Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat

Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm. Qualitative traits in buckwheat were greatly influenced by the altitudinal variations.A total of 34,978 evenly distributed single nucleotide polymorphisms across eight chromosomes in buckwheat were identified.A total of 71 significant quantitative trait loci revealed the genomic regions associated with major yield-attributing traits.The identified marker-trait associations have implications on improvement of economically important traits. Buckwheat is a nutrient dense pseudo cereal crop. Despite its obvious potential as a functional food, Buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, frost susceptibility. The inadequate availability of genomics resources in Buckwheat is one of the major reasons for it. In the present study, genome-wide association mapping (GWAS) was conducted to identify regions for various morphological and yield traits in buckwheat. 71 significant marker-trait associations (genomic regions) across eight chromosomes were identified in this study. These genomic regions will assist in tracking the desirable alleles of target genes within the Buckwheat breeding populations/germplasm for the improvement of economically important traits.