Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study

Hea-Young Lee; Na-Young Ro; Abhinandan Patil; Joung-Ho Lee; Jin-Kyung Kwon; Byoung-Cheorl Kang

doi:10.3389/fpls.2020.01100

Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study

Front Plant Sci. 2020 Jul 23:11:1100. doi: 10.3389/fpls.2020.01100. eCollection 2020.

Authors

Hea-Young Lee¹, Na-Young Ro², Abhinandan Patil¹, Joung-Ho Lee¹, Jin-Kyung Kwon¹, Byoung-Cheorl Kang¹

Affiliations

¹ Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.
² National Academy of Agricultural Science, National Agrobiodiversity Center, Rural Development Administration, Jeonju, South Korea.

Abstract

All modern pepper accessions are products of the domestication of wild Capsicum species. However, due to the limited availability of genome-wide association study (GWAS) data and selection signatures for various traits, domestication-related genes have not been identified in pepper. Here, to address this problem, we obtained data for major fruit-related domestication traits (fruit length, width, weight, pericarp thickness, and fruit position) using a highly diverse panel of 351 pepper accessions representing the worldwide Capsicum germplasm. Using a genotype-by-sequencing (GBS) method, we developed 187,966 genome-wide high-quality SNP markers across 230 C. annuum accessions. Linkage disequilibrium (LD) analysis revealed that the average length of the LD blocks was 149 kb. Using GWAS, we identified 111 genes that were linked to 64 significant LD blocks. We cross-validated the GWAS results using 17 fruit-related QTLs and identified 16 causal genes thought to be associated with fruit morphology-related domestication traits, with molecular functions such as cell division and expansion. The significant LD blocks and candidate genes identified in this study provide unique molecular footprints for deciphering the domestication history of Capsicum. Further functional validation of these candidate genes should accelerate the cloning of genes for major fruit-related traits in pepper.

Keywords: Capsicum; domestication; fruit-related traits; genome-wide association study; genotype-by-sequencing; linkage disequilibrium; quantitative trait locus.