Genome-Wide Association Study of the Resilience to High Temperature of Faba Bean (Vicia faba L.) Germplasm

Abstract

Our research on enhancement of faba bean (Vicia faba L.) has the objectives of increasing resilience to temperature extremes and improving nutritional quality. We conduct traditional field/greenhouse experiments and adopt contemporary genomics approaches in our independent and collaborative research projects at the Western Regional Plant Introduction Station (WRPIS), one of the four regional plant introduction stations in the US Department of Agriculture-ARS National Plant Germplasm System (NPGS) with the mission of acquiring, documenting, maintaining, characterizing, evaluating and distributing plant genetic resources to the global research community to improve agricultural productivity for food security. In collaboration with the International Center for Agricultural Research in the Dry Areas, Terbol, Lebanon and supported by a grant from the CGIAR-U.S. University Linkages Program, we collected data for eight agronomic traits on a Generation Challenge Program (GCP) reference set of 140 faba bean accessions grown under high temperature at different locations in Lebanon and USA. We also genotyped the reference set with the genotyping by sequencing (GBS) technique which produced approximately 4 million reads per genotype on an Illumina HiSeq 2500 Sequencer. The single nucleotide polymorphism (SNP) marker calling pipeline UNEAK (Universal Network Enabled Analysis Kit) found 10,950 variant loci from the sequence data. After fileting SNPs with missing rate over 60% and minor allele frequency less than 5%, 2,632 SNPs were obtained for final analyses. The final dataset contained 131 accessions with SNP call rate above 70%. The missing SNPs were imputed by LinkImpute. Genome-Wide Association Study (GWAS) was performed using the program BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway). Four SNP markers were identified to be significantly associated with plant height (2 SNPs) and seed size (2SNPs). Upon further validation, these markers will be useful for marker-assisted selection to breed faba bean variety with increased resilience to high temperature.