CBGG

Genome-wide association studies (GWAS) are one of the foundations for modern molecular breeding for plant genetic improvement. Single-locus GWAS methodologies impose constraints in association mapping due to the complex nature of quantitative traits and the often-stringent thresholds used. Multi-locus models, therefore, serve as alternative approaches in identifying significant marker-trait associations. This study used six multi-locus models to determine quantitative trait loci (QTL) associated with yield and agronomic traits in a diverse population of chile pepper evaluated in New Mexico, USA. Using the GWAS models, eight genotyping-by-sequencing (GBS)-derived single nucleotide polymorphism (SNP) markers across six chromosomes were identified to be associated with multiple traits. Plant height shared similar genetic control with plant width, whereas total yield per plant had common QTL with yield components. Epigenetic mechanisms such as methylation and chromatin remodeling and organization were predicted for first pod date and flowering time. The diverse functions of candidate genes identified reflect the complex genomic architecture of the evaluated traits. Allele specific assays for the identified QTL will be developed and validated for marker-assisted selection and genome-wide selection towards the genetic improvement of chile pepper.

genome-wide association study; genotyping-by-sequencing; marker-assisted selection; quantitative trait loci; single nucleotide polymorphisms