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Genetic resistance is the primary means for control of Bean golden yellow mosaic virus (BGYMV) in common bean (Phaseolus vulgaris L.). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving marker-assisted selection (MAS) for the recessive bgm-1 gene and identifying and developing MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations and genome-wide association study (GWAS) in a large breeding population and two diversity panels revealed a candidate gene for bgm-1 and three QTL BGY4.1, BGY7.1, and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene Phvul.003G027100 on chromosome Pv03 corresponded with the recessive bgm-1 resistance allele. The five bp deletion in exon 2 starting at 20 bp (Pv03: 2,601,582) is expected to cause a stop codon at codon 23 (Pv03: 2,601,625), disrupting further translation of the gene. A Tm-shift assay marker named PvNAC1 was developed to track bgm-1. PvNAC1 corresponded with bgm-1 across ∼1,000 lines which trace bgm-1 back to a single landrace “Garrapato” from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with bgm-1. BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with bgm-1. Tm-shift assay markers were generated for MAS of the QTL, but their effectiveness requires further validation.

Background White mold (WM) is a major disease in common bean ( Phaseolus vulgaris L.), and its complex quantitative genetic control has limited the development of WM resistant cultivars. WM2.2 is one of the nine meta-QTL that has a major effect on WM tolerance. This QTL explains up to 35% of the phenotypic variation and was previously mapped to a large interval on Pv02. Our objective was to narrow the interval of this QTL using QTL-based bulk segregant analysis.Results The phenotypic and genotypic data from two RIL populations (R31 and Z0726-9), which possess different genetic backgrounds for white mold resistance, were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing, and reads were aligned against the sequence of the resistance parent. The QTL physical intervals for each RIL population were mapped by fixed SNPs in 10kb-2kb sliding windows. WM2.2 QTL was split into two regions WM2.2a (3.54-4.56 Mbp; euchromatic) and WM 2.2b (12.19 to 26.41 Mbp; heterochromatic) in populations R31 and Z0726-9, respectively. For each QTL interval, the possible functional contribution of significant non-synonymous and synonymous polymorphisms was investigated. Gene models encoding for pentatricopeptide repeat, gibberellin 2-oxidase, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein and a EF-TU receptor are potential candidate genes associated with WM2.2b resistance and most likely trigger a physiological resistance response to WM.Conclusion QTL-based pooled sequencing analysis revealed that the large genomic region associated with WM2.2 meta QTL consists of two major QTL each associated with a different WM resistance function. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b region triggers physiological resistance.

Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin&ndash, Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.

Multi-environment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET datasets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for over 70 years in the United States and Canada, consisting of 20 to 50 entries each year at 10 to 20 locations. The CBDN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association (GWAS) using best linear unbiased predictions (BLUPs) derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2M SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. The first use of mash on an agricultural dataset discovered two genomic regions with pleiotropic effects on multiple phenotypes, likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that by applying multiple statistical genomic approaches on data mined from MET phenotypic data sets, significant genetic effects that define genomic regions associated with crop improvement can be discovered.

Common bean ( L.) is the most consumed edible grain legume worldwide and contains a wide range of nutrients for human health including dietary fiber. Diets high in beans are associated with lower rates of chronic diseases such as obesity and type 2 diabetes, and the content of dietary fibers varies among different market classes of dry bean. In this study, we evaluated the dietary fiber content in a Middle American diversity panel (MDP) of common bean and evaluated the genetic architecture of the various dietary fiber components. The dietary fiber components included insoluble and soluble dietary fibers as well as the antinutritional raffinose family of oligosaccharides (RFOs; raffinose, stachyose, and verbascose). All variables measured differed among market classes and entries. Colored bean seeds had higher levels of insoluble dietary fibers with the black market class showing also the highest raffinose and stachyose content. Cultivars and lines released since 1997 had higher insoluble dietary fibers and RFO content in race Durango. Higher levels of RFOs were also observed in cultivars with type II growth habit that was a recent breeding target in Durango race germplasm. Candidate genes for dietary fiber traits, especially homologs to two main genes in the RFO biosynthesis pathway, were identified. The knowledge of diversity of dietary fibers in the MDP accompanied with the identification of candidate genes could effectively improve dietary fiber components in common bean.

Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes.

Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

White mold, caused by the necrotrophic fungus (Lib.) de Bary, is a major disease of common bean ( L.). WM7.1 and WM8.3 are two quantitative trait loci (QTL) with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI) population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs) relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.

Genotyping by sequencing (GBS) is a technique to discover large numbers of single nucleotide polymorphisms (SNPs) within a sample pool. The standard version of the GBS method uses a pool of relatively large DNA fragments and is typically sequenced at low coverage (1×). This often results in mis-scoring of heterozygotes as homozygotes and a high rate (≥30 %) of missing data points. The purpose of this study was to improve the quality and the coverage of GBS data in common bean (Phaseolus vulgaris L.) in order to increase the number of SNPs available for genome-wide association studies (GWAS). An improved and Phaseolus-specific GBS method was developed, which utilizes an in silico digest of the bean genome to predict the best fragment density and length, a double digest with the restriction enzymes MseI and TaqαI, and size selection after library preparation to achieve a reduced fragment pool that can be sequenced at higher coverage. The study consisted of 25 diverse common bean genotypes belonging to the Mesoamerican gene pool and compared libraries using ApeKI fragments with MseI/TaqαI double-digest fragments. The new improved bean-specific GBS library provided a 3.8- to 12.5-fold increase in SNPs, based on a minimum coverage (3×, 5× and 8×). These results provide insight for future GBS library constructs, and how to achieve a higher SNP density for GWAS studies.

Genetic diversity data were collected from a large population of common bean (Phaseolus vulgaris L.) landraces representing the United States Department of Agriculture core collection. The data were based on microsatellite data from all linkage groups. A procedure was developed to determine if we collected sufficient marker data to adequately estimated pairwise diversity. The diversity data were used to define populations using distance and model-based approaches. Genetic differentiation and genetic isolation by distance data were collected. Diversity was also compared for markers linked and unlinked to domestication loci. Using a model-based approach, the landraces were divided into the traditional Middle American and Andean gene pools. Diversity was greater for the Middle American gene pool. Six Middle American and three Andean subpopulations were defined, and the Middle American subpopulations exhibited strong geographic identity. Unlike other studies, seed size varied considerably with subpopulations, and a number of the subpopulations contained landraces from multiple common bean races. All of the subpopulations were highly differentiated, with the Middle American subpopulations showing the greatest differentiation. Genetic isolation by distance was observed among the Middle American and Andean subpopulations but not among subpopulations within a gene pool. Within each gene pool, diversity was lower for markers linked to domestication loci.

Molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris, common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana, genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana. Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris. Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD

Inheritance of the strong greenish-yellow (SGY) seedcoat color in `Wagenaar' common bean (Phaseolus vulgaris L.) was investigated. Line 5-593 is a determinate, Florida dry bean breeding line (with small black seeds) used as the recurrent parent in the development of many genetic stocks, e.g., g b v BC3 5-593. Through crosses with genetic tester stocks, the seedcoat genotype of `Wagenaar' was confirmed to be C J g b vlae Rk. Three randomly amplified polymorphic DNA markers (OAP7850, OAP31400, and OU14950) that cosegregated with the G seedcoat color locus were developed from the F2 population derived from the cross g b v BC2 5-593 × G b v BC3 5-593. From the cross `Wagenaar' × g b v BC3 5-593, 80 F2 plants were classified into 54 non-SGY and 16 SGY seedcoat color plants. When the OAP7850 marker was applied to that population, linkage was not observed with the non-SGY and SGY phenotypes. Conversely, a molecular marker (OAP12400, that was developed from the F2 from the cross `Wagenaar' × g b v BC3 5-593) linked to the locus controlling the SGY phenotype segregated independently of the G locus. Therefore, SGY phenotype is not controlled by the G locus. An F3 progeny test of 76 F2 plants from the cross `Wagenaar' × g b v BC3 5-593 confirmed the hypothesis that a single recessive gene (for which we propose the symbol gy) controls the seedcoat color change from pale greenish yellow (PGY) to SGY. Through crosses with genetic tester stocks, the seedcoat genotype of `Enola' was determined to be C J g b vlae Rk. The test cross `Enola' × `Wagenaar' demonstrated that `Enola' also carries the gy gene. The relationship of `Enola' to the `Mayocoba' market class of common bean and to `Azufrado Peruano 87' is discussed.

Two common bean (Phaseolus vulgaris L.) genes, J (modifies seedcoat color and pattern) and L (modifies partly colored seedcoat pattern), were tested for allelism using genetic tester stocks. Those stocks have a common genetic background by backcrossing to the recurrent parent, Florida dry bean breeding line 5-593, that has black self-colored seeds and purple flowers due to the genotype T P [C r] Z J G B V Rk. Specifically, the L gene from `Thuringia' and the lers gene from `Early Wax' were tested for allelism with the j gene from various genetic tester stocks. L was found to be identical with j, but lers was a different allele at J. We propose the gene symbols J (formerly l), j (formerly L), and jers (formerly lers). The seedcoat genotype of `Thuringia' was found to be t P C z j g b vlae rkd. A new seedcoat pattern called reverse margo was found to be determined by the genotype T/t z/z j/jers in a P C G B V genetic background. A randomly amplified polymorphic DNA marker was developed for the j gene (formerly L) from `Thuringia' using bulk segregant analysis in an F2 population segregating for j vs. J in a t z genetic background, i.e., from the cross t z j × t z J in BC1 to 5-593. The linkage distance between marker OL4525 and j was determined to be 1.2 cM. In a population segregating for J and jers, the distance between the marker and jers was determined to be 4.7 cM. The utility of marker OL4525 is limited primarily to the Middle American gene pool.

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.

Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users., Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users.

Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation-migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (π(sil)=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (F(st)=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.

Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.

Determinacy is an agronomically important trait associated with the domestication in soybean ( Glycine max ). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas Glycine soja , the wild progenitor of soybean, is indeterminate. Indeterminate ( Dt1/Dt1 ) and determinate ( dt1/dt1 ) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that Dt1 is a homolog (designated as GmTfl1 ) of Arabidopsis terminal flower 1 ( TFL1 ), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype, but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis . However, the GmTfl1 homeolog, despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1 , appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.

Background Understanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species. Results Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points. Conclusion The collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.

Association mapping is an alternative to mapping in a biparental population. A key to successful association mapping is to avoid spurious associations by controlling for population structure. Confirming the marker/trait association in an independent population is necessary for the implementation of the marker in other genetic studies. Two independent soybean populations consisting of advanced breeding lines representing the diversity within maturity groups 00, 0, and I were screened in multi-site, replicated field trials to discover molecular markers associated with iron deficiency chlorosis (IDC), a major yield-limiting factor in soybean. Lines with extreme phenotypes were initially screened to identify simple sequence repeat (SSR) markers putatively associated with the IDC. Marker data collected from all lines were used to control for population structure and kinship relationships. Single factor analysis of variance (SFA) and mixed linear model (MLM) analyses were used to discover marker/trait associations. The MLM analyses, which include population structure, kinship or both factors, reduced the number of markers significantly associated with IDC by 50% compared with SFA. With the MLM approach, three markers were found to be associated with IDC in the first population. Two of these markers, Satt114 and Satt239, were also found to be associated with IDC in the second confirmation population. For both populations, those lines with the tolerance allele at both these two marker loci had significantly lower IDC scores than lines with one or no tolerant alleles.

Common bean (Phaseolus vulgaris L.) exhibits a wide variety of seed coat patterns and colors. From a historical perspective, extensive genetic analyses have identified specific genes that control seed coat pattern (T, Z, L, J, Bip, and Ana) and color (P, C, R, J, D, G, B, V, and Rk). Many of these genes exhibit epistatic interactions with other genes, interactions that define the many seed coat patterns and colors observed within the species. To better understand these complex interactions, we began a molecular marker discovery program that previously identified random amplified polymorphic DNA (RAPD) markers linked to many of these genes. We report here the discovery of RAPD markers linked to three additional genes-C, G, and V. These markers, and five RAPD markers we previously discovered linked to other seed coat pattern and color genes, were converted into easily scorable sequence tagged site (STS) markers. We next placed these markers onto a common molecular map shared by the Phaseolus research community and demonstrated a generally wide distribution of the genes throughout the common bean genome. A few previously unrecognized linkages were discovered. The probable existence of multiple genes controlling growth habit in common bean is discussed. Our approach demonstrates the usefulness and feasibility of marker discovery in one population followed by accurate mapping of that marker onto a core, community-wide map.