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• Modern varieties are derived from wild progenitors through crop domestication. • Limited genetic diversity is a constraint of crop improvement programs to keep pace with the challenges of climate change. • Crop wild relatives and their rich reservoir of gene pool provide the armor against crop stresses. • Genome editing tools are used to explore the germplasm of popular crops for domestication and climate-resilient genes. • Crop domestication is accelerated by Cis-regulating mutation, CRISPR-Cas-, and multiplex editing. Crop domestication is one of the oldest crop improvement methods, significantly impacting socioeconomic conditions globally. Modern varieties are derived from wild progenitors through crop domestication. These varieties are generated by crossing compatible genotypes to obtain the desired phenotype-containing progenies. The uncertainties and stress conditions caused by climate change deeply impact the current agricultural scenario. However, limited genetic diversity is the major constraint of the present crop improvement programs in keeping pace with climate change and several resulting biotic and abiotic stresses. Therefore, using crop wild relative and their rich reservoir of resistant genes to biotic and abiotic stressors must provide the armors against the crop stresses. However, crop wild relatives are unsuitable for direct intensive cropping because of many undesirable agronomic traits and are incompatible for gene transfer with conventional breeding. With the dawn of new-generation sequencing techniques and genome editing tools, scientists are trying to explore the germplasm of popular crops for domestication and climate-resilient genes. Considering the above context, the present review discusses the genetics of crop domestication, different strategies for a targeted mutation to accelerate crop domestication, and the current status of various crops. Further, it will discuss current challenges and the future fate of crop domestication using advanced biotechnological tools. [ABSTRACT FROM AUTHOR]

Alternaria leaf spot is a major disease of Brassica crops, and it causes huge economic loss to both the cultivated Brassica oilseeds and vegetables. The present study was aimed to develop a non-destructive robust method for screening of wild Brassica species and to find resistant wild species against Alternaria brassicicola (Schw.) Wiltsh. For this, 38 wild species of Brassicaceae were screened at adult plant stage by an in vitro detached leaf inoculation method in three consecutive years i.e. 2019–2020, 2020–2021 and 2021–2022. The new screening protocol created favourable environment (temperature 25 ± 2 °C; relative humidity > 90%) for the pathogen by using incubator. The host leaves were retained in turgid condition by placing sucrose 5% w/v on slanting cut at petiolar base. The consistency in reactions of the wild species against A. brassicicola during all three years of testing indicates the robustness of the protocol. Multiple parameters were recorded on leaf condition and disease response of the wild species and devised a score system for disease rating. Complete resistance was observed in Capsella while resistance in Lepidium, Camelina and Biscutella. Both Capsella bursa pastoris (L.) Medik (early) and C. bursa pastoris (late) were symptomless resistant. Camelina sativa (L.) Crantz, Diplotaxis erucoides (L.) DC and Diplotaxis gomez-campoi Mart.-Laborde were found to be resistant against A. brassicicola. The significant correlation between disease parameters indicates the robustness and effectiveness of the screening protocol for wild Brassica species. [ABSTRACT FROM AUTHOR]

Forty-two accessions of eggplant were screened against Ralstonia solanacearum in screen-house environments. This was followed by an assessment of the genetic diversity of the 42 eggplant successions originating from Bangladesh, China, Thailand and Malaysia, accomplished by exploring SSR markers for germplasm characterisation. Five selected resistant genotypes used as a rootstock were further assessed with UPMSE16 strain in a subsequent trial. The pathogenicity test based on area under the disease progress curve (AUDPC) and disease severity index (DSI) at four weeks after inoculation indicated that genotypes TB3, TB6, TB7, MB16 and BB9 had the greatest degree of resistance. Also, the results of the second trial for grafted and control plants based on DSI and AUDPC at 4 WAI showed that grafted plants had resistance to UPMSE16 strain with no symptoms at 4 WAI. The 42 accessions were grouped into nine major clusters based on SSR markers using Unweighted Pair Group Method with Arithmetic mean. Hence, the phenotyping screening reveals that five eggplant accessions were resistant to R. solanacearum and can be used as potential rootstock. As a result, the discovered SSR markers may be effective in marker-assisted selection for future use in developing new rootstock. [ABSTRACT FROM AUTHOR]

Cyclamen, a popular decorative plant, is commonly found in gardens and pots. Since wild Cyclamen are endangered, a study was conducted to explore the genetic potential of wild Cyclamen, focusing on their morphology and chromosomal diversity among eight accessions. A total of 23 phenotypic-biochemical traits were evaluated along with chromosome counting. The morphological measures showed a humble range of variation, particularly in the number of flowers, peduncle diameter, number of leaves, hypocotyl length, and hypocotyl weight, with the Kordkuy accession being the largest and the Deylaman accession the most seeded. Cyclamen chromosome counting indicated 15 chromosomal levels, implying a significant chromosomal diversity among the accessions, with the Pasand accession exhibiting the highest level of chromosomal diversity (14 chromosomal levels). Furthermore, only the Pasand accession had the greatest chromosomal level (2n=48) among the accessions. By describing the results based on the median, the smallest chromosomal diversity was recorded in the Kordkuy accession. Cyclamen accessions were divided into two main clusters and a single accession. The Kordkuy accession was separated from the other accessions. HCA analysis confirmed the separation of the Kordkuy accession from the other accessions, as expected from its superiority in most morphological traits. The current findings can be used for improving Cyclamen breeding programs as well as evolutionary studies. We suggest more focus on the utilization of wild genetic resources to conserve Cyclamen varieties and strengthen their genetic background. [ABSTRACT FROM AUTHOR]

Abstract Elucidating genetic diversity within wild forms of modern crops is essential for understanding domestication and the possibilities of wild germplasm utilization. Gossypium hirsutum is a predominant source of natural plant fibers and the most widely cultivated cotton species. Wild forms of G. hirsutum are challenging to distinguish from feral derivatives, and truly wild populations are uncommon. Here we characterize a population from Mound Key Archaeological State Park, Florida using genome-wide SNPs extracted from 25 individuals over three sites. Our results reveal that this population is genetically dissimilar from other known wild, landrace, and domesticated cottons, and likely represents a pocket of previously unrecognized wild genetic diversity. The unexpected level of divergence between the Mound Key population and other wild cotton populations suggests that the species may harbor other remnant and genetically distinct populations that are geographically scattered in suitable habitats throughout the Caribbean. Our work thus has broader conservation genetic implications and suggests that further exploration of natural diversity in this species is warranted.

Maize, a salt-sensitive crop, frequently suffers severe yield losses due to soil salinization. Enhancing salt tolerance in maize is crucial for maintaining yield stability. To address this, we developed an introgression line (IL76) through introgressive hybridization between maize wild relatives Zea perennis, Tripsacum dactyloides, and inbred Zheng58, utilizing the tri-species hybrid MTP as a genetic bridge. Previously, genetic variation analysis identified a polymorphic marker on Zm00001eb244520 (designated as ZmSC), which encodes a vesicle-sorting protein described as a salt-tolerant protein in the NCBI database. To characterize the identified polymorphic marker, we employed gene cloning and homologous cloning techniques. Gene cloning analysis revealed a non-synonymous mutation at the 1847th base of ZmSCIL76, where a guanine-to-cytosine substitution resulted in the mutation of serine to threonine at the 119th amino acid sequence (using ZmSCZ58 as the reference sequence). Moreover, homologous cloning demonstrated that the variation site derived from Z. perennis. Functional analyses showed that transgenic Arabidopsis lines overexpressing ZmSCZ58 exhibited significant reductions in leaf number, root length, and pod number, alongside suppression of the expression of genes in the SOS and CDPK pathways associated with Ca2+ signaling. Similarly, fission yeast strains expressing ZmSCZ58 displayed inhibited growth. In contrast, the ZmSCIL76 allele from Z. perennis alleviated these negative effects in both Arabidopsis and yeast, with the lines overexpressing ZmSCIL76 exhibiting significantly higher abscisic acid (ABA) content compared to those overexpressing ZmSCZ58. Our findings suggest that ZmSC negatively regulates salt tolerance in maize by suppressing downstream gene expression associated with Ca2+ signaling in the CDPK and SOS pathways. The ZmSCIL76 allele from Z. perennis, however, can mitigate this negative regulatory effect. These results provide valuable insights and genetic resources for future maize salt tolerance breeding programs. [ABSTRACT FROM AUTHOR]

Cowpea, Vigna unguiculata, is an important food legume in the tropics and subtropics. However, cowpea is a complex species with more than 10 subspecies that can hybridize and produce intermediate offspring. Partly because of the complex organization of the cowpea gene pool and the lack of adequate markers for these infraspecific units, cowpea breeders are not using the wild part of the cowpea gene pool. Here, we report the molecular characterization of 34 representative accessions with 18 polymorphic simple sequence repeat (SSR) markers from coding regions. Although the SSRs failed to separate the closest groups, i.e., subsp. alba, subsp. tenuis and the perennial groups from subsp. unguiculata, a combination of 11 SSR markers could properly identify the main cowpea subspecies. Regarding the infraspecific phylogeny of cowpea, the SSR markers confirmed the special status of the annual subsp. unguiculata versus the different perennial subspecies. They suggested that subsp. protracta is the oldest subspecies, making the origin of the species in southern Africa likely. All the taxa of hybrid origin, i.e., subsp. alba, subsp. tenuis, subsp. pubescens, and the BWA group of subsp. unguiculata, are in a single clade clearly separated from subsp. unguiculata. Although a limited number of markers were tested, considering that several hundred cowpea SSRs are available, the present work shows that SSR markers can be used for the molecular characterization of cowpea subspecies and can be very helpful for understanding the complex evolutionary history of cowpea. [ABSTRACT FROM AUTHOR]

Main conclusion: Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding. [ABSTRACT FROM AUTHOR]

Summary: Global agriculture faces increasing pressure to produce more food with fewer resources. Drought, exacerbated by climate change, is a major agricultural constraint costing the industry an estimated US$80 billion per year in lost production. Wild relatives of domesticated crops, including wheat (Triticum spp.) and barley (Hordeum vulgare L.), are an underutilized source of drought tolerance genes. However, managing their undesirable characteristics, assessing drought responses, and selecting lines with heritable traits remains a significant challenge. Here, we propose a novel strategy of using multi‐trait selection criteria based on high‐throughput spectral images to facilitate the assessment and selection challenge. The importance of measuring plant capacity for sustained carbon fixation under drought stress is explored, and an image‐based transpiration efficiency (iTE) index obtained via a combination of hyperspectral and thermal imaging, is proposed. Incorporating iTE along with other drought‐related variables in selection criteria will allow the identification of accessions with diverse tolerance mechanisms. A comprehensive approach that merges high‐throughput phenotyping and de novo domestication is proposed for developing drought‐tolerant prebreeding material and providing breeders with access to gene pools containing unexplored drought tolerance mechanisms. [ABSTRACT FROM AUTHOR]

The concentration of mineral nutrients in plants is associated with bioavailabilities of soil mineral nutrients, which are regulated by various soil physio-chemical properties. A pot experiment was conducted to investigate the effects of soil type on grain and straw zinc (Zn), iron (Fe) and selenium (Se) concentrations of wheat/Amblyopyrum muticum and wheat/Triticum urartu doubled haploid lines. A set of 42 treatments in a factorial combinationwith 21 genotypes and two soil types collected fromNgabu and Chitedze Research Stations in Malawi was laid in a randomisedcompleteblockdesign (RCBD) in three replicates. Pre-experiment soil Zn and Fe were extracted using DTPA extraction method followed by analysis with inductively coupled plasma-mass spectrometry (ICP-MS). Aqua-regia hotplate acid digestion was used to extract soil Se and analysis was done using ICPM-MS. Grain and straw samples were digested using nitric acid digestion (HNO3) and analysed using ICP-MS. Soil analysis results showed that the two soils had the same textural class (Sandy clay loam), but different mineral concentrations, pH levels and percentage organic matter. Analysis of variance revealed a ~two-fold higher Zn concentration in grains grown in low pH, high Zn soils (Chitedze soils) compared to grains grown in high pH, low Zn soils (Ngabu soils). Variation in grain Zn concentrationwas associated with the genotypes (p = 0002), soil type (p = <0.0001), and their interaction (p = 0.035). Grain Fe was 1.3-fold higher in low pH than in high pH soils, and itwas influenced by genotypes (p = < 0.0001) and soil type (p = <0.0001). Grain Se was highly associated with soil type (p = <0.0001), and it was 30-fold higher in high pH than in low pH soils. Straw Zn was generally higher in plants grown in Chitedze soils than Ngabu soils, whilst strawSewas higher in plants grown in Ngabu soils than Chitedze soils. The findings demonstrate the significance of soil physio-chemical properties for mineral accumulation and distribution to plant parts, thus informing future breeding programs on important considerations on crop genetic biofortification with the three mineral elements. [ABSTRACT FROM AUTHOR]

Concerns about food security worldwide have been raised due to the adverse impacts of climate change on agricultural productivity. Utilizing wild relatives of cultivated plants in breeding schemes is a potential solution to address the abovementioned challenges. Wild relatives refer to indigenous plant species that share genetic ancestry with recently cultivated plants. The capacity of plants to withstand abiotic stresses and enhance crop yield stability in cold and arid environments renders them a valuable prospective resource for breeding programs. Molecular markers are employed to assess the genetic variability of cultivated plants and their wild relatives under investigation. This study employed a set of five primers derived from ISSR (Inter Simple Sequence Repeats) and SCoT (Start Codon Targeted) to assess comparative research between cultivated species and their wild relatives from three families: Apiaceae (Apium gravolens L., A. leptophyllum (Pers.) F.Muell., Daucus carota L.& D. litoralis Sm.), Asteraceae (Lactuca sativa L. & L. serriola L.) and Brassicaceae (B. oleracea L., Brassica tourneforttii Gouan., Raphanus sativus L. & R. raphanistrum L.). The ISSR technique yields approximately 206 bands, whereas the SCoT primers generate approximately 207 bands. The ISSR primers yielded 169 polymorphic bands, exhibiting a polymorphism rate of 82.04%, whereas the SCoT primers produced 169 polymorphic bands with a polymorphism rate of 81.64%. The Brassicaceae has been found to exhibit the highest resolving power (RP) of 48.25, as determined by ISSR. The primary objective of DNA barcoding is to create a communal database of DNA sequences that can be utilized to identify organisms and clarify their taxonomic classification. The findings indicate that the internal transcribed spacer (ITS) regions exhibit high efficacy as a DNA barcoding tool. Overall, the results obtained from two molecular markers and DNA barcoding analyses suggest a significant degree of genetic diversity and relatedness among the cultivated taxa and their wild relatives examined in this study. [ABSTRACT FROM AUTHOR]

Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome's polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era. [ABSTRACT FROM AUTHOR]

The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

Lowering nitrogen inputs is a major goal for sustainable agriculture. In the present study, a set of 10 Solanum melongena introgression lines (ILs) developed using Solanum incanum as the exotic donor parent were grown under two nitrogen fertilization doses supplied with the irrigation system: 1) 8.25 mmol · L−1 NH4NO3, corresponding to the high nitrogen treatment (HN), and 2) no external nitrogen supply, corresponding to the low nitrogen treatment (LN). Twenty traits, including plant growth and yield parameters, fruit size and morphology, nitrogen and carbon content in leaf and fruit, and phenolics content in fruit, were evaluated. The aim was to select of potential materials for eggplant breeding under low N inputs, as well as to identify and locate putative QTLs associated with the traits evaluated. No significant differences were observed between the soil characteristics of the HN and LN treatments, except for nitrogen and iron content, which was slightly lower in the HN, probably as a consequence of higher nutrient removal from soil by plants in the latter group. Analysis of variance showed that lowering nitrogen inputs did not significantly affect the final yield, fruit morphology, size and phenolics content. Most agronomic traits were highly and positively correlated with each other under both treatments, as well as total phenolics with chlorogenic acid content. The assessment of the differences between each IL and the recipient parent resulted in the identification of 36 QTLs associated with most of the traits—12 were specific to the HN, 17 specific to the LN, and 7 were stable across treatments. The introgressed fragment of S. incanum generally had a negative effect on the trait, except for QTLs for fruit dry matter, for fruit length on chromosome 10 under the HN, and for fruit pedicel length on chromosome 9 under the LN. The increase over AN-S-26 of the allele of S. incanum for the QTLs detected ranged between −73.98% and 26.03% in HN and −73.67% and 34.43% in LN. These findings provide useful tools for the utilization of S. incanum in eggplant breeding under lower nitrogen fertilization.

Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety 'Nachit' derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum,and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference 'Svevo' genome assembly. Kinship distinguished the progenies in three cladesmatching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were namedQ.ICD.NAM-04,Q.ICD.NAM-14, andQ.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding. [ABSTRACT FROM AUTHOR]

• In vegetatively propagated crops, the loss of sexual reproduction capacity has been recognized as a domestication syndrome. • Results of pairwise PERMANOVA comparisons showed significant divergence between wild and domesticated enset in terms of their fruit and seed morphological characters. • Fruit weight, fruit length, fruit circumference, and number of seeds per fruit were the traits that differed most between cultivated and wild enset; significantly greater in the wild population. • Our results point to the possibility of complex evolutionary dynamics of both cultivated and wild forms. Enset is a single-stemmed plant; i.e., non-suckering naturally both in wild and cultivated states. There are great differences in their life cycles between the wild and cultivated populations of enset. Wild enset reproduce naturally via seeds. As cultivated enset is usually harvested before or shortly after flowering, the development of flowers and fruits is rarely encountered in cultivation. As a result, cultivated enset is propagated vegetatively, with adventitious buds sprouting from the corm after the removal of the apical meristem. In vegetatively propagated crops, the loss of sexual reproduction capacity has been recognized as a domestication syndrome. The present study was performed to determine the pattern of fruit and seed variation between and within wild and cultivated populations, by measuring morphological differences in fruit and seed traits (number of hands per bunch, number of fruit per mid-hand, mean fruit weight, fruit length, fruit circumference, seed number per fruit, seed weight and seed diameter) in wild and cultivated plants. Results of pairwise PERMANOVA comparisons showed significant difference between wild and domesticated enset in terms of their fruit and seed morphological characters. Among the traits studied, average fruit weight, fruit length, fruit circumference, and number of seeds per fruit were the traits that differed most between cultivated and wild. These characters were significantly greater in the wild population than in cultivated. We suggest that these traits could define the domestication syndrome of this plant. Despite significant divergences between wild and cultivated ensets, some cultivated accessions, were certainly domesticated landrace are placed together with wild accessions in PCA biplot. Our results point to the possibility of complex evolutionary dynamics of both cultivated and wild forms, and gave an insight that there is huge potential to improve this crop through hybridization and clonal selection methods. Furthermore, the present results provide useful indications on how to act for more rational planning in reproductive material management and genetic resource conservation strategies. [ABSTRACT FROM AUTHOR]

Background and Aims Gigantism is a key component of the domestication syndrome, a suite of traits that differentiates crops from their wild relatives. Allometric gigantism is strongly marked in horticultural crops, causing disproportionate increases in the size of edible parts such as stems, leaves or fruits. Tomato (Solanum lycopersicum) has attracted attention as a model for fruit gigantism, and many genes have been described controlling this trait. However, the genetic basis of a corresponding increase in size of vegetative organs contributing to isometric gigantism has remained relatively unexplored. Methods Here, we identified a 0.4-Mb region on chromosome 7 in introgression lines (ILs) from the wild species Solanum pennellii in two different tomato genetic backgrounds (cv. 'M82' and cv. 'Micro-Tom') that controls vegetative and reproductive organ size in tomato. The locus, named ORGAN SIZE (ORG), was fine-mapped using genotype-by-sequencing. A survey of the literature revealed that ORG overlaps with previously mapped quantitative trait loci controlling tomato fruit weight during domestication. Key Results Alleles from the wild species led to lower cell number in different organs, which was partially compensated by greater cell expansion in leaves, but not in fruits. The result was a proportional reduction in leaf, flower and fruit size in the ILs harbouring the alleles from the wild species. Conclusions Our findings suggest that selection for large fruit during domestication also tends to select for increases in leaf size by influencing cell division. Since leaf size is relevant for both source–sink balance and crop adaptation to different environments, the discovery of ORG could allow fine-tuning of these parameters. [ABSTRACT FROM AUTHOR]

Cucurbita ficifolia is a squash grown from Mexico to Bolivia. Its ancestor is unknown, but it has limited compatibility with wild xerophytic Cucurbita from Mexico's highlands. We assembled the reference genome of C. ficifolia and assessed the genetic diversity and historical demography of the crop in Mexico with 2524 nuclear single nucleotide polymorphisms (SNPs). We also evaluated the gene flow between C. ficifolia and xerophytic taxa with 6292 nuclear and 440 plastome SNPs from 142 individuals sampled in 58 sites across their area of sympatry. Demographic modelling of C. ficifolia supports an eight-fold decrease in effective population size at about 2409 generations ago (95% CI = 464–12,393), whereas plastome SNPs support the expansion of maternal lineages ca. 1906–3635 years ago. Our results suggest a recent spread of C. ficifolia in Mexico, with high genetic diversity (π = 0.225, FST = 0.074) and inbreeding (FIS = 0.233). Coalescent models suggest low rates of gene flow with C. radicans and C. pedatifolia, whereas ABBA-BABA tests did not detect significant gene flow with wild taxa. Despite the ecogeographic proximity of C. ficifolia and its relatives, this crop persists as a highly isolated lineage of puzzling origin. [ABSTRACT FROM AUTHOR]

Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change. [ABSTRACT FROM AUTHOR]

Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop. [ABSTRACT FROM AUTHOR]

Lowering nitrogen inputs is a major goal for sustainable agriculture. In the present study, a set of 10 Solanum melongena introgression lines (ILs) developed using Solanum incanum as the exotic donor parent were grown under two nitrogen fertilization doses supplied with the irrigation system: 1) 8.25 mmol $ L-1 NH4NO3, corresponding to the high nitrogen treatment (HN), and 2) no external nitrogen supply, corresponding to the low nitrogen treatment (LN). Twenty traits, including plant growth and yield parameters, fruit size and morphology, nitrogen and carbon content in leaf and fruit, and phenolics content in fruit, were evaluated. The aim was to select of potential materials for eggplant breeding under low N inputs, as well as to identify and locate putative QTLs associated with the traits evaluated. No significant differences were observed between the soil characteristics of the HN and LN treatments, except for nitrogen and iron content, which was slightly lower in the HN, probably as a consequence of higher nutrient removal from soil by plants in the latter group. Analysis of variance showed that lowering nitrogen inputs did not significantly affect the final yield, fruit morphology, size and phenolics content. Most agronomic traits were highly and positively correlated with each other under both treatments, as well as total phenolics with chlorogenic acid content. The assessment of the differences between each IL and the recipient parent resulted in the identification of 36 QTLs associated with most of the traitsd12 were specific to the HN, 17 specific to the LN, and 7 were stable across treatments. The introgressed fragment of S. incanum generally had a negative effect on the trait, except for QTLs for fruit dry matter, for fruit length on chromosome 10 under the HN, and for fruit pedicel length on chromosome 9 under the LN. The increase over AN-S-26 of the allele of S. incanum for the QTLs detected ranged between -73.98% and 26.03% in HN and -73.67% and 34.43% in LN. These findings provide useful tools for the utilization of S. incanum in eggplant breeding under lower nitrogen fertilization. [ABSTRACT FROM AUTHOR]

Black gram is one of the most important short duration grain legume, which contributes significantly towards nutritional security and environmental sustainability. The virus specific primers confirms the presence of mungbean yellow mosaic India virus (MYMIV) in representative samples. A total of 27 cultivated and two wild species were found as highly resistant (HR) to MYMIV and validated through molecular markers. The start codon target (SCoT) markers analysis revealed that the SCoT loci, namely, SCoT‐4 (2200 bp), SCot‐9 (1150/ 1200 bp), SCoT‐15 (1150/1100 bp), SCoT‐16 (700 bp), SCoT‐24 (2500 bp), SCoT‐25 (700 bp), SCoT‐33 (900/1000 bp), and SCoT‐34 (600 bp), were found unique, able to distinguish HR and highly susceptible (HS) genotypes. Biochemical characterization and gene expression profiling revealed the higher expression of antioxidants and R‐genes just after pathogen inoculation indicated the activation of defence mechanism in both cultivated and its wild relatives, which modulates the resistant responses in cultivated and wild accessions. These information will be really helpful in accelerating resistance breeding in black gram. [ABSTRACT FROM AUTHOR]

Aims: Domestication and crop breeding has improved plants for human use, but may have unintended consequences for traits that are not selected upon. Disruption in the mycorrhizal mutualism has been observed in crops; possibly due to breeding in fertilised soil. Little is known about whether the legume-rhizobia mutualism can be disrupted by domestication and crop evolution, despite the importance of symbiotic nitrogen fixation. We aimed to identify differences in mutualistic outcomes between five legume cultivars and their wild progenitors in terms of their reactions across varying nitrogen levels. Methods: With five greenhouse experiments, we characterised symbiosis traits in chickpea, lentil, pea, peanut, and soybean across a gradient of N fertilisation to characterise whether symbiosis traits differ context specifically between wild and domesticated lines. Results: At lower levels of N addition, wild soybean benefited more from rhizobia than domesticated soybean. Chickpea cultivars abandoned symbiosis at lower N than wild chickpea accessions. Chickpea cultivars reduced per-nodule colony forming units (CFU) in response to N addition more than wild chickpeas, but lentil cultivars reduced CFU less than lentil accessions. The lentil, pea, and peanut cultivars did not differ from their wild relatives in rhizobial benefit, nor in nodulation response to N addition. Conclusions: Differences in the regulation of the root nodule symbiosis are evident between domesticated and wild chickpea and soybean, but not lentil, pea, or peanut. This indicates that mutualism disruption—a decrease in the magnitude of the mutually symbiotic interaction—is a possible, but not necessary, consequence of domestication. [ABSTRACT FROM AUTHOR]

Timothy grass (Phleum pratense L.) is one of the most important forage crops in temperate regions. Forage production, however, faces many challenges, and new cultivars adapted to a changing climate are needed. Wild populations and relatives of timothy may serve as valuable genetic resources in the breeding of improved cultivars. The aim of our study is to provide knowledge about the phenotypic diversity in domesticated (cultivars, breeding lines and landraces) and wild timothy and two closely related species, P. nodosum (lowland species) and P. alpinum, (high altitude species) to identify potential genetic resources. A total of 244 accessions of timothy and the two related species were studied for growth (plant height, fresh and dry weight) and plant development (days to stem elongation, days to booting and days to heading) in the field and in a greenhouse. We found a large diversity in development and growth between the three Phleum species, as well as between the accessions within each species. Timothy showed the highest growth, but no significant difference was found between wild accessions and cultivars of timothy in fresh and dry weight. However, these two groups of accessions showed significant differences in plant development, where timothy cultivars as a group reached flowering earlier than the wild accessions. This suggests that there has not been a strong directional selection towards increased yield during the domestication and breeding of timothy; rather, timothy has been changed for other traits such as earlier heading. Principal component analysis and cluster analysis based on all traits revealed distinct clusters. Accessions falling within the same cluster showed similarities in the development and growth rather than the type of accession. The large diversity found in this study shows the potential of using timothy accessions as genetic resources in crosses with existing cultivars. Also, accessions of P. nodosum with favorable traits can be candidates for the domestication of a novel forage crop, and the high-altitude relative P. alpinum may be a source of genes for the development of more cold and stresstolerant cultivars. [ABSTRACT FROM AUTHOR]

The concentration of mineral nutrients in plants is associated with bioavailabilities of soil mineral nutrients, which are regulated by various soil physio-chemical properties. A pot experiment was conducted to investigate the effects of soil type on grain and straw zinc (Zn), iron (Fe) and selenium (Se) concentrations of wheat/Amblyopyrum muticum and wheat/Triticum urartu doubled haploid lines. A set of 42 treatments in a factorial combination with 21 genotypes and two soil types collected from Ngabu and Chitedze Research Stations in Malawi was laid in a randomised complete block design (RCBD) in three replicates. Pre-experiment soil Zn and Fe were extracted using DTPA extraction method followed by analysis with inductively coupled plasma-mass spectrometry (ICP-MS). Aqua-regia hotplate acid digestion was used to extract soil Se and analysis was done using ICPM-MS. Grain and straw samples were digested using nitric acid digestion (HNO3) and analysed using ICP-MS. Soil analysis results showed that the two soils had the same textural class (Sandy clay loam), but different mineral concentrations, pH levels and percentage organic matter. Analysis of variance revealed a ~two-fold higher Zn concentration in grains grown in low pH, high Zn soils (Chitedze soils) compared to grains grown in high pH, low Zn soils (Ngabu soils). Variation in grain Zn concentration was associated with the genotypes (p = 0002), soil type (p =

In recent decades, genetic advances in yield improvement in the major cereal crops, including wheat, has stagnated or proceeded at a slower rate than is required to meet future global food demand, particularly in the face of climate change. To reverse this situation, and in view of the future climate scenario, there is a need to increase the genetic diversity of wheat to increase its productivity, quality, stability, and adaptation to local agro-environments. The abundant genetic resources and literature are a basis for wheat improvement. However, many species, such as wild relatives, landraces, and old cultivars have not been studied beyond their agronomic characteristics, highlighting the lack of understanding of the physiological and metabolic processes (and their integration) associated with higher productivity and resilience in limiting environments. Retrospective studies using wheat ancestors and modern cultivars may identify novel traits that have not previously been considered, or have been underestimated, during domestication and breeding, but that may contribute to future food security. This review describes existing wheat genetic diversity and changes that occurred during domestication and breeding, and considers whether mining natural variation among wheat ancestors offers an opportunity to enhance wheat agronomic performance, spike architecture, canopy- and organ-level photosynthetic capacity, and responses to abiotic stress, as well as to develop new wheat hybrids.

Terminal drought is one of the most common and devastating climatic stress factors affecting durum wheat (Triticum durum Desf.) production worldwide. The wild relatives of this crop are deemed a vast potential source of useful alleles to adapt to this stress. A nested association mapping (NAM) panel was generated using as a recurrent parent the Moroccan variety ‘Nachit’ derived from Triticum dicoccoides and known for its large grain size. This was recombined to three top-performing lines derived from T. dicoccoides, T. araraticum, and Aegilops speltoides, for a total of 426 inbred progenies. This NAM was evaluated across eight environments (Syria, Lebanon, and Morocco) experiencing different degrees of terminal moisture stress over two crop seasons. Our results showed that drought stress caused on average 41% loss in yield and that 1,000-kernel weight (TKW) was the most important trait for adaptation to it. Genotyping with the 25K TraitGenetics array resulted in a consensus map of 1,678 polymorphic SNPs, spanning 1,723 cM aligned to the reference ‘Svevo’ genome assembly. Kinship distinguished the progenies in three clades matching the parent of origin. A total of 18 stable quantitative trait loci (QTLs) were identified as controlling various traits but independent from flowering time. The most significant genomic regions were named Q.ICD.NAM-04, Q.ICD.NAM-14, and Q.ICD.NAM-16. Allelic investigation in a second germplasm panel confirmed that carrying the positive allele at all three loci produced an average TKW advantage of 25.6% when field-tested under drought conditions. The underlying SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers and successfully validated in a third germplasm set, where they explained up to 19% of phenotypic variation for TKW under moisture stress. These findings confirm the identification of critical loci for drought adaptation derived from wild relatives that can now be readily exploited via molecular breeding.

The transition from annual to perennial growth habits can contribute to increased sustainability and diversification of staple cropping systems like those based on annual wheat. Amphiploids between Triticum aestivum and Thinopyrum spp. can present a wheat-like morphology and post sexual cycle regrowth. The complex and unpredictable nature of the chromosomal rearrangements typical of inter-generic hybrids can hamper progress in the development of this new crop. By using fluorescence in situ hybridization, we described the genomic constitution of three perennial wheat breeding lines that regrew and completed a second year of production in field conditions in Washington state (USA). Two breeding lines presented stable, 56-chromosome partial amphiploids; however, their chromosome composition differed significantly. The third breeding line presented an unstable karyotype with a chromosome number ranging from 53 to 58 across eight individuals. The agronomic performance of the perennial breeding lines was evaluated for two growing seasons from 2020 to 2022. The grain yields of the perennial lines were lower than the grain production of the annual wheat control line in the first season. The perennial lines displayed vigorous regrowth after the initial harvest; however, worsening environmental conditions in the second season of growth hampered subsequent growth and grain yield. This information facilitates the breeding work necessary to improve key traits by grouping agronomically valuable individuals according to their genomic constitution. [ABSTRACT FROM AUTHOR]

Lentil (Lens culinaris Medik.) is commonly grown in drought-prone areas where terminal heat and drought are frequent. The limited-transpiration (TRlim) trait under high vapor pressure deficit (VPD) could be a way to conserve water and increase yield under water deficit conditions. The TRlim trait was examined in cultivated and wild lentil species together with its evolution throughout the breeding pipeline. Sixty-one accessions representing the six wild lentil species (L. orientalis , L. tomentosus , L. odemensis , L. lamottei , L. ervoides , and L. nigricans) and 13 interspecific advanced lines were evaluated in their transpiration response to high VPD. A large variation in transpiration rate (TR) response to increased VPD was recorded among wild lentil accessions, with 43 accessions exhibiting a breakpoint (BP) in their TR response to increasing VPD, with values ranging from 0.92 kPa to 3.38 kPa under greenhouse conditions. Ten genotypes for the interspecific advanced lines displayed a BP with an average of 1.95 kPa, much lower than previously reported for cultivated lentil. Results from field experiments suggest that the TRlim trait (BP=0.97 kPa) positively affected yield and yield-related parameters during the years with late-season water stress. The selection of TRlim genotypes for high VPD environments could improve lentil productivity in drought-prone areas. [ABSTRACT FROM AUTHOR]

Eggplant (S. melongena L.) belongs to Solanaceae and is cultivated worldwide. Root-knot nematodes (RKN), Meloidogyne spp., are among the most important pathogens affecting eggplant production both in greenhouse and open field cultivation. Chemical control was carried out for many years, but their excessive usage is harmful for both human and environmental health. Genetic improvement of eggplant is the best environmentally friendly alternative method for the containment of pests, also providing sustainable production in growing areas. Thus, it is necessary to characterize the available germplasm of cultivated eggplant as well as of allied and wild species to uncover potential sources of resistance exploitable for breeding. To date, there is no sufficient information available on resistance sources to nematodes for eggplant. In this study, some new potential resistance sources to M. incognita race 1, the most common nematode species affecting eggplant worldwide, were investigated. Plantlets of 15 genotypes, including eggplant varieties, heirlooms, allied species, and interspecific hybrids, were inoculated with second stage juveniles (J2), and disease assessment was performed by visually evaluating galls on the roots using a 0–5 scale and by counting egg masses/galls on plant root system and J2 in soil. Among the genotypes tested, a strong resistance source was detected in both S. torvum and S. tomentosum, being this latter the best candidate exploitable for breeding programs as this species is crossable with eggplant and ILs are already available. [ABSTRACT FROM AUTHOR]

In recent decades, genetic advances in yield improvement in the major cereal crops, including wheat, has stagnated or proceeded at a slower rate than is required to meet future global food demand, particularly in the face of climate change. To reverse this situation, and in view of the future climate scenario, there is a need to increase the genetic diversity of wheat to increase its productivity, quality, stability, and adaptation to local agro-environments. The abundant genetic resources and literature are a basis for wheat improvement. However, many species, such as wild relatives, landraces, and old cultivars have not been studied beyond their agronomic characteristics, highlighting the lack of understanding of the physiological and metabolic processes (and their integration) associated with higher productivity and resilience in limiting environments. Retrospective studies using wheat ancestors and modern cultivars may identify novel traits that have not previously been considered, or have been underestimated, during domestication and breeding, but that may contribute to future food security. This review describes existing wheat genetic diversity and changes that occurred during domestication and breeding, and considers whether mining natural variation among wheat ancestors offers an opportunity to enhance wheat agronomic performance, spike architecture, canopy- and organ-level photosynthetic capacity, and responses to abiotic stress, as well as to develop new wheat hybrids. [ABSTRACT FROM AUTHOR]

Genetic divergence analysis in brinjal genetic resources consisting of landraces, related cultivated species and wild relatives based on 22 morphological descriptors revealed distinct variation between cultivated and wild genotypes for the plant, flowering and fruiting characters. The multivariate D2 analysis grouped the 30 accessions into eight clusters revealing a clear separation of wild relatives and cultivated types. The characters fruit yield per plant, leaf size and fruit number had high contribution towards the genetic divergence. SM- 27 (cluster V), SM- 25 (cluster III) and SM-23, SM-24,SM-20, SM-18, SM-10 and SM- 8 (cluster I) were the promising accessions identified based on superior performance for three yield attributes viz., fruit weight, number of fruits per plant and fruit yield per plant. The accessions SM- 25, SM- 27, SM- 28 (Solanum incanum) and SM-30 (Solanum insanum) of highly divergent clusters III, V and VIII respectively were identified as potential parents for future introgression breeding.

Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome’s polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.

A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication However, the lack of genome sequences of these wild watermelon species has limited their utilization in watermelon breeding. Bitter or bland-tasting wild watermelons, such as I C. mucosospermus i , I C. amarus i and I C. colocynthis i , have been used in watermelon breeding to introduce disease resistance to modern cultivars (Levi I et al i ., [2]). Keywords: watermelon; super-pangenome; wild relatives; domestication; disease resistance EN watermelon super-pangenome wild relatives domestication disease resistance 1926 1928 3 09/20/23 20231001 NES 231001 Cultivated watermelon ( I Citrullus lanatus i subsp. I vulgaris i ) has a narrow genetic base due to domestication and breeding focusing primarily on fruit quality traits. [Extracted from the article]

Camelina or false flax (Camelina sativa) is an emerging oilseed crop and a feedstock for biofuel production. This species is believed to originate from Western Asian and Eastern European regions, where the center of diversity of the Camelina genus is located. Cultivated Camelina species arose via a series of polyploidization events, serving as bottlenecks narrowing genetic diversity of the species. The genetic paucity of C. sativa is foreseen as the most crucial limitation for successful breeding and improvement of this crop. A potential solution to this challenge could be gene introgression from Camelina wild species or from resynthesized allohexaploid C. sativa. However, both approaches would require a complete comprehension of the evolutionary trajectories that led to the C. sativa origin. Although there are some studies discussing the origin and evolution of Camelina hexaploid species, final conclusions have not been made yet. Here, we propose the most complete integrated evolutionary model for the Camelina genus based on the most recently described findings, which enables efficient improvement of C. sativa via the interspecific hybridization with its wild relatives. We also discuss issues of interspecific and intergeneric hybridization, aimed on improving C. sativa and overcoming the genetic paucity of this crop. The proposed comprehensive evolutionary model of Camelina species indicates that a newly described species Camelina neglecta has a key role in origin of tetra- and hexaploids, all of which have two C. neglecta-based subgenomes. Understanding of species evolution within the Camelina genus provides insights into further research on C. sativa improvements via gene introgression from wild species, and a potential resynthesis of this emerging oilseed crop.

Background: In the Sesamum species complex, the lack of wild species genomic resources hinders the evolutionary comprehension of phylogenetic relationships. Results: In the present study, we generated complete chloroplast genomes of six wild relatives (Sesamum alatum, Sesamum angolense, Sesamum pedaloides, Ceratotheca sesamoides (syn. Sesamum sesamoides), Ceratotheca triloba (syn. Sesamum trilobum), and Sesamum radiatum) and a Korean cultivar, Sesamum indicum cv. Goenbaek. A typical quadripartite chloroplast structure, including two inverted repeats (IR), a large single copy (LSC), and a small single copy (SSC), was observed. A total of 114 unique genes encompassing 80 coding genes, four ribosomal RNAs, and 30 transfer RNAs were counted. The chloroplast genomes (152, 863–153, 338 bp) exhibited the IR contraction/expansion phenomenon and were quite conserved in both coding and non-coding regions. However, high values of the nucleotide diversity index were found in several genes, including ndhA, ndhE, ndhF, ycf1, and psaC–ndhD. Concordant tree topologies suggest ndhF as a useful marker for taxon discrimination. The phylogenetic inference and time divergence dating indicate that S. radiatum (2n = 64) occurred concomitantly with the sister species C. sesamoides (2n = 32) approximately 0.05 million years ago (Mya). In addition, S. alatum was clearly discriminated by forming a single clade, showing its long genetic distance and potential early speciation event in regards to the others. Conclusion: Altogether, we propose to rename C. sesamoides and C. triloba as S. sesamoides and S. trilobum, respectively, as suggested previously based on the morphological description. This study provides the first insight into the phylogenetic relationships among the cultivated and wild African native relatives. The chloroplast genome data lay a foundation for speciation genomics in the Sesamum species complex. [ABSTRACT FROM AUTHOR]

Deleterious mutations are common in plant genomes and present both challenges and opportunities for domesticated crops. While many deleterious mutations can negatively impact crop performance, some deleterious mutations are associated with breeding-relevant phenomena, such as heterosis, genetic variation, and key loss-of-function domestication traits that underpin crop production. Breeding may hasten the accumulation of deleterious variants. Crop species vary in their pattern and distribution of deleterious mutations, and differences are noted among mating systems, ploidy levels, and propagation systems. Current efforts focus on predicting functional consequences of deleterious mutations on a genome-wide scale and comparing the effects across species. Strategies for removal of deleterious variants with techniques such as gene editing may facilitate breeding and accelerate the redomestication of crops from wild species. Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations. [ABSTRACT FROM AUTHOR]

Abstract The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.

Mangosteen (Garcinia mangostana var. mangostana) is a popular tropical fruit, yet many aspects of its biology and evolutionary history are little known. Its origin remains contentious, although recent findings suggest G. mangostana L. var. malaccensis (Hook. f.) Nazre (synonym: G. malaccensis Hook. f.) as the sole progenitor. We review hypotheses on the origin of mangosteen and clarify points that have been affected by errors of fact and interpretation. The narrow focus and lack of detail in published results make their interpretation difficult. When possible, we support our interpretations with field observations and examination of herbarium specimens. We outline the main biological traits (e.g., dioecy, facultative apomixis, and polyploidy) of mangosteen and its wild relatives to infer traits that might have evolved during domestication of mangosteen. We find no clear indication that apomixis and polyploidy evolved during domestication. Polyploidy is known in the wild relatives, but apomixis has not yet been demonstrated. Also, we propose a testable new evolutionary‐ecological framework that we call "Forest‐Dusun Interface" to infer processes in the origin of mangosteen. Dusun (Malay) refers to subsistence orchards in this context. Lastly, we propose future studies to address identified knowledge gaps. [ABSTRACT FROM AUTHOR]