Genome wide association studies correcting population stratification in pepper core collection

Abstract

Genome-wide association study (GWAS) is an effective approach for identifying genetic variants associated to useful agronomic traits. GWAS has emerged as a powerful approach for identifying genes underlying complex diseases or morphological traits at an unprecedented rate. In such studies, it is very important to correct for population stratification, which refers to allele frequency differences between cases and controls due to systematic ancestry differences. Population stratification can cause false positive findings if not adjusted properly. As we are performing GWAS for various agronomic traits in pepper, a genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>33,000 SNPs) for a 250 pepper core collection. Using GBS platform, high density haplotype map was constructed and various stratification methods, including distance based phylogenetic methods, principal component analysis (PCA), and bayesian phylogenetic methods (STRUCTURE) were performed to show the genetic diversity and population stratification. As a result, MLM using Q values combined with k-medoids clustering estimated from stratification methods were used to identify quantitative trait loci controlling the variation of ten agronomic traits. These results will help to understand associations between phenotype and genotype and also use for validate the candidate genes or quantitative trait loci previously identified in pepper.