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Tepary bean (Phaseolus acutifolius A. Gray) is a drought and high ambient temperature tolerant crop native to the Sonoran Desert, the hottest and driest region in the United States and Mexico. Although tepary bean is an orphan crop with little current commercial production, there was a brief period of larger scale production in the early 1900s in California. Tepary bean has great potential as a novel crop in a warmer world climate and can be introduced as an alternative pulse crop in hot and/or dry regions worldwide. TARS-Tep 23 (Reg. no. GP-309, PI 698457) is an improved tepary bean germplasm with wide-ranging adaptation to tropical and temperate regions experiencing high temperature and drought stress conditions, with broad resistance to bean rust and with resistance to common bacterial blight. It has a flat, mottled black seed type with good seed size, a Type III plant habit, and a short crop cycle of 55–61 d in the environments tested. This germplasm was developed cooperatively by the USDA-ARS, Zamorano University, the University of California–Davis, and the University of Nebraska. The use of this improved germplasm by farmers in production zones affected by abiotic and biotic stresses, or by breeding programs, can potentially increase seed yields of this climate-resilient crop.

Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC1S4) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from -164 to 277 kg ha-1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from drought-stressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression.

BackgroundCommon bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed quality. Previous studies have shown that photosynthate remobilization and partitioning is one of the main mechanisms of drought tolerance and overall productivity in common bean.ResultsIn this study, we sought to determine the inheritance of pod harvest index (PHI), a measure of the partitioning of pod biomass to seed biomass, relative to that of grain yield. We evaluated a recombinant inbred population of the cross of ICA Bunsi and SXB405, both from the Mesoamerican gene pool, to determine the effects of intermittent and terminal drought stresses on the genetic architecture of photosynthate allocation and remobilization in pods of common bean. The population was grown for two seasons, under well-watered conditions and terminal and intermittent drought stress in one year, and well-watered conditions and terminal drought stress in the second year. There was a significant effect of the water regime and year on all the traits, at both the phenotypic and QTL levels. We found nine QTLs for pod harvest index, including a major (17% of variation explained), stable QTL on linkage group Pv07. We also found eight QTLs for yield, three of which clustered with PHI QTLs, underscoring the importance of photosynthate remobilization in productivity. We also found evidence for substantial epistasis, explaining a considerable part of the variation for yield and PHI.ConclusionOur results highlight the genetic relationship between PHI and yield and confirm the role of PHI in selection of both additive and epistatic effects controlling drought tolerance. These results are a key component to strengthen the robustness of common bean against drought stresses.

BackgroundCommon bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed quality. Previous studies have shown that photosynthate remobilization and partitioning is one of the main mechanisms of drought tolerance and overall productivity in common bean.ResultsIn this study, we sought to determine the inheritance of pod harvest index (PHI), a measure of the partitioning of pod biomass to seed biomass, relative to that of grain yield. We evaluated a recombinant inbred population of the cross of ICA Bunsi and SXB405, both from the Mesoamerican gene pool, to determine the effects of intermittent and terminal drought stresses on the genetic architecture of photosynthate allocation and remobilization in pods of common bean. The population was grown for two seasons, under well-watered conditions and terminal and intermittent drought stress in one year, and well-watered conditions and terminal drought stress in the second year. There was a significant effect of the water regime and year on all the traits, at both the phenotypic and QTL levels. We found nine QTLs for pod harvest index, including a major (17% of variation explained), stable QTL on linkage group Pv07. We also found eight QTLs for yield, three of which clustered with PHI QTLs, underscoring the importance of photosynthate remobilization in productivity. We also found evidence for substantial epistasis, explaining a considerable part of the variation for yield and PHI.ConclusionOur results highlight the genetic relationship between PHI and yield and confirm the role of PHI in selection of both additive and epistatic effects controlling drought tolerance. These results are a key component to strengthen the robustness of common bean against drought stresses.

Significance: Plant domestication has radically modified crop morphology and development. Nevertheless, many crops continue to display some atavistic characteristics that were advantageous to their wild ancestors, such as pod dehiscence (PD). Domesticated common bean (Phaseolus vulgaris), a nutritional staple for millions of people globally, shows considerable variation in PD. Here, we identified multiple genetic regions controlling PD in common bean grown throughout geographically distributed lineages. For example, on chromosome Pv03, PvPdh1 shows a single base-pair substitution that is strongly associated with decreased PD and expansion of the crop into northern Mexico, where the arid conditions promote PD. The environmental dependency and genetic redundancy explain the maintenance of atavistic traits under domestication. Knowledge of PD genetics will assist in developing aridity-adapted varieties. A reduction in pod dehiscence (PD) is an important part of the domestication syndrome in legumes, including common bean. Despite this, many modern dry bean varieties continue to suffer yield reductions due to dehiscence, an atavistic trait, which is particularly problematic in hot, dry environments. To date, the genetic control of this important trait has been only partially resolved. Using QTL mapping and GWAS, we identified major PD QTLs in dry beans on chromosomes Pv03, Pv05, Pv08, and Pv09, three of which had not been described previously. We further determined that the QTL on chromosome Pv03, which is strongly associated with PD in Middle American beans, includes a dirigent-like candidate gene orthologous to Pod dehiscence 1 (Pdh1) of soybean. In this gene, we identified a substitution in a highly conserved amino acid that is unique to PD-resistant varieties. This allele is associated with the expansion of Middle American domesticated common beans into the arid environments of northern Mexico, resulting in a high allelic frequency in the domesticated ecogeographic race Durango. The polygenic redundancy and environmental dependency of PD resistance may explain the maintenance of this atavistic characteristic after domestication. Use of these alleles in breeding will reduce yield losses in arid growing conditions, which are predicted to become more widespread in coming decades.

Widespread adoption of new varieties can be valuable, especially where improved agricultural production technologies are hard to access. However, as farmers adopt new varieties, in situ population structure and genetic diversity of their seed holdings can change drastically. Consequences of adoption are still poorly understood due to a lack of crop genetic diversity assessments and detailed surveys of farmers' seed management practices. Common bean (Phaseolus vulgaris) is an excellent model for these types of studies, as it has a long history of cultivation among smallholder farmers, exhibits eco-geographic patterns of diversity (e.g., Andean vs. Mesoamerican gene-pools), and has been subjected to post-Columbian dispersal and recent introduction of improved cultivars. The Hoima district of western Uganda additionally provides an excellent social setting for evaluating consequences of adoption because access to improved varieties has varied across farmer groups in this production region. This study establishes a baseline understanding of the common bean diversity found among household producers in Uganda and compares the crop population structure, diversity and consequences of adoption of household producers with different adoption practices. Molecular diversity analysis, based on 4,955 single nucleotide polymorphism (SNP) markers, evaluated a total of 1,156 seed samples that included 196 household samples collected from household producers in the Hoima district, 19 breeder-selected varieties used in participatory breeding activities that had taken place prior to the study in the region, and a global bean germplasm collection. Households that had participated in regional participatory breeding efforts were more likely to adopt new varieties and, consequently, diversify their seed stocks than those that had not participated. Of the three farmer groups that participated in breeding efforts, households from the farmer group with the longest history of bean production were more likely to conserve "Seed Engufu", a local "Calima"-type variety of the Andean bean gene pool, and, at the same time, introduce rare Mesoamerican gene pool varieties into household seed stocks.

A limited transpiration rate under high vapor pressure deficit (VPD) could be used to conserve soil water for later use under drought conditions. Many crops show this behavior either as limited transpiration or decreases in stomatal conductance. However, little work has been done in Phaseolus. Four experiments evaluated stomatal closure across a range of VPD for well-watered plants, each experiment using varying combinations of genotypes of common (15), lima (6) and tepary beans (7 genotypes). A two-year experiment found genotypic variation in average stomatal conductance, but genotypes only had 14% stomatal closure between a VPD of 1–4kPa. In comparison, soybean, which is known to close stomata, had a 40% decrease for similar conditions in Davis, CA, USA. In a second field experiment and outdoor pot experiments, genotypes from the three species displayed, on average, a 34, 50–45% increase in stomatal conductance with increasing VPD. Six genotypes were statistically indistinguishable from a 40% decrease, but all had low probability (p

A limited transpiration rate under high vapor pressure deficit (VPD) could be used to conserve soil water for later use under drought conditions. Many crops show this behavior either as limited transpiration or decreases in stomatal conductance. However, little work has been done in Phaseolus. Four experiments evaluated stomatal closure across a range of VPD for well-watered plants, each experiment using varying combinations of genotypes of common (15), lima (6) and tepary beans (7 genotypes). A two-year experiment found genotypic variation in average stomatal conductance, but genotypes only had 14% stomatal closure between a VPD of 1–4kPa. In comparison, soybean, which is known to close stomata, had a 40% decrease for similar conditions in Davis, CA, USA. In a second field experiment and outdoor pot experiments, genotypes from the three species displayed, on average, a 34, 50–45% increase in stomatal conductance with increasing VPD. Six genotypes were statistically indistinguishable from a 40% decrease, but all had low probability (p

Next-generation sequencing technologies have increased markedly the throughput of genetic studies, allowing the identification of several thousands of SNPs within a single experiment. Even though sequencing cost is rapidly decreasing, the price for whole-genome re-sequencing of a large number of individuals is still costly, especially in plants with a large and highly redundant genome. In recent years, several reduced representation library approaches have been developed for reducing the sequencing cost per individual. Among them, genotyping-by-sequencing (GBS) represents a simple, cost-effective, and highly multiplexed alternative for species with or without an available reference genome. However, this technology requires specific optimization for each species, especially for the restriction enzyme (RE) used. Here we report on the application of GBS in a test experiment with 18 genotypes of wild and domesticated Phaseolus vulgaris. After an in silico digestion with different RE of the P. vulgaris genome reference sequence, we selected CviAII as the most suitable RE for GBS in common bean based on the high frequency and even distribution of restriction sites. A total of 44,875 SNPs, 1940 deletions, and 1693 insertions were identified, with 50 % of the variants located in genic sequences and tagging 11,027 genes. SNP and InDel distributions were positively correlated with gene density across the genome. In addition, we were able to also identify putative copy number variations of genomic segments between different genotypes. In conclusion, GBS with the CviAII enzyme results in thousands of evenly spaced markers and provides a reliable, high-throughput, and cost-effective approach for genotyping both wild and domesticated common beans.

Next-generation sequencing technologies have increased markedly the throughput of genetic studies, allowing the identification of several thousands of SNPs within a single experiment. Even though sequencing cost is rapidly decreasing, the price for whole-genome re-sequencing of a large number of individuals is still costly, especially in plants with a large and highly redundant genome. In recent years, several reduced representation library approaches have been developed for reducing the sequencing cost per individual. Among them, genotyping-by-sequencing (GBS) represents a simple, cost-effective, and highly multiplexed alternative for species with or without an available reference genome. However, this technology requires specific optimization for each species, especially for the restriction enzyme (RE) used. Here we report on the application of GBS in a test experiment with 18 genotypes of wild and domesticated Phaseolus vulgaris. After an in silico digestion with different RE of the P. vulgaris genome reference sequence, we selected CviAII as the most suitable RE for GBS in common bean based on the high frequency and even distribution of restriction sites. A total of 44,875 SNPs, 1940 deletions, and 1693 insertions were identified, with 50 % of the variants located in genic sequences and tagging 11,027 genes. SNP and InDel distributions were positively correlated with gene density across the genome. In addition, we were able to also identify putative copy number variations of genomic segments between different genotypes. In conclusion, GBS with the CviAII enzyme results in thousands of evenly spaced markers and provides a reliable, high-throughput, and cost-effective approach for genotyping both wild and domesticated common beans.