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Heat stress is a major abiotic stress factor reducing crop productivity and climate change models predict increasing temperatures in many production regions. Common bean ( Phaseolus vulgaris L .) is an important crop for food security in the tropics and heat stress is expected to cause increasing yield losses. To study physiological responses and to characterize the genetics of heat stress tolerance, we evaluated the recombinant inbred line (RIL) population IJR (Indeterminate Jamaica Red) x AFR298 of the Andean gene pool. Heat stress (HS) conditions in the field affected many traits across the reproductive phase. High nighttime temperatures appeared to have larger effects than maximum daytime temperatures. Yield was reduced compared to non-stress conditions by 37% and 26% in 2016 and 2017 seasons, respectively. The image analysis tool HYRBEAN was developed to evaluate pollen viability (PolVia). A significant reduction of PolVia was observed in HS and higher viability was correlated with yield only under stress conditions. In susceptible lines the reproductive phase was extended and defects in the initiation of seed, seed fill and seed formation were identified reducing grain quality. Higher yields under HS were correlated with early flowering, high pollen viability and effective seed filling. Quantitative trait loci (QTL) analysis revealed a QTL for both pod harvest index and PolVia on chromosome Pv05, for which the more heat tolerant parent IJR contributed the positive allele. Also, on chromosome Pv08 a QTL from IJR improved PolVia and the yield component pods per plant. HS affected several traits during the whole reproductive development, from floral induction to grain quality traits, indicating a general heat perception affecting many reproductive processes. Identification of tolerant germplasm, indicator traits for heat tolerance and molecular tools will help to breed heat tolerant varieties to face future climate change effects.

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.

In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and increasingly available genotypic data. This enables the adoption of genomic selection also in under-used legume crops such as common bean. Beans are an important staple food in the tropics and mainly grown by smallholders under limiting environmental conditions such as drought or low soil fertility. Therefore, genotype-by-environment interactions (G × E) are an important consideration when developing new bean varieties. However, G × E are often not considered in genomic prediction models nor are these models implemented in current bean breeding programs. Here we show the prediction abilities of four agronomic traits in common bean under various environmental stresses based on twelve field trials. The dataset includes 481 elite breeding lines characterized by 5,820 SNP markers. Prediction abilities over all twelve trials ranged between 0.6 and 0.8 for yield and days to maturity, respectively, predicting new lines into new seasons. In all four evaluated traits, the prediction abilities reached about 50-80% of the maximum accuracies given by phenotypic correlations and heritability. Predictions under drought and low phosphorus stress were up to 10 and 20% improved when G × E were included in the model, respectively. Our results demonstrate the potential of genomic selection to increase the genetic gain in common bean breeding. Prediction abilities improved when more phenotypic data was available and G × E could be accounted for. Furthermore, the developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.

Common bean productivity is reduced by several abiotic stress factors like drought and low soil fertility, leading to yield losses particularly in low input smallholder farming systems in the tropics. To understand the genetics of stress tolerance, and to improve adaptation of common bean to adverse environments, the BAT 881 x G21212 population of 95 recombinant inbred lines (RILs) was evaluated under different abiotic stress conditions in 15 trials across four locations in Colombia, representing two higher altitude (Darién, Popayán) and two lower altitude (Palmira, Quilichao) locations. Stress vs non-stress treatments showed that yields were reduced in drought trials in Palmira by 13 and 31%, respectively, and observed yield reductions in low phosphorus stress were 39% in Quilichao, 16% in Popayán, and 71% in Darién, respectively. Yield components and biomass traits were also reduced. Traits linked to dry matter redistribution from stems, leaves and pods to seed, such as pod harvest index and total non-structural carbohydrates, were found to be important factors contributing to yield in all conditions. In contrast, early maturity was correlated with improved yield only in lower altitude locations, whereas in higher altitudes delayed maturity promoted yield. Superior RILs that combine stress tolerance and high cross-location productivity were identified. Lines that showed good yield under strong stress conditions also performed well under non-stress conditions, indicating that breeder's selection can be applied for both conditions at the same time. Quantitative trait loci (QTL) analyses revealed a stable yield QTL on chromosome Pv04, detected individually in all locations, several stress treatments and in best linear unbiased predictions (BLUPs) across all trials. Furthermore, two QTL hotspots for maturity traits were identified on Pv01 and Pv08, which are the most stable QTL. The constitutive yield QTL could serve as a good candidate for marker development and could be used in marker assisted selection. Increased understanding of the physiology of abiotic stress tolerance, combined with the availability of superior germplasm and molecular tools, will aid breeding efforts for further improvement of these plant traits.

Cooking time of the common bean is an important trait for consumer preference, with implications for nutrition, health, and environment. For efficient germplasm improvement, breeders need more information on the genetics to identify fast cooking sources with good agronomic properties and molecular breeding tools. In this study, we investigated a broad genetic variation among tropical germplasm from both Andean and Mesoamerican genepools. Four populations were evaluated for cooking time (CKT), water absorption capacity (WAC), and seed weight (SdW): a bi-parental RIL population (DxG), an eight-parental Mesoamerican MAGIC population, an Andean (VEF), and a Mesoamerican (MIP) breeding line panel. A total of 922 lines were evaluated in this study. Significant genetic variation was found in all populations with high heritabilities, ranging from 0.64 to 0.89 for CKT. CKT was related to the color of the seed coat, with the white colored seeds being the ones that cooked the fastest. Marker trait associations were investigated by QTL analysis and GWAS, resulting in the identification of 10 QTL. In populations with Andean germplasm, an inverse correlation of CKT and WAC, and also a QTL on Pv03 that inversely controls CKT and WAC (CKT3.2/WAC3.1) were observed. WAC7.1 was found in both Mesoamerican populations. QTL only explained a small part of the variance, and phenotypic distributions support a more quantitative mode of inheritance. For this reason, we evaluated how genomic prediction (GP) models can capture the genetic variation. GP accuracies for CKT varied, ranging from good results for the MAGIC population (0.55) to lower accuracies in the MIP panel (0.22). The phenotypic characterization of parental material will allow for the cooking time trait to be implemented in the active germplasm improvement programs. Molecular breeding tools can be developed to employ marker-assisted selection or genomic selection, which looks to be a promising tool in some populations to increase the efficiency of breeding activities.

Crop improvement efforts have exploited new methods for modeling spatial trends using the arrangement of the experimental units in the field. These methods have shown improvement in predicting the genetic potential of evaluated genotypes. However, the use of these tools may be limited by the exposure and accessibility to these products. In addition, these new methodologies often require plant scientists to be familiar with the programming environment used to implement them; constraints that limit data analysis efficiency for decision-making. These challenges have led to the development of Mr.Bean, an accessible and user-friendly tool with a comprehensive graphical visualization interface. The application integrates descriptive analysis, measures of dispersion and centralization, linear mixed model fitting, multi-environment trial analysis, factor analytic models, and genomic analysis. All these capabilities are designed to help plant breeders and scientist working with agricultural field trials make informed decisions more quickly. Mr.Bean is available for download at https://github.com/AparicioJohan/MrBeanApp .

Common bean ( Phaseolus vulgaris L.) is the most important legume for direct human consumption worldwide. It is a rich and relatively inexpensive source of proteins and micronutrients, especially iron and zinc. Bean is a target for biofortification to develop new cultivars with high Fe/Zn levels that help to ameliorate malnutrition mainly in developing countries. A strong negative phenotypic correlation between Fe/Zn concentration and yield is usually reported, posing a significant challenge for breeders. The objective of this study was to investigate the genetic relationship between Fe/Zn. We used Quantitative Trait Loci (QTLs) mapping and Genome-Wide Association Studies (GWAS) analysis in three bi-parental populations that included biofortified parents, identifying genomic regions associated with yield and micromineral accumulation. Significant negative correlations were observed between agronomic traits (pod harvest index, PHI; pod number, PdN; seed number, SdN; 100 seed weight, 100SdW; and seed per pod, Sd/Pd) and micronutrient concentration traits (SdFe and SdZn), especially between pod harvest index (PHI) and SdFe and SdZn. PHI presented a higher correlation with SdN than PdN. Seventy-nine QTLs were identified for the three populations: 14 for SdFe, 12 for SdZn, 13 for PHI, 11 for SdN, 14 for PdN, 6 for 100SdW, and 9 for Sd/Pd. Twenty-three hotspot regions were identified in which several QTLs were co-located, of which 13 hotpots displayed QTL of opposite effect for yield components and Fe/Zn accumulation. In contrast, eight QTLs for SdFe and six QTLs for SdZn were observed that segregated independently of QTL of yield components. The selection of these QTLs will enable enhanced levels of Fe/Zn and will not affect the yield performance of new cultivars focused on biofortification.

Core Ideas Inter–gene pool introgressions illustrate multiple admixture events and the breeding history of beans. A catalog of 40 million genomic variants is available for research on bean genetics. Genome‐wide variability is a valuable tool for molecular marker development. Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and is a major nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to P. vulgaris, Phaseolus acutifolius (A. Gray), and Phaseolus coccineus L. were sequenced by whole‐genome sequencing, identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between P. vulgaris and the two other domesticated Phaseolus species, but also within P. vulgaris, affecting hundreds of protein‐coding genomic regions. A large number of inter–gene pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed single nucleotide polymorphism markers within previously discovered quantitative trait loci for common bacterial blight and angular leaf spot provides improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.

Angular leaf spot (ALS) is one of the most devastating diseases of common bean ( Phaseolus vulgaris L.) and causes serious yield losses worldwide. ALS resistance is reportedly pathotype-specific, but little is known about the efficacy of resistance loci against different pathotypes. Here, we report on ALS resistance evaluations of 316 bean lines under greenhouse and field conditions at multiple sites in Colombia and Uganda. Surprisingly, genome-wide association studies revealed only two of the five previously described resistance loci to be significantly associated with ALS resistance. Phg-2 on chromosome eight was crucial for ALS resistance in all trials, while the resistance locus Phg-4 on chromosome 4 was effective against one particular pathotype. Further dissection of Phg-2 uncovered an unprecedented diversity of functional haplotypes for a resistance locus in common bean. DNA sequence-based clustering identified eleven haplotype groups at Phg-2 . One haplotype group conferred broad-spectrum ALS resistance, six showed pathotype-specific effects, and the remaining seven did not exhibit clear resistance patterns. Our research highlights the importance of ALS pathotype-specificity for durable resistance management strategies in common bean. Molecular markers co-segregating with resistance loci and haplotypes will increase breeding efficiency for ALS resistance and allow to react faster to future changes in pathogen pressure and composition.

Common bean ( Phaseolus vulgaris L.) is an important legume crop worldwide and is a major nutrient source in the tropics. Common bean reproductive development is strongly affected by heat stress, particularly overnight temperatures above 20°C. The desert Tepary bean ( Phaseolus acutifolius A. Gray) offers a promising source of adaptative genes due to its natural acclimation to arid conditions. Hybridization between both species is challenging, requiring in vitro embryo rescue and multiple backcrossing cycles to restore fertility. This labor-intensive process constrains developing mapping populations necessary for studying heat tolerance. Here we show the development of an interspecific mapping population using a novel technique based on a bridging genotype derived from P. vulgaris , P. Acutifolius and P. parvifolius named VAP1 and is compatible with both common and tepary bean. The population was based on two wild P. acutifolius accessions, repeatedly crossed with Mesoamerican elite common bush bean breeding lines. The population was genotyped through genotyping-by-sequencing and evaluated for heat tolerance by genome-wide association studies. We found that the population harbored 59.8% introgressions from wild tepary, but also genetic regions from Phaseolus parvifolius , a relative represented in some early bridging crosses. We found 27 significative quantitative trait loci, nine located inside tepary introgressed segments exhibiting allelic effects that reduced seed weight, and increased the number of empty pods, seeds per pod, stem production and yield under high temperature conditions. Our results demonstrate that the bridging genotype VAP1 can intercross common bean with tepary bean and positively influence the physiology of derived interspecific lines, which displayed useful variance for heat tolerance.