Background: Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS. Results: Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color. Conclusions: GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.

Background: A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species. Results: A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes. Conclusions: Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89–6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.

White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods were used in the GWAS. Response to this fungus showed a continuous distribution, and 28 lines were identified as potential resistance sources, including lines of Andean and Mesoamerican origin, as well as intermediate lines between the two gene pools. Twenty-two significant associations were identified, which were organized into 15 quantitative trait intervals (QTIs) located on chromosomes Pv01, Pv02, Pv03, Pv04, Pv08, and Pv09. Seven of these QTIs were identified for the first time, whereas eight corresponded to chromosome regions previously identified in the WM resistance. In all, 468 genes were annotated in these regions, 61 of which were proposed potential candidate genes for WM resistance, based on their function related to the three main defense stages on the host: recognition (22), signal transduction (8), and defense response (31). Results obtained from this work will contribute to a better understanding of the complex quantitative resistance to WM in common bean and reveal information of significance for future breeding programs.

Snap beans are a group of bean cultivars grown for their edible immature pods. The objective of this work was to characterize the diversity of pod phenotypes in a snap bean panel (SBP), comprising 311 lines collected in Europe, and establish a core set (Core-SBP) with the maximum diversity of pod phenotypes. Phenotyping of the SBP was carried out over two seasons based on 14 quantitative pod dimension traits along with three qualitative traits: pod color, seed coat color, and growth habit. Phenotypes were grouped into 54 classes using a hierarchical method, and a Core-SBP with one line per phenotype class was established. A further field-based evaluation of the Core-SBP revealed higher diversity index values than those obtained for the SBP. The Core-SBP was also genotyped using 24 breeder-friendly DNA markers tagging 21 genomic regions previously associated with pod trait control. Significant marker-trait associations were found for 11 of the 21 analyzed regions as well as the locus fin. The established Core-SBP was a first attempt to classify snap bean cultivars based on pod morphology and constituted a valuable source of characteristics for future breeding programs and genetic analysis.