Genome-Wide Association Study for Seed Quality Traits in Chickpea
Chickpeas (Cicer arietinum L.) are an important source of nutrition for the world’s population. Global demand for high quality chickpeas is growing . Canadian chickpea production is expected to increase as a result. Breeding efforts for Canadian varieties are increasingly targeting seed quality. Seed protein and oil content are important, quantitatively inherited traits . To improve nutrition and functional quality of chickpeas an understanding of the genetic basis and underlying traits is crucial. Genome-wide association studies (GWAS) have been employed in breeding populations to aid marker assisted selection (MAS) and genomic selection (GS) applications . A panel of diverse chickpea accessions including materials developed at the Canadian breeding program were grown during the summers of 2016-18. The population was grown at two locations each year, with three replicates per location. The panel was phenotyped for total crude protein and oil content. Over 60K single nucleotide polymorphisms (SNP) derived from whole genome sequences were used to analyze genetic diversity and population structure of the accessions. After data quality screening 170 out of 184 accessions remained, consisting of 45 Desis and 125 Kabulis. Roughly 30 600 SNPs remained after filtering for quality and a 10% minor allele frequency (MAF). Population structure analysis revealed several distinct groups primarily divided by market class. Linkage disequilibrium decay was determined to be between 390 and 380 kilobases. There was a moderate negative correlation shared between the traits (r=-0.57) as well as a genotype by environment interaction. It was determined that year was a greater source of phenotypic variation than growing location. QTLs and candidate genes associated with total protein and oil content were identified through GWAS, with potential markers for both traits on the q arm of chromosome 5.
Chickpea, GWAS, Marker-assisted Selection, Genomic Selection
Soils and Crops Workshop