---
identifier: mixed.gwas.Oladzad_Porch_2019
taxid: 3885
scientific_name: Phaseolus vulgaris
scientific_name_abbrev: phavu
genotype: 
  - "Bean Abiotic Stress Evaluation (BASE) panels for genetic discovery in Phaseolus vulgaris, that included variation in high temperature and drought stress responses, were assembled using genotypes relevant to agriculture in Central America and Africa. BASE panels included the BASE_120 [genotypes from 93 Middle American (MA), 22 Andean, 4 Tepary bean pools], BASE_Meso [119 genotypes mostly from Race Mesoamerica], and BASE_Andean [124 Andean genotypes]."
synopsis: GWAS of production traits under heat and drought stress in Common bean, relative to the the G19833 assembly 2.
genotyping_platform: Andean_MidAmer_GBS
genotyping_method: Illumina HiSeq GBS
description: 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.
data_curators: Scott Kalberer, Steven Cannon
publication_doi: 10.1534/g3.119.400072
citation: "Oladzad A, Porch T, Rosas JC, Moghaddam SM, Beaver J, Beebe SE, Burridge J, Jochua CN, Miguel MA, Miklas PN, Raatz B, White JW, Lynch J, McClean PE. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3 (Bethesda). 2019 Jun 5;9(6):1881-1892. doi: 10.1534/g3.119.400072. Erratum in: G3 (Bethesda). 2020 Jun 1;10(6):2129. PMID: 31167806; PMCID: PMC6553540."
publication_title: Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments.
contributors: Oladzad A, Porch T, Rosas JC, Moghaddam SM, Beaver J, Beebe SE, Burridge J, Jochua CN, Miguel MA, Miklas PN, Raatz B, White JW, Lynch J, McClean PE.