Phenotypic Diversity for Seed Mineral Concentration in North American Dry Bean Germplasm of Middle American Ancestry

Dry bean (Phaseolus vulgaris L.) seeds are a major protein, carbohydrate, and mineral source in the human diet of peoples in multiple regions of the world. Seed mineral biofortification is an ongoing objective to improve this important food source. The objective of this research was to assess the seed mineral concentration of five macroelements and eight microelements in a large panel (n = 277) of modern race Durango and race Mesoamerica genotypes to determine if variability existed that could be exploited for targeted seed biofortification. Varieties that derive from these races are found in many diets throughout the world. The panel was grown in replicated trials under typical production conditions in the major bean growing regions of the United States, and a subset of the panel was also grown in replicated trials at three locations under control and terminal drought conditions. Except for K, seed mineral concentrations were higher for race Mesoamerica genotypes. Significantly higher seed concentrations for the majority of the minerals were observed for white-seeded genotypes and race Durango genotypes with the now preferred indeterminate, upright growth habit. Modern genotypes (since 1997) had equal or increased mineral concentrations compared with older genotypes. Drought affected mineral content differentially, having no effect on the microelement content but increased Co, Fe, and Ni concentrations. The correlation of Ca and Mn concentrations suggests that these elements may share seed deposition mechanisms. The high heritability for seed mineral concentration implies that breeding progress can be achieved by parental selection from this panel

Genome wide association studies and QTL mapping in chickpeas for resistance to Ascochyta Blight and Pythium Ultimum

Ascochyta blight, caused by Ascochyta rabiei, is globally the most destructive disease of chickpea. Chickpeas also suffer from emerging diseases, including seed rot and damping-off caused by Pythium ultimum. The objectives of this study were to detect molecular markers associated with resistance in chickpea to these two diseases. Plant materials included 177 chickpea recombinant inbred lines derived from an interspecific cross [C. reticulatum (PI 599072) x C. arietinum (FLIP 84-92C)] and 209 chickpea accessions representing an ICRISAT ‘mini-core’ collection. Disease screenings were conducted in a growth chamber (Pythium) or greenhouse (Ascochyta) in repeated experiments. A linkage map was developed for the C. reticulatum x C. arietinum population that included 1032 single nucleotide polymorphisms (SNPs) across eight linkage groups covering 965cM. Recombinant inbred lines were evaluated for reaction to seed rot and pre-emergence damping-off caused by metalaxyl resistant P. ultimum. A single significant QTL was detected on LG4 by composite interval mapping that explained 41.8 % of total phenotypic variation for disease reaction. Conversely, a genome wide association study (GWAS) approach was used to detect markers associated with resistance in the ICRISAT mini-core collection to Pythium seed rot and Ascochyta blight. A total of 302,902 single nucleotide polymorphisms (SNPs) equally distributed across the chickpea genome were examined with ADMIXTURE to determine population structure. Genomic regions were evaluated separately to establish marker-trait associations by employing FarmCPU and multiple loci mixed linear models (MMLM). For Pythium disease resistance, a total of 15 significant SNPs were detected and three candidate genes identified. One candidate gene and a total of 10 and 18 significant SNPs were detected for resistance to A. rabiei pathotype 1 (AR19) and pathotype 2 (AR628), respectively. SNPs and candidate genes identified in this study can be used for marker-assisted selection to develop superior chickpea varieties with improved disease resistance

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Common bean (Phaseolus vulgaris 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 \u3e150,000 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