Pilot-scale genome-wide association mapping in diverse sorghum germplasms identified novel genetic loci linked to major agronomic, root and stomatal traits

Abstract

This genome-wide association studies (GWAS) used a subset of 96 diverse sorghum accessions, constructed from a large collection of 219 accessions for mining novel genetic loci linked to major agronomic and physiological traits including root. The subset yielded 43,452 high quality single nucleotide polymorphic (SNP) markers exhibiting high allelic diversity. Population stratification showed distinct separation between caudatum and durra races. Linkage disequilibrium (LD) decay was rapidly declining with increasing physical distance across all chromosomes. The initial 50% LD decay was ~ 5Kb and background level was within or below ~ 80Kb. Plant height and grain color identified significant SNPs co-localized with dwarfing dw2 locus and chalcone synthase, respectively, indicating the representativeness of the population and reliability of methods. AP2-like ethylene-responsive transcription factor and gibberellin receptor GID1L2 affecting single plant yield and biomass respectively were identified. The study detected novel genetic loci linked to drought avoidance traits viz., Leucine rich repeat family protein (root biomass and root architecture), AP2 domain containing protein (intrinsic water use efficiency) and serine/threonine protein kinase (abaxial stomatal complex total area). This study justified that the constructed subset of diverse sorghums can be used as a panel for mapping other key traits to accelerate molecular breeding in sorghum.