Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments

Authors: OLADZAD, ATENA - North Dakota State University; Porch, Timothy - Tim; ROSAS, JUAN - Catie Tropical Agricultural Research; MOGHADDAM, SAMIRA MAFI - 22nd Century Group Inc; BEAVER, JAMES - University Of Puerto Rico; BEEBE, STEVE - Catie Tropical Agricultural Research; BURRIDGE, JIMMY - Pennsylvania State University; JOCHUA, CELESTINA - Michigan State University; MAGALHAES, AMADE - Mozambique Agronomic Research Institute; Miklas, Phillip - Phil; RATZ, BODO - International Center For Tropical Agriculture (CIAT); White, Jeffrey; LYNCH, JONATHAN - Pennsylvania State University; MCCLEAN, PHILLIP - North Dakota State University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2019
Publication Date: 6/6/2019
Citation: Oladzad, A., Porch, T.G., Rosas, J.C., Moghaddam, S., Beaver, J., Beebe, S.E., Burridge, J., Jochua, C.N., Magalhaes, A.M., Miklas, P.N., Ratz, B., White, J.W., Lynch, J., McClean, P.E. 2019. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3, Genes/Genomes/Genetics. 9(6):1881-1892. https://doi.org/10.1534/g3.119.400072.

Interpretive Summary: the genetic improvement of economically important production traits of dry bean 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 DNA sequence data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of DNA sequences identifying over 200k sequence variations, single nucleotide polymorphisms (SNP), for each gene pool against the most recent assembly of the common bean genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of common bean varieties appropriate for production in Central America and Africa, were assembled. Evolutionary, or phylogenetic, analyses demonstrated that the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Genetic studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments in Central America using the BASE panels. Multiple effect, or pleiotropic, genetic factors were discovered using a multiple trait mixed model analysis. SNPs within or near candidate genes known to be associated with responses to abiotic stresses were identified and can be used as genetic markers. Potential gene candidates were identified that are thought to be associated with stress response, such as hormone signaling, epigenetic regulation, and ROS detoxification, under abiotic stress conditions. Ashy stem blight disease resistance was mapped to a group of genes, a malectin/receptor kinase cluster, on chromosome Pv04. This new genetic understanding and novel molecular markers can potentially be employed to improve common bean response to heat and drought stress and thus provide crop resiliency to farmers.

Technical Abstract: 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 in Central America using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes known to be associated with responses to abiotic stresses were identified and can be used as genetic markers. The candidate genes were associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions. Macrophomina resistance was mapped to a malectin/receptor kinase cluster on Pv04.