Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments

The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs. Includes Corrigendu

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions

Phene Synergism between Root Hair Length and Basal Root Growth Angle for Phosphorus Acquisition

Shallow basal root growth angle (BRGA) increases phosphorus acquisition efficiency by enhancing topsoil foraging because in most soils, phosphorus is concentrated in the topsoil. Root hair length and density (RHL/D) increase phosphorus acquisition by expanding the soil volume subject to phosphorus depletion through diffusion. We hypothesized that shallow BRGA and large RHL/D are synergetic for phosphorus acquisition, meaning that their combined effect is greater than the sum of their individual effects. To evaluate this hypothesis, phosphorus acquisition in the field in Mozambique was compared among recombinant inbred lines of common bean (Phaseolus vulgaris) having four distinct root phenotypes: long root hairs and shallow basal roots, long root hairs and deep basal roots, short root hairs and shallow basal roots, and short root hairs and deep basal roots. The results revealed substantial synergism between BRGA and RHL/D. Compared with short-haired, deep-rooted phenotypes, long root hairs increased shoot biomass under phosphorus stress by 89%, while shallow roots increased shoot biomass by 58%. Genotypes with both long root hairs and shallow roots had 298% greater biomass accumulation than short-haired, deep-rooted phenotypes. Therefore, the utility of shallow basal roots and long root hairs for phosphorus acquisition in combination is twice as large as their additive effects. We conclude that the anatomical phene of long, dense root hairs and the architectural phene of shallower basal root growth are synergetic for phosphorus acquisition. Phene synergism may be common in plant biology and can have substantial importance for plant fitness, as shown here

Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments

The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs. Includes Corrigendu

Seedling root architecture and its relationship with seed yield across diverse environments in \u3ci\u3ePhaseolus vulgaris\u3c/i\u3e

Seedling root phenotypes may have important impacts on fitness and are more easily measured than mature root phenotypes. We phenotyped the roots of 577 genotypes of common bean (Phaseolus vulgaris), representing the bulk of the genetic diversity for recent cultivars and landraces in this species. Root architectural phenotypes of seedlings germinated for nine days were compared to root architectural phenotypes in the field as well as seed yield across 51 environments with an array of abiotic stresses including drought, nutrient deficiency, and heat, as well as non-stress conditions. We observed repeatability ranging from 0.52–0.57 for measures of root phenotypes in seedlings, significant variation in root phene states between gene pools and races, relationships between seedling and field phenotypes, and varying correlations between seedling root phenes and seed yield under a variety of environmental conditions. Seed yield was significantly related to seedling basal root number in 22% of environments, seedling adventitious root abundance in 35% of environments, and seedling taproot length in 12% of environments. Cluster analysis grouped genotypes by their aggregated seedling root phenotype, and variation in seed yield among these clusters under non-stress, drought, and low fertility conditions was observed. These results highlight the existence and influence of integrated root phenotypes for adaptation to edaphic stress, and suggest root phenes have value as breeding targets under real-world conditions