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.
Highlights
Pepper (Capsicum species), like other Solanaceae family members including tomato and potato, is a New World genus with a primary center of diversity in Bolivia and Peru (Nee et al, 2006)
To confirm the genome-wide association study (GWAS) results, we examined QTLs for four major fruit-related domestication traits (FL, fruit width (FWd), fruit weight (FWg), fruit position (FP)) using 120 recombinant inbred lines (RILs) derived from a cross between C. annuum ‘Perennial’ and C. annuum ‘Dempsey’ (PDRIL); in these lines, 86 QTLs for 17 horticultural traits were previously mapped (Han et al, 2016)
GWAS is often used to explore the genetic basis of complex traits in field-grown and horticultural crops due to its efficient detection of many natural allelic variations underlying phenotypic diversity (Brachi et al, 2011)
Summary
Pepper (Capsicum species), like other Solanaceae family members including tomato and potato, is a New World genus with a primary center of diversity in Bolivia and Peru (Nee et al, 2006). Among Solanaceae species, domestication-related traits have been described for tomato (Bai and Lindhout, 2007; Giovannoni 2018), potato (Li et al, 2018), and eggplant (Doganlar et al, 2002; Meyer et al, 2012). These traits are generally referred to as “domestication syndrome” because they can be used to distinguish cultivated crops from their progenitors (Doebley et al, 2006).
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