum commersonii Dun. (cmm; 2n = 2x = 24, 1 EBN) is a native species to southern Brazil, Uruguay and Argentina with desirable traits for introgressive hybridisation breeding into cultivated potato such as resistance to R. solanacearum. In Uruguay, successful crosses between cmm and Solanum tuberosum Group Tuberosum (tbr; 2n = 4x = 48, 4 EBN) have been carried out with this objective, resulting in backcross 1, 2 and 3 progenies. The aim of this study was to characterise one backcross 3 progeny (BC3) using cytogenetic, genetic, morphological and agronomic descriptors. Resistance to R. solanacearum showed transgressive segregation and an association with plant architecture. Fifty-two percent of individuals had chromosome numbers close to cultivated potato with no evidence of preferential loss of cmm chromosomes. All BC3 individuals showed male sterility, probably due to nuclear-cytoplasmic interactions. Although there was wide segregation in morphological traits, most individuals resembled the recurrent tbr parents. A few more backcrosses combined with screening for bacterial wilt resistance may be necessary to allow for further recombination and removal of undesirable traits from cmm. The presence of BC3 individuals with chromosome numbers close to 2n = 48, combining morphological traits from tbr with good levels of resistance, suggests the occurrence of introgression events. This points to S. commersonii as one of the most promising genetic resources for potato breeding from the Southern Atlantic region.

We identified cryptic early blight resistance introgressions in tomato breeding lines and demonstrated efficient genotypic selection for resistance in the context of a tomato breeding program. Early blight is a widespread and problematic disease affecting tomatoes (Solanum lycopersicum). Caused by the fungal pathogen Alternaria linariae (syn. A. tomatophila), symptoms include lesions on tomato stems, fruit, and foliage, often resulting in yield losses. Breeding tomatoes with genetic resistance would enhance production sustainability. Using cross-market breeding populations, we identified several quantitative trait loci (QTL) associated with early blight resistance. Early blight resistance putatively derived from ‘Campbell 1943′ was confirmed in modern fresh market tomato breeding lines. This resistance offered substantial protection against early blight stem lesions (collar rot) and moderate protection from defoliation. A distinctive and potentially novel form of early blight foliar resistance was discovered in a processing tomato breeding line and is probably derived from S. pimpinellifolium via ‘Hawaii 7998’. Additional field trials validated the three most promising large-effect QTL, EB-1.2, EB-5, and EB-9. Resistance effects for EB-5 and EB-9 were consistent across breeding populations and environments, while EB-1.2’s effect was population specific. Using genome-wide marker-assisted backcrossing, we developed fresh market tomato lines that were near-isogenic for early blight QTL. Resistance in these lines was largely mediated by just two QTL, EB-5 and EB-9, that together captured 49.0 and 68.7% of the defoliation and stem lesion variance, respectively. Our work showcases the value of mining cryptic introgressions in tomato lines, and across market classes, for use as additional sources of disease resistance.

The wild species of rice, Oryza rufipogon, is a source of genetic variation for yield-enhancing traits and blast resistance. With the objective to genetically enhance the elite rice cultivar, ‘Samba Mahsuri’, a set of 192 BC2F2 and BC2F3 lines developed from O. rufipogon was characterized for yield-enhancing traits and blast resistance. The study revealed the presence of significant genetic variability and transgressive segregation for productive tillers, spikelets per panicle, and grain yield per plant. The study also identified several introgression lines superior to the recurrent parent for yield enhancing traits and blast resistance. Molecular characterization of 26 blast resistant lines identified multiple blast resistance genes in IL-136 [Pib, Pi9 (t), Pi54, Pi38, Pitp and Pi20(t)], IL-3 [Pib, Pi54, Pi38, Pitp and Pi20(t)], and IL-140 [Pib, Pi9(t), Pi54, Pi38, and Pitp]. Based on the performance of yield-enhancing traits and blast resistance, seven lines (IL-27, IL-28, IL-29, IL-72, IL-139, IL-158 and IL-171) showed merit. Estimation of the recovery of the recurrent parental genome by using 117 polymorphic SSR markers revealed that recurrent-parental genome recovery varied from 54.0 (IL-158) to 92.3% (IL-27). These promising, high-yielding introgression lines with multiple blast-resistance genes can serve as important genetic resources for yield and blast resistance improvement in rice, especially for the southern India.

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

Drought tolerance of plants is related to their root system architecture. The architecture of a mature plant root system is closely linked to seminal root growth at the seedling stage; hence, selection for root characteristics at the seedling stage may identify genotypes better suited for drought conditions. Here, the genetics of seminal root angle and number were investigated in three doubled haploid mapping populations of wheat. All populations showed significant phenotypic variation for both traits and each demonstrated transgressive segregation. In total, 34 genomic regions were associated with seminal root traits; however, most QTLs were variable from year to year and were population specific. Considering only the results consistent across both years of experiments, five QTLs for seminal root angle were identified on chromosomes 2DS, 5BS, 6AL, 7A, and 7BS, but only the 2DS QTL appeared in two of the three populations. For the seminal root number, one QTL was identified on 4BL. Correlation analyses for seminal root angle, number, and seed weight revealed interesting relationships to consider for future research. In one population, those interactions wrongfully identified QTLs for seed weight as QTLs for seminal root traits. Our findings demonstrate that seminal root angle and number are complex traits and despite high heritability, may be more difficult to unwind than previously proposed.

Head smut (HS) is one of the most devastating diseases in spring maize growing region. To provide theoretical and applied basics for breeding resistant maize to HS, quantitative trait loci (QTL) for HS resistance was identified in this study. The resistant QTL to HS was studied by the F2:3 population derived from the cross T32 (highly resistant genotype) × HC (highly susceptible genotype). Analysis for each environment and joint analysis across three environments were used to identify QTL for the F2:3 population. A significant difference in HS resistance was found between inbred lines ‘T32’ and ‘HC’. A large genetic variation and transgressive segregation of the F2:3 population were observed among three different sites, Guian (GA), Huaxi (HX), and Pingba (PB). Two stable QTL for resistance to HS were detected in different environments, located in the interval umc1177 to umc2224 on chromosome 1 and in the interval umc1006 to nc013 on chromosome 6. Both of these QTL can be used for further marker-assisted selection (MAS) breeding and theoretical study of maize resistance to HS.

FAPEMIG - Fundação de Amparo a Pesquisa do Estado de Minas Gerais O uso de cultivares resistentes é o método ideal para o controle de nematoide das galhas em alface. Conhecer aspectos genéticos relacionados à resistência ao patógeno, torna-se importante, para a tomada de decisões e o estabelecimento de estratégias de melhoramento. Portanto o objetivo da pesquisa foi estimar e analisar parâmetros genéticos e fenotípicos para a reação de resistência da alface ao nematoide das galhas Meloidogyne incognita. Utilizaram-se como genitores as cultivares Salinas 88 (resistente) e Regina 71 (suscetível), para cruzamento e obtenção das populações F1 e F2 a serem avaliadas, juntamente com os genitores, quanto à resistência ao M. incognita. As características avaliadas foram: número de ovos totais por planta (NO), número de ovos por grama de raiz (NOGR), índice de reprodução (IR), índice de reprodução por grama de raiz (IRGR) e fator de reprodução (FR). Os parâmetros estimados foram: variâncias fenotípica e genotípica, herdabilidade no sentido amplo, grau médio de dominância, medida dos efeitos aditivos e de dominância e ganhos por seleção. As populações foram também classificadas quanto a reação de resistência a partir do percentual de redução do fator de reprodução (RFR). Foi possível observar herdabilidade no sentido amplo relativamente alta, presença de efeitos aditivos dos alelos e ocorrência de segregação transgressiva, especialmente para as características de NO e IRGR, o que indica a possibilidade de ganhos na seleção. A cultivar ‘Regina 71’ foi classificada como altamente suscetível, ‘Salinas 88’ como moderadamente resistente e as gerações F1 e F2 como suscetíveis. Por fim, concluiu-se que existe variabilidade genética para resistência ao M. incognita, a partir do cruzamento entre as cultivares Regina 71 e Salinas 88 e que a cultivar Salinas 88 mostrou-se como uma viável fonte de resistência ao M. incognita para ser usada em programas de melhoramento. The use of resistant cultivars is the ideal method for the control of root-knot nematode on lettuce. Knowing genetic aspects related to resistance to the pathogen becomes important for decision making and the establishment of improvement strategies. Therefore, the objective of the research was to estimate and analyze genetic and phenotypic parameters for the resistance reaction of lettuce to the root-knot nematode Meloidogyne incognita. The cultivars Salinas 88 (resistant) and Regina 71 (susceptible) were used as parents to cross and obtain the F1 and F2 populations to be evaluated, together with the parents, for resistance to M. incognita. The characteristics evaluated were: number of total eggs per plant (NE), number of eggs per gram of root (NEGR), reproduction index (RI), reproduction index per gram of root (RIGR) and reproduction factor (RF). The estimated parameters were: phenotypic and genotypic variances, broad-sense heritability, average degree of dominance, measure of additive and dominance effects, and gains by selection. Populations were also classified for resistance reaction based on percentage reduction in reproduction factor (RRF). It was possible to observe relatively high broad-sense heritability, presence of additive effects of alleles and occurrence of transgressive segregation, especially for NE and RIGR traits, which indicates the possibility of gains in selection. Cultivar 'Regina 71' was classified as highly susceptible, 'Salinas 88' as moderately resistant and F1 and F2 generations as susceptible. Finally, it was concluded that there is genetic variability for resistance to M. incognita, from the crossing between the cultivars Regina 71 and Salinas 88 and that the cultivar Salinas 88 proved to be a viable source of resistance to M. incognita to be used in breeding programs. Dissertação (Mestrado)

Hybrid bermudagrass (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) is widely used for turf throughout subtropical and tropical climates because of its superior quality and performance. Development of cultivars adapted to broad range of environments is the main goal of many breeding programs. There is large variation for turfgrass characteristics and drought resistance among native bermudagrass (C. dactylon) germplasm originating from the Mediterranean region. Hence, the aim of this study was to develop triploid turf-type bermudagrass hybrids by making use of native genetic resources. Drought resistant tetraploid C. dactylon genotypes originating from the Mediterranean coastal region of Turkey were crossed with a diploid accession of C. transvaalensis from South Africa in 2011 and 2012. The hybrids were first identified using SRAP molecular markers. Then, phenotypic pre-selection was made for leaf shape, color and density and 273 hybrids were transplanted into the field. Two SSR markers further confirmed the true hybridity of 170 (62%) of these genotypes. Establishment rates in 2013, and turfgrass characteristics in 2014 and 2015 were recorded. Transgressive segregation was evident for estabilishment rate, turfgrass quality and color, and shoot density among progenies. Correlation analysis indicated that selection for shoot density, leaf texture, and prostrate growth habit could increase turf quality. The genotypes ‘45’ and ‘150’ were identified as promising parents for future breeding efforts as they provided positive general combining ability. The best ten hybrids with acceptable turfgrass characteristics were evaluated further under replicated field trials and line T4-C3 has just been released for commercial use.

Phenotypic characteristics, as well as the relation between carotenoid accumulation and gene expression during ripening were determined in fruits of five new hybrids between tangor cv. ‘Murcott’ and sweet orange cv. ‘Pera’. The genotypes were classified into the orange-like group, showing mainly epoxycarotenoids, oval fruit shape and yellowish color, or in the mandarin-like group, showing mainly β-cryptoxanthin, flattened shape and deep-orange coloration; although some hybrids presented intermediate characteristics. The diversity in carotenoid composition of hybrids and genitors were mostly explained by patterns of gene expression. High carotenoid (250–426 μg/g dry weight [dw]) and β-cryptoxanthin (81–125 μg/g dw) contents, observed in the mandarin-like group, were generally associated with high expression of upstream genes (GGPPS1, PSY, PDS). On the other hand, low expression/repression of these genes and high expression of downstream genes (BCHX and ZEP) were associated with low carotenoid (~158 μg/g dw) and β-cryptoxanthin (5–22 μg/g dw) contents and epoxycarotenoid accumulation, as occurred in the orange-like group. Breeding experiments resulted in hybrids with outstanding higher carotenoid contents than both genitors (up to 426 μg/g dw versus 158–250 μg/g dw in genitors), which was attributed to transgressive segregation. Differences among genotypes have great impact on commercial fruit quality and potential health benefits, such as the provitamin A content.

Zoysia germplasm exhibit different levels of sensitivity to fluazifop-P-butyl, but the genetic factors responsible for such differences are unknown. Segregation patterns of the fluazifop-P-butyl tolerance trait were studied under greenhouse conditions. In total, 244 F1 lines were generated from multiple crosses between the tolerant line 5337-2 (non–target site tolerance) and three more-sensitive lines (123, 252, and 5330-23). Progeny segregation showed that fluazifop-P-butyl tolerance within zoysiagrass (Zoysia spp.) is expressed as a quantitative trait with a wide range of intermediate phenotypes between parental phenotypes. Transgressive segregation was extensive and largely favored susceptibility in most families, but was especially evident for 5337-2 × 123 and 5337-2 × 5330-23. The segregation patterns for biomass reduction and percent injury were different within reciprocal crosses and among three different family crosses. Reciprocal effects were observed in growth reduction for 5337-2 × 5330-23, in percent injury at 3 wk after the treatment (WAT), and for 5337-2 × 252 at 6 WAT. This indicated that fluazifop-P-butyl tolerance was not completely controlled by nuclear genetic factors in 5337-2 and maternal/cytoplasmic inheritance was also partially responsible. These results suggested that fluazifop-P-butyl tolerance may be attributed to multiple genetic mechanisms, which could present a challenge for future breeding efforts because of the difficulty of fixing multiple traits within a breeding population.

Heterosis might be used in a strategic way to increase yields of flue-cured tobacco (Nicotiana tabacum L.), but previous reports have suggested levels of heterosis to be low for F₁ hybrids of this market class. Based on analysis of a 14-parent diallel, we found average levels of F₁ midparent heterosis to be 10.3%, a level that is substantially higher than previous estimates from the 1960s. Thirteen of ninety-one tested hybrids significantly outyielded the highest yielding parental lines. Heterosis might also be an indicator of superior allelic complementation by parental lines that, in principle, could be fixed in derived inbred lines. We compared F₃:₄ families derived from three high heterotic crosses and three low heterotic crosses and observed positive correlations between F₁ heterosis and desirable transgressive segregation. Hence, the data support the use of F₁ heterosis as a predictor of breeding crosses with increased potential for desired outcomes. Several derived F₃:₄ families exhibited yields that were comparable with, or significantly better than, corresponding heterotic F₁ hybrids, indicating that heterotic effects could be fixed within inbred lines. Results suggest a reconsideration of heterosis for increasing yields of flue-cured tobacco.

Adaptation of pigeonpea [Cajanus cajan (L.) Millspaugh], a short-day species, is restricted due to its sensitivity to photo-period. Earliness in this crop is reported to be linearly associated with photo-insensitivity; and this provides an opportunity to breed widely adapted cultivars through the selection for earliness. This research note reports breeding of the earliest maturing pigeonpea germplasm at ICRISAT. This germplasm, nicknamed as ‘super early’ and bred through the selection of transgressive segregants matured in

Background Water supply limits agricultural productivity of many crops including lettuce. Identifying cultivars within crop species that can maintain productivity with reduced water supply is a significant challenge, but central to developing resilient crops for future water-limited climates. We investigated traits known to be related to water-use efficiency (WUE) and yield in lettuce, a globally important leafy salad crop, in a recombinant inbred line (RIL) lettuce mapping population, produced from a cross between the cultivated Lactuca sativa L. cv. Salinas and its wild progenitor L. serriola L. Results Wild and cultivated lettuce differed in their WUE and we observed transgressive segregation in yield and water-use traits in the RILs. Quantitative trait loci (QTL) analysis identified genomic regions controlling these traits under well-watered and droughted conditions. QTL were detected for carbon isotope discrimination, transpiration, stomatal conductance, leaf temperature and yield, controlling 4–23 % of the phenotypic variation. A QTL hotspot was identified on chromosome 8 that controlled carbon isotope discrimination, stomatal conductance and yield under drought. Several promising candidate genes in this region were associated with WUE, including aquaporins, late embryogenesis abundant proteins, an abscisic acid-responsive element binding protein and glutathione S-transferases involved in redox homeostasis following drought stress were also identified. Conclusions For the first time, we have characterised the genetic basis of WUE of lettuce, a commercially important and water demanding crop. We have identified promising candidate genomic regions determining WUE and yield under well-watered and water-limiting conditions, providing important pre-breeding data for future lettuce selection and breeding where water productivity will be a key target.

Spot blotch (SB) disease caused by the hemibiotrophic pathogen Bipolaris sorokiniana inflicting major losses to the wheat grown in warm and highly humid areas of the Indian subcontinent, including Bangladesh, necessitates identification of QTLs stably expressing in Indian subcontinent conditions. Thus, two RIL mapping populations, i.e., WC (WUYA × CIANO T79) and KC (KATH × CIANO T79), were phenotyped at Dinajpur, Bangladesh for three consecutive years (2013-2015) and genotyped on a DArTseq genotyping by sequencing (GBS) platform at CIMMYT, Mexico. In both populations, quantitative inheritance along with transgressive segregation for SB resistance was identified. The identified QTLs were mostly minor and were detected on 10 chromosomes, i.e., 1A, 1B, 2A, 2B, 2D, 4B, 4D, 5A, 5D, and 7B. The phenotypic variation explained by the identified QTLs ranged from 2.3–15.0%, whereby QTLs on 4B (13.7%) and 5D (15.0%) were the largest in effect. The identified QTLs upon stacking showed an additive effect in lowering the SB score in both populations. The probable presence of newly identified Sb4 and durable resistance gene Lr46 in the identified QTL regions indicates the importance of these genes in breeding for SB resistance in Bangladesh and the whole of South Asia.

Hybridization between more divergent organisms is likely to generate progeny with more novel genetic interactions and genetic variations. However, the relationship between parental genetic divergence and progeny phenotypic variation remains largely unknown. Here, using strains of the human pathogenic Cryptococcus, we investigated the patterns of such a relationship. Twenty-two strains with up to 15% sequence divergence were mated. Progeny were genotyped at 16 loci. Parental strains and their progeny were phenotyped for growth ability at two temperatures, melanin production at seven conditions, and susceptibility to the antifungal drug fluconazole. We observed three patterns of relationships between parents and progeny for each phenotypic trait, including (i) similar to one of the parents, (ii) intermediate between the parents, and (iii) outside the parental phenotypic range. We found that as genetic distance increases between parental strains, progeny showed increased fluconazole resistance and growth at 37 °C but decreased melanin production under various oxidative and nitrosative stresses. Our findings demonstrate that, depending on the traits, both evolutionarily more similar strains and more divergent strains may be better parents to generate progeny with hybrid vigor. Together, the results indicate the enormous potential of Cryptococcus hybrids in their evolution and adaptation to diverse conditions.

Background Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major production constraint for common bean, a situation that will be aggravated with current climate change scenarios. In this context, new tools designed to understand the genetic basis governing the phenotypic responses to abiotic stress are required to improve transfer of desirable traits into cultivated beans. Results A multiparent advanced generation intercross (MAGIC) population of common bean was generated from eight Mesoamerican breeding lines representing the phenotypic and genotypic diversity of the CIAT Mesoamerican breeding program. This population was assessed under drought conditions in two field trials for yield, 100 seed weight, iron and zinc accumulation, phenology and pod harvest index. Transgressive segregation was observed for most of these traits. Yield was positively correlated with yield components and pod harvest index (PHI), and negative correlations were found with phenology traits and micromineral contents. Founder haplotypes in the population were identified using Genotyping by Sequencing (GBS). No major population structure was observed in the population. Whole Genome Sequencing (WGS) data from the founder lines was used to impute genotyping data for GWAS. Genetic mapping was carried out with two methods, using association mapping with GWAS, and linkage mapping with haplotype-based interval screening. Thirteen high confidence QTL were identified using both methods and several QTL hotspots were found controlling multiple traits. A major QTL hotspot located on chromosome Pv01 for phenology traits and yield was identified. Further hotspots affecting several traits were observed on chromosomes Pv03 and Pv08. A major QTL for seed Fe content was contributed by MIB778, the founder line with highest micromineral accumulation. Based on imputed WGS data, candidate genes are reported for the identified major QTL, and sequence changes were identified that could cause the phenotypic variation. Conclusions This work demonstrates the importance of this common bean MAGIC population for genetic mapping of agronomic traits, to identify trait associations for molecular breeding tool design and as a new genetic resource for the bean research community.

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait values or novel trait combinations and such transgressive phenotypes may allow some hybrids to explore ecological niches neither of the parental species could tap into. Here, we investigate the potential of second‐generation (F2) hybrids between two generalist cichlid species from Lake Malawi to exploit a resource neither parental species is specialized on: feeding by sifting sand. Some of the F2 hybrids phenotypically resembled fish of species that are specialized on sand sifting. We combined experimental behavioral and morphometric approaches to test whether the F2 hybrids are transgressive in both morphology and behavior related to sand sifting. We then performed a quantitative trait loci (QTL) analysis using RADseq markers to investigate the genetic architecture of morphological and behavioral traits. We show that transgression is present in several morphological traits, that novel trait combinations occur, and we observe transgressive trait values in sand sifting behavior in some of the F2 hybrids. Moreover, we find QTLs for morphology and for sand sifting behavior, suggesting the existence of some loci with moderate to large effects. We demonstrate that hybridization has the potential to rapidly generate novel and ecologically relevant phenotypes that may be suited to a niche neither of the parental species occupies. Interspecific hybridization may thereby contribute to the rapid generation of ecological diversity in cichlid radiations., Interspecific hybrids can have transgressive phenotypes that may allow them to explore novel ecological niches. Using a combination of behavioral assays, morphometric analyses, and genetic mapping, we demonstrate transgressive segregation in morphology and in a novel trophic behavior in F2 hybrids between two generalist cichlid species from Lake Malawi. Such rapid generation of novel ecologically relevant phenotypes might contribute to the rapid generation of ecological diversity in cichlid fish adaptive radiations.

Breeding for thermotolerance in processes determining fruit set and pollen germination is increasingly needed as global warming progresses. We previously reported good yields at high temperatures from the F1 hybrid of the Capsicum chinense cultivars ‘Sy-2’ and ‘No. 3686’, both of which yield poorly at high temperatures. Moreover, the percentages of fruit set at high temperature in the F2 population segregated quantitively. In addition, percentages of fruit set in some F2 individuals exceeded those of the F1 hybrid. Analysis of the F2 population using double-digest restriction site-associated DNA sequencing (ddRAD-Seq) shows that the percentage of fruit set under high temperature is strongly associated to single nucleotide polymorphisms (SNPs) in a certain gene region of chromosome 6 and weakly associated to a gene region on the chromosome 3. Furthermore, the pollen germination rate is strongly associated to SNPs of the same regions on chromosomes 3 and 6. Analysis of the genotypes and traits in another F2 population shows that the genotype determined by the cleaved amplified polymorphic sequence marker designed on the candidate gene region is associated to the percentage of fruit set and the pollen germination rate at high temperatures, supporting the results of ddRAD-Seq. The presence of alleles from both the gene regions of chromosome 3 from ‘No. 3686’ and chromosome 6 from ‘Sy-2’ increased the percentage of fruit set additively. We suggest that genes controlling fruit set and pollen germination at high temperature are located in these two gene regions.

Flower shape and colour are key plant traits which are often strongly correlated with pollinator choice and reproductive isolation. To understand the genetic changes underlying variation in these traits, we performed the first QTL analyses of these traits in Streptocarpus (Gesneriaceae) using a segregating backcross (BC) population of (S. rexii × S. grandis) × S. grandis. Composite traits of floral dimensions were dissected into smallest definable subtraits to examine the efficiency of QTL mapping and correlation between composite and subtrait-specific QTLs. Strong dominance effects were observed in the F1 for many S. rexii traits but for few S. grandis traits. In the BC plants new phenotypes appeared that may be the result of transgressive segregation. Many phenotypic correlations were found between floral dimension traits, which was probably due to the co-localisation of QTLs on the linkage groups. Two regions were associated with large numbers of size and shape traits (17 linked on LG1 and eight linked on LG12), to which the first principal component was also mapped. QTLs of composite traits were mostly overlapping with subtraits, although a few QTLs were newly discovered in subtrait mapping. Strong QTLs were detected for time to flowering and for floral pigmentation traits, ventral lobe pigmentation and the yellow spot. The absence of linkage of floral dimension traits and flower pigmentation suggests that genetic regulation of floral form in Streptocarpus allows versatility, perhaps allowing fast response to changing selective pressures from pollinators.

Background Wheat blast, caused by Magnaporthe oryzae Triticum (MoT) pathotype, is a global threat to wheat (Triticum aestivum L.) production. Few blast resistance (R) genes have been identified to date, therefore assessing potential sources of resistance in wheat is important. The Brazilian wheat cultivar BR 18-Terena is considered one of the best sources of resistance to blast and has been widely used in Brazilian breeding programmes, however the underlying genetics of this resistance are unknown. Results BR 18-Terena was used as the common parent in the development of two recombinant inbred line (RIL) F6 populations with the Brazilian cultivars Anahuac 75 and BRS 179. Populations were phenotyped for resistance at the seedling and heading stage using the sequenced MoT isolate BR32, with transgressive segregation being observed. Genetic maps containing 1779 and 1318 markers, were produced for the Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179 populations, respectively. Five quantitative trait loci (QTL) associated with seedling resistance, on chromosomes 2B, 4B (2 QTL), 5A and 6A, were identified, as were four QTL associated with heading stage resistance (1A, 2B, 4A and 5A). Seedling and heading stage QTL did not co-locate, despite a significant positive correlation between these traits, indicating that resistance at these developmental stages is likely to be controlled by different genes. BR 18-Terena provided the resistant allele for six QTL, at both developmental stages, with the largest phenotypic effect conferred by a QTL being 24.8% suggesting that BR 18-Terena possesses quantitative resistance. Haplotype analysis of 100 Brazilian wheat cultivars indicates that 11.0% of cultivars already possess a BR 18-Terena-like haplotype for more than one of the identified heading stage QTL. Conclusions This study suggests that BR 18-Terena possesses quantitative resistance to wheat blast, with nine QTL associated with resistance at either the seedling or heading stage being detected. Wheat blast resistance is also largely tissue-specific. Identification of durable quantitative resistances which can be combined with race-specific R gene-mediated resistance is critical to effectively control wheat blast. Collectively, this work facilitates marker-assisted selection to develop new varieties for cultivation in regions at risk from this emerging disease.

Funding support was provided by NERC grants to N.W.B. (NE/G014906/1, NE/L011255/1), NERC (NE/G00949X/1) and ARC grants to J.H (DP180101708), and an Orthopterists’ Society grant to P.A.M. Speciation research dissects the genetics and evolution of reproductive barriers between parental species. Hybrids are the ‘gatekeepers’ of gene flow, so it is also important to understand the behavioural mechanisms and genetics of any potential isolation from their parental species. We tested the role of multiple behavioural barriers in reproductive isolation among closely related field crickets and their hybrids (Teleogryllus oceanicus and T. commodus). These species hybridize in the laboratory, but the behaviour of hybrids is unusual and there is little evidence for gene flow in the wild. We found that heterospecific pairs exhibited reduced rates of courtship behaviour due to discrimination by both sexes, and that this behavioural isolation was symmetrical. However, hybrids were not sexually selected against and exhibited high rates of courtship behaviour even though hybrid females are sterile. Using reciprocal hybrid crosses, we characterized patterns of interspecific divergence and inheritance in key sexual traits that might underlie the mating patterns we found: calling song, courtship song and cuticular hydrocarbons (CHCs). Song traits exhibited both sex linkage and transgressive segregation, whereas CHCs exhibited only the latter. Calculations of the strength of isolation exerted by these sexual traits suggest that close‐range signals are as important as long‐distance signals in contributing to interspecific sexual isolation. The surprisingly weak mating barriers observed between hybrids and parental species highlight the need to examine reproductive isolating mechanisms and their genetic bases across different potential stages of introgressive hybridization. Postprint

Glyphosate-resistant (GR) Palmer amaranth (Amaranthus palmeriS. Watson) is considered one of the most troublesome weeds in the southern and central United States, but results of previous research to determine the mode of inheritance of this trait have been conflicting and inconclusive. In this study, we examined segregation patterns ofEPSPSgene-copy numbers in F1and F2generations ofA. palmeriand found no evidence of a Mendelian single-gene pattern of inheritance. Transgressive segregation for copy number was exhibited by several F1and all of the F2families, most likely the product ofEPSPScopy-number variation within each plant. This variation was confirmed by assaying gene-copy number across clonal generations and among individual shoots on the same plant, demonstrating thatEPSPSamplification levels vary significantly within a single plant. Increases and decreases in copy number occurred in a controlled, stress-free environment in the absence of glyphosate, indicating thatEPSPSgene amplification is a random and variable process within the plant. The ability ofA. palmerito gain or loseEPSPSgene copies is a valuable adaptive trait, allowing this species to respond rapidly to selection pressures and changing environments.

Picea purpurea originated from the homoploid hybrid speciation, which occupy novel alpine habitats in the north-east region of the Qinghai-Tibet Plateau (QTP) where its progenitors, P. wilsonii and P. likiangensis are excluded. Alpine habitats are usually characterized by low atmospheric CO2 concentrations and strong solar radiation with a large fraction of shortwave radiation (i.e. blue light). To test whether P. purpurea has the transgressive segregation in photosynthetic capacity and stomatal characteristics contributed to occupying such extreme habitats, we investigated the leaf gas exchange properties at two level of CO2 concentration (Ca: 200 and 400 μmol mol−1), light responsive curves of photosynthesis under three light qualities (red, blue and a mixture of both red and blue light at the ratio of 94:6), stomatal and other relative physiological traits for all three species. Our results show evidence of transgressive segregation in hybrid species; for instance, under blue and red light P. p...

Pythium root rot is one of the significant diseases of soybean (Glycine max (L.) Merr.) in the United States. The causal agent of the disease is a soil-borne oomycete pathogen Pythium irregulare, the most prevalent and aggressive species of Pythium in North Central United States. However, few studies have been conducted in soybean for the identification of quantitative trait loci (QTL) for tolerance to P. irregulare. In this study, two recombinant inbred line (RIL) populations (designated as POP1 and POP2) were challenged with P. irregulare (isolate CMISO2-5-14) in a greenhouse assay. POP1 and POP2 were derived from ‘E09014’ × ‘E05226-T’ and ‘E05226-T’ × ‘E09088’, and contained 113 and 79 lines, respectively. Parental tests indicated that ‘E05226-T’ and ‘E09014’ were more tolerant than ‘E09088’, while ‘E09088’ was highly susceptible to the pathogen. The disease indices, root weight of inoculation (RWI) and ratio of root weight (RRW) of both populations showed near normal distributions, with transgressive segregation, suggesting the involvement of multiple QTL from both parents contributed to the tolerance. All the lines were genotyped using Illumina Infinium BARCSoySNP6K iSelect BeadChip and yielded 1373 and 1384 polymorphic markers for POP1 and POP2, respectively. Notably, despite high density, polymorphic markers coverage was incomplete in some genomic regions. As such, 28 and 37 linkage groups were obtained in POP1 and POP2, respectively corresponding to the 20 soybean chromosomes. Using RRW, one QTL was identified in POP1 on Chromosome 20 that explained 12.7–13.3% of phenotypic variation. The desirable allele of this QTL was from ‘E05226-T’. Another QTL was found in POP2 on Chromosome 11. It explained 15.4% of the phenotypic variation and the desirable allele was from ‘E09088’. However, no QTL were identified using RWI in either population. These results supported that RRW was more suitable to be used to evaluate P. irregulare tolerance in soybean.

A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve important horticultural traits in garden petunia. An F7 recombinant inbred population derived between Petunia axillaris and P. exserta was phenotyped for plant height, plant spread, plant size, flower counts, flower diameter, flower length, and days to anthesis in Florida in two consecutive years. Transgressive segregation was observed for all seven traits in both years. The broad-sense heritability estimates for the traits ranged from 0.20 (days to anthesis) to 0.62 (flower length). A genome-wide genetic linkage map consisting of 368 single nucleotide polymorphism bins and extending over 277 cM was searched to identify QTL for these traits. Nineteen QTL were identified and localized to five linkage groups. Eleven of the loci were identified consistently in both years; several loci explained up to 34.0% and 24.1% of the phenotypic variance for flower length and flower diameter, respectively. Multiple loci controlling different traits are co-localized in four intervals in four linkage groups. These intervals contain desirable alleles that can be introgressed into commercial petunia germplasm to expand the genetic base and improve plant performance and flower characteristics in petunia.

Breeding for resistance to flower bud thrips (Megalurothrips sjostedti) in cowpea has been hindered by the quantitative nature of resistance. To identify simple sequence repeat (SSR) markers associated with resistance to flower bud thrips that could be used for marker-assisted breeding, a F2 population was generated from a cross between genotypes TVU-123 (resistant) and WC36 (susceptible). The population was evaluated for thrips damage scores, thrips counts, and pods number per plant under artificial infestation. Sixty-six microsatellites markers were screened between the two parental lines and seven polymorphic markers were used to genotype 100 F2 plants. Single marker analysis was used to evaluate an association between the markers and traits. Transgressive segregation among the F2 plants for resistance to flower thrips was observed. A significant negative relationship was observed between thrips damage scores and pods number per plant. Markers CP37/38 and CP215/216 were significantly associated with thrips damage scores and thrips counts, respectively. The two markers explained 7 and 11.2% of the total variation in thrips damage scores and thrips counts with positive and negative effects, respectively. Mainly additive gene effects were observed. A more detailed study using more markers on these loci should provide better understanding of this complex trait. Key words: Cowpea, single marker analysis, polymorphism, simple sequence repeat (SSR) markers.

Sugarcane is among the most efficient crops in converting solar energy into chemical energy. However, due to its complex genome structure and inheritance, the genetic and molecular basis of biomass yield in sugarcane is still largely unknown. We created an F2 segregating population by crossing S. officinarum and S. spontaneum and evaluated the biomass yield of the F2 individuals. The F2 individuals exhibited clear transgressive segregation in biomass yield. We sequenced transcriptomes of source and sink tissues from 12 selected extreme segregants to explore the molecular basis of high biomass yield for future breeding of high-yielding energy canes. Among the 103,664 assembled unigenes, 10,115 and 728 showed significant differential expression patterns between the two extreme segregating groups in the top visible dewlap leaf and the 9th culm internode, respectively. The most enriched functional categories were photosynthesis and fermentation in the high-biomass and the low-biomass groups, respectively. Our results revealed that high-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. Group-specific expression alleles which can be applied in the development of new high-yielding energy cane varieties via molecular breeding were identified.

Six parents, i.e. Gemmeiza 9, Sids 12, Misr 1, Misr 2, Sids 1 and Sham 4, were used and evaluated with corresponding 15 F2 crosses. The parents in each cross were significantly different for most of these characters, revealing the different genetic background of the parents involved. The phenotypic variances in the F2 crosses were differed significantly from the environmental variances in the corresponding parents in most cases. The parents Gemmeiza 9, Sids 12, Misr 1, Misr 2 were resistant for leaf rust and Gemmeiza 9, Sids 12 and Sids 1 were resistant to stem rust. Among the crosses, three crosses, i.e. Misr 2 x Sids 1, Misr 1 x Sids 1 and Gemmeiza 9 x Sids 1 gave the highest grain yield. The means of F2 hybrids were higher than the means of the parents for most studied characters. The ranges of the F2 values went out the ranges of the two parents in most cases, exhibiting transgressive segregation. Most characters showed moderate to high values of broad sense heritabilities. The studied plants in the F2 ‘s crosses segregated and gave ratios fitted the ratios 9:7, 9:7, 3:1, 1:3, 13:3 and 3:13 for leaf rust and 9:7, 7: 9, 3:1, 1:3, 3:13 and 1:15 for stem rust with insignificant χ2 values, indicating that the resistant parents for leaf and stem rusts had one or two genes and were complimentary dominance, recessive or independent in their expressions. Based on the resistance to leaf and stem rusts, suitable plant height (90-110 cm) and grain yield higher than the highest parent, 8-17 plants were selected from seven crosses.

Rapid hybrid speciation in Darwin's finches Galapagos finches have driven hypotheses of how speciation occurs. Most commonly, it is assumed that natural selection separates species originating from a single population on the basis of variation in traits that confer advantages for survival and reproduction. Lamichhaney et al. document a case where cross-species hybridization established a reproductively isolated lineage, which demonstrates a process known as homoploid hybrid speciation in action (see the Perspective by Wagner). The authors used genetic markers and phenotypic analyses to create a pedigree that revealed how a cross-island migrant bred with a native species to form a self-perpetuating hybrid population that was reproductively isolated from both parental species. Science , this issue p. 224 ; see also p. 157

Vigour control in grapevine can be achieved by grafting with particular rootstocks, and may become especially important under climate change. This research studied the F1 progeny from the cross of 'Ramsey' × 'Riparia Gloire de Montpellier' rootstocks, known to confer high and low vigour, respectively. We hypothesized that vigour correlates with growth rate, leaf area, biomass partitioning, plant hydraulics and gas exchange; and that these variables could be associated with genetic markers. We evaluated 138 seedlings from this cross, three replicates each, for 60 days in a greenhouse at UC Davis, California, during summer 2014 and 2015. Each plant was pruned to a single shoot and watered daily. Shoot growth rate, leaf area and dry biomass were measured for the complete population, both years. In 2014, after day 45, 40 genotypes were subjected to a 50% water deficit, based from initial weight at full pot capacity, and plant and root hydraulic conductance's, stomatal conductance and water potential were measured. The progeny showed transgressive segregation and significant differences in vigour. A PCA analysis showed a strong role for shoot growth rate, specific leaf area, plant hydraulics and partitioning indices for vigour determination. Under water stress, larger plants showed less specific hydraulic and stomatal conductance's, indicating higher sensibility upon drought. Significant QTLs for leaf area, specific leaf area and partitioning indices were found on chromosomes 1, 4, 16, and 5; accounting for 20% of explained variability for leaf area, and from 10 to 14% of explained variability for specific leaf area and partitioning indices in 2014. Mapping data from 2015 is being analysed.

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis × Miscanthus sacchariflorus F1 population and two intraspecific M. sinensis F1 populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data were collected in 2012 and 2013 for fourteen yield traits. Six high-density parental genetic maps, as well as a consensus genetic map integrating M. sinensis and M. sacchariflorus, were developed via the pseudotestcross strategy for noninbred parents with ≥1214 single-nucleotide polymorphism markers generated from restriction site-associated DNA sequencing. We confirmed for the first time a whole-genome duplication in M. sacchariflorus relative to Sorghum bicolor, similar to that observed previously for M. sinensis. Four quantitative trait locus (QTL) analysis methods for detecting marker-trait associations were compared: (1) individual parental map composite interval mapping analysis, (2) individual parental map stepwise analysis, (3) consensus map single-population stepwise analysis and (4) consensus map joint-population stepwise analysis. These four methods detected 288, 264, 133 and 109 total QTLs, which resolved into 157, 136, 106 and 86 meta-QTLs based on QTL congruency, respectively, including a set of 59 meta-QTLs common to all four analysis methods. Composite interval mapping and stepwise analysis co-identified 118 meta-QTLs across six parental maps, suggesting high reliability of stepwise regression in QTL detection. Joint-population stepwise analysis yielded the highest resolution of QTLs compared to the other three methods across all meta-QTLs. Strong, frequently advantageous transgressive segregation in the three populations indicated a promising future for breeding new higher-yielding cultivars of Miscanthus.

We used the ‘Baronesse’/‘Full Pint’ doubled haploid population to analyse the genetic factors controlling flowering date under South American conditions. Both parents have similar heading dates, but the population shows transgressive segregation. Two genes, eps2S on chromosome 2H and sdw1 on chromosome 3H, explained most of the phenotypic variation for anthesis date, with the later allele carried by ‘Baronesse’ and ‘Full Pint’ , respectively. Both effects were completely additive with no interaction. We studied three plant developmental periods: seedling emergence to tillering (Z10–Z20), tillering (Z20–Z30) and end of tillering to anthesis (Z30–Z49) under field conditions at three contrasting planting dates. Z10–Z20 was also measured under semi-controlled conditions. eps2S controlled Z30–Z49 periods, while sdw1 controlled Z20–Z30. Each of the two genes for the end-point phenotype—anthesis date—was a determinant of flowering at a different developmental stage. No gene x planting date interactions were detected.

Seed starch content (SSC) greatly affects the taste, flavour and processing properties of soy foods. The objective in this study was to identify quantitative trait loci (QTL) for SSC in soybean. A total in 169 recombinant inbred lines (RILs) derived from a cross in ‘Williams 82’ and ‘PI 366121’ were grown for three consecutive years. The SSC of the RILs displayed continuous variation with transgressive segregation and hence amenable for QTL mapping. Nine significant QTL exhibiting 5.6–11.3% of the total phenotypic variation (PVE) were identified. The QTL qSTR06_2 showed highest PVE (9.1–11.3%) at LOD values of 4.25–5.39. No stable QTL over 3 years were identified, indicating strong environmental influence on SSC. The QTL qSTR11_1 and qSTR20_1 were found to colocalize with some of the previously reported QTL for sucrose content in soybean, implying the interrelationship between starch and sucrose biosynthesis. As the carbohydrate components may affect key constituents such as oil and protein in soybean seed, findings of the study may be useful in breeding soybeans with improved seed composition.

Root growth angle (RGA) is one of the major morphological traits that determine whether a plant develops a shallow or deep root system. To date, however, no genetic information has been available regarding RGA in apple (Malus domestica Borkh.). In this study, phenotypic variation in RGA was investigated using deep-rooted Baleng Crab (BC), shallow-rooted M9, and 115 intraspecific hybrid progenies derived from a BC × M9 cross. Auxin (IAA) content and the expression of genes that control RGA and root gravitropism, MdDROs and MdPIN11, were also analyzed. The results revealed that M9 had a smaller RGA than Baleng Crab. The IAA level and the expression of both MdDRO1 and MdPIN11 were significantly lower in the roots of M9 than in those of Baleng Crab, indicating the potential importance of auxin signaling and these two genes in the control of RGA. Furthermore, fewer amyloplasts were detected in columella cells in the root cap of M9 in comparison with Baleng Crab. Both RGA and root length showed a normal distribution and transgressive segregation in hybrid progeny, suggesting that both these traits are quantitative in nature and controlled by polygenes. We conclude that both RGA and root length are important traits contributing to deep rooting in M. domestica and that these might be influenced by MdDRO1 and MdPIN11.

Heading date is an important event to ensure successful seed production. Although foxtail millet (Setaria italica (L.) P.Beauv.) is an important foodstuff in semiarid regions around the world, the genetic basis determining heading date is unclear. To identify genomic regions regulating days to heading (DTH), we conducted a QTL-seq analysis based on combining whole-genome re-sequencing and bulked-segregant analysis of an F2 population derived from crosses between the middle-heading cultivar Shinanotsubuhime and the earlyheading cultivar Yuikogane. Under field conditions, transgressive segregation of DTH toward late heading was observed in the F2 population. We made three types of bulk samples: Y-bulk (early-heading), S-bulk (late-heading) and L-bulk (extremely late-heading). By genome-wide comparison of SNPs in the Y-bulk vs. the S-bulk and the Y-bulk vs. the L-bulk, we identified two QTLs associated with DTH. The first QTL, qDTH2, was detected on chromosome 2 from the Y-bulk and S-bulk comparison. The second QTL, qDTH7, was detected on chromosome 7 from the Y-bulk and L-bulk comparison. The Shinanotsubuhime allele for qDTH2 caused late heading in the F2 population, whereas the Yuikogane allele for qDTH7 led to extremely late heading. These results suggest that allelic differences in both qDTH2 and qDTH7 determine regional adaptability in S. italica.

Hybridization might promote offspring fitness via a greater tolerance to environmental stressors due to heterosis and higher levels of phenotypic plasticity. Thus, analyzing the phenotypic expression of hybrids provides an opportunity to elucidate further plant responses to environmental stress. In the case of coastal salt marshes, sea level rise subjects hybrids, and their parents, to longer tidal submergence and higher salinity. We analyzed the phenotypic expression patterns in the hybrid Spartina densiflora x foliosa relative to its parental species, native S. foliosa, and invasive S. densiflora, from the San Francisco Estuary when exposed to contrasting salinities and inundations in a mesocosm experiment. 37% of the recorded traits displayed no variability among parents and hybrids, 3% showed an additive inheritance, 37% showed mid-parent heterosis, 18% showed best-parent heterosis, and 5% presented worst-parent heterosis. Transgressivity, rather than phenotypic plasticity, in key functional traits of the hybrid, such as tiller height, conveyed greater stress tolerance to the hybrid when compared to the tolerance of its parents. As parental trait variability increased, phenotypic transgressivity of the hybrid increased and it was more important in response to inundation than salinity. Increases in salinity and inundation associated with sea level rise will amplify the superiority of the hybrid over its parental species. These results provide evidence of transgressive traits as an underlying source of adaptive variation that can facilitate plant invasions. The adaptive evolutionary process of hybridization is thought to support an increased invasiveness of plant species and their rapid evolution.

To identify cold tolerance at the reproductive stage in rice (Oryza sativa L.), the cold susceptible accession, IAPAR-9 (tropical japonica) was crossed with the cold tolerant accessions Akihikari and Liaoyan241 (temperate japonica) to construct two recombinant inbred lines (RIL) to detected QTLs related to cold-tolerance of rice through analyze phenotypic variation. The two RILs and their parents were experimentally grown in natural conditions and cold water irrigation at one site, Gongzhuling Jilin (China), and at natural low temperature in another site, Kunming Yunnan (China). We measured plant height, panicle length, number of panicles per plant, grain number per panicle, seed setting rate and panicle exsertion of parents and RIL populations in the maturation stage. In the three treatment environments, the traits of the two RILs showed normal distributions, and both exhibited transgressive segregation. Low temperature stress had greater influence on number of panicles per plant and grain number per panicle and lower influence on plant height and panicle length. Seventeen quantitative trait locus (QTLs) were detected, distributed on chromosomes 1, 3-6, 8, 11 and 12. Among these, four QTLs had values of phenotypic variance explained that were greater than 10%. There were two QTLs, qPN12-2E2 and qPN12-2E3, detected in the IAPAR-9/Akihikari RIL population in same region under cold water irrigation condition in Gongzhuling Jilin and natural low temperature in Kunming Yunnan. Major regions related to cold tolerance QTLs in these two populations was on chromosome 12 from RM511 to RM3739. The cold tolerance allele was from the Akihikari and Liaoyan241 in the respective populations for both QTL regions.

The anemone-type inflorescence of chrysanthemum features prominent, colored tubular florets. Here, the inheritance of a set of traits associated with floral form was investigated using a quantitative trait locus (QTL) mapping approach applied to a segregating population bred from a cross between the two varieties ‘Nannong Xuefeng’ and ‘Monalisa’. The coefficient of variation of the various traits ranged from 12.8 to 59.2%, with an average of 28.0%, and there was notable transgressive segregation in both directions. A set of 26 QTL was uncovered, explaining a portion of the variation in eight of the eleven traits; individually, the loci accounted for between 6.3 and 11.9% of the phenotypic variation. A further 16 pairs of epistatically acting QTL were identified, associated with a contribution of between 3.7 and 13.6% of the phenotypic variance; the majority of these interactions involved background loci. The conclusion was that both additive and epistatic effects were involved in the genetic determination of floral form in chrysanthemum.

Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.

Improved salt tolerance is a major goal for maize breeders, but the control of salt tolerance-related traits in maize is poorly understood. A set of 209 doubled haploid (DH) lines derived from the maize hybrid Xianyu335 was genotyped using 1335 single-nucleotide polymorphism (SNP) markers. Biomass-related traits under salt stress were used as salt tolerance indicators, and a quantitative trait loci (QTL) analysis was conducted in hydroponic culture under salt-stress and normal conditions. Fourteen traits showed significant phenotypic differences between parents, and 16 traits showed transgressive segregation in the DH population. We detected 65 QTL: 41 associated with salt tolerance and 24 related to normal growth. Salt tolerance-related QTL clustered on chromosomes 1, 3, 7, and 9, among which 13 major effect QTL on chromosome 1 individually explained more than 21% of the phenotypic variation. Of these large-effect QTL, QTL controlling seven traits upon salt treatment and two salt tolerance indexes were co-located; they extensively overlapped with the remaining four co-localized QTL related to four other salt tolerance indexes. The QTL identified here shed new light on the molecular mechanism of salt tolerance in maize and may provide robust functional markers for marker-assisted selection of salt tolerant maize varieties.

Variation in gene expression promotes adaptive divergence. In this study, we performed comparative transcriptomics on Melastoma candidum, M. sanguineum and their F1 hybrid to investigate the role of gene expression in plant species diversification and hybridization. Differentially expressed genes were mostly found between the two parental species, and were related to adaptive traits that limit the species to their habitats. In the F1 hybrid, although the expression levels of most genes were similar to either parent, a small number of genes had expression levels exceeding both parents, possibly explaining its vigour in certain morphological and adaptive traits., Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.

Inheritance of adult-plant resistance to leaf rust, caused by Puccinia triticina, was studied in the progeny of a one-way diallel cross involving five CIMMYT-derived adult-plant resistant wheat (Triticum aestivum) genotypes and a susceptible wheat ‘Avocet-YrA’. F1 progenies, F2 populations, F2-derived F3, and F4-derived F5 lines were field evaluated under artificial epidemics with leaf rust race MCJ/SP. Adult-plant resistance to leaf rust was incompletely dominant in crosses with the susceptible parent and was found to be controlled by additive interactions of Lr34 with at least two to three additional genes. Transgressive segregation giving rise to plants or lines with higher and lower levels of resistance than the parents was observed in all F2 and F5 derivatives of the resistant-parent intercrosses and suggested that, apart from Lr34, some of the other additive genes were nonallelic. Although specific combining ability was significant in some generations, general combining ability was found to be the major component of variation. Among generations, the estimates of the narrow-sense heritability of adult-plant resistance to leaf rust ranged from 0.67 to 0.97.

Significance Most plants resist most plant pathogens. Barley resists wheat-infecting powdery mildew races (and vice versa), and both barley and wheat resist potato late blight. Such “nonhost” resistance could result because the pathogen fails to suppress defense or triggers innate immunity due to failure to evade detection. Albugo candida causes white rust on most Brassicaceae, and we investigated Arabidopsis NHR to Brassica-infecting races. Transgressive segregation for resistance in Arabidopsis recombinant inbred lines revealed genes encoding nucleotide-binding, leucine-rich repeat (NLR) immune receptors. Some of these NLR-encoding genes confer resistance to white rust in Brassica sp. This genetic method thus provides a route to reveal resistance genes for crops, widening the pool from which such genes might be obtained., Arabidopsis thaliana accessions are universally resistant at the adult leaf stage to white rust (Albugo candida) races that infect the crop species Brassica juncea and Brassica oleracea. We used transgressive segregation in recombinant inbred lines to test if this apparent species-wide (nonhost) resistance in A. thaliana is due to natural pyramiding of multiple Resistance (R) genes. We screened 593 inbred lines from an Arabidopsis multiparent advanced generation intercross (MAGIC) mapping population, derived from 19 resistant parental accessions, and identified two transgressive segregants that are susceptible to the pathogen. These were crossed to each MAGIC parent, and analysis of resulting F2 progeny followed by positional cloning showed that resistance to an isolate of A. candida race 2 (Ac2V) can be explained in each accession by at least one of four genes encoding nucleotide-binding, leucine-rich repeat (NLR) immune receptors. An additional gene was identified that confers resistance to an isolate of A. candida race 9 (AcBoT) that infects B. oleracea. Thus, effector-triggered immunity conferred by distinct NLR-encoding genes in multiple A. thaliana accessions provides species-wide resistance to these crop pathogens.

Petunia is a very important flower in the global floriculture industry and has played a critical role as a model in plant genetic studies. Owing to limited genetic variability in commercial germplasm, development of novel petunia phenotypes and new varieties has become increasingly difficult. To enrich petunia germplasm and facilitate genetic improvement, it is important to explore genetic variation in progenitor species that may contain highly valuable genes/alleles. In this study, an interspecific recombinant inbred population (168 recombinant inbreds) derived from Petunia integrifolia × P. axillaris were phenotyped for days to anthesis (DTA), flower count (Flower_C), flower diameter (Flower_D), flower length (Flower_L), plant height (Plant_H), plant spread (Plant_S), and plant size (Plant_Z) in 2014 and 2015. Transgressive segregation was observed for all traits in both years. The broad-sense heritability on a 2-year basis varied from 0.38 (Flower_C) to 0.82 (Flower_L). Ten QTL were consistently identified in both years and by two mapping strategies [multiple QTL mapping (MQM) in MapQTL and inclusive composite interval mapping (ICIM) in IciMapping]. Major QTL explained up to 30.2, 35.5, and 47.1% of the total phenotypic variation for Plant_S, Flower_L, and Flower_D, respectively. These findings should be of significant values for introgression of desirable genes from wild petunias into commercial varieties and future genetic improvement of this important flower. Uncovering the genetics behind desirable traits in petunia plants could help improve commercial cultivars. While petunia plants are a key feature of the global horticultural industry, the limited genetic variability in commercial plants makes it difficult to improve desired plant traits. Zhanao Deng at the University of Florida, US, and co-workers conducted a genome-wide QTL identification study using a crossbred population combining two petunia species, P. integrifolia and P. axillaris. The team phenotyped the petunias in an open-air sub-tropical field rather than in an artificial environment like previous studies. They identified and characterized 17 genetic loci for seven important aesthetic traits, ranging from flower count to plant size. The petunia species had very different genetic backgrounds, likely stemming from their different geographic origins. The two species each can contribute novel genes for enhancing cultivated petunia cultivars.