Abstract
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.
Highlights
The pepper genus Capsicum originated in Bolivia and consists of 25 to 30 species; five are domesticated: C. annuum, C. baccatum, C. chinense, C. frutescens, and C. pubescens[1,2]
A total of 66,960 single nucleotide polymorphisms (SNPs) were identified from the reads obtained for the 94 diverse C. annuum accessions studied; 7678, 7751, 8201, 6285, 4724, 6087, 5230, 3873, 3826, 4279, 3768 and 5268 SNPs were mapped to the whole-genome sequence (WGS) draft (Kim et al.8) and located on chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 and 12, respectively
Principal component analysis (PCA), model based population structure and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions were in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome
Summary
The pepper genus Capsicum originated in Bolivia and consists of 25 to 30 species; five are domesticated: C. annuum, C. baccatum, C. chinense, C. frutescens, and C. pubescens[1,2]. Trade routes between Europe, Middle-East and Asia promoted additional introductions and reciprocal exchanges, so multiple introductions were rapidly cultivated in most tropical, Mediterranean and temperate regions of the world In these secondary diversification centers, thousands of landraces have been selected for 4 to 5 centuries by growers to fit new environments and local consumption habits and trade, which has resulted in wide phenotypic diversity of pepper cultivars[5,6,7]. Despite several QTL studies of pepper[15,16,17,18,19,20], the current study is unique in that it utilizes WGS drafts for anchoring SNPs and systematic GWAS pipelines to identify SNP markers for various fruit-related traits with special reference to capsaicinoid content and fruit weight (FW) It aims to identify genome-wide effects on capsaicinoid content and fruit weight (FW) in C. annuum populations by using SNPs identified by GBS
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