Abstract
Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9–2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.
Highlights
Chile peppers (Capsicum spp.) are represented by at least 32 species, of which Capsicum annuum, Capsicum baccatum L. var. pendulum (Willd.) Eshbaugh, Capsicum chinense Jacq., Capsicum frutescens L., and Capsicum pubescens Ruiz & Pavon represent domesticated taxa (Heiser and Smith, 1953; Eshbaugh, 1980; Pickersgill, 1991; Bosland and Votava, 1999; Chiou and Hastorf, 2014)
A total of 77,407 single nucleotide polymorphisms (SNPs) were isolated from the nucleotide sequence obtained for the 283 C. baccatum and 94 C. annuum accessions studied; a total of 8661, 8086, 9843, 6197, 5688, 7410, 5588, 5086, 4472, 5336, 5079, and 5961 SNPs were mapped to the whole genome sequence (WGS) draft and located on chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, respectively
The flow of the river Rio Mizque from the south to join the Amazon is through lowland tropical Bolivia and the Amazon Basin and includes both the range of the C. baccatum group and a portion of the range of the C. annuum group (Eshbaugh, 1980)
Summary
Chile peppers (Capsicum spp.) are represented by at least 32 species, of which Capsicum annuum, Capsicum baccatum L. var. pendulum (Willd.) Eshbaugh, Capsicum chinense Jacq., Capsicum frutescens L., and Capsicum pubescens Ruiz & Pavon represent domesticated taxa (Heiser and Smith, 1953; Eshbaugh, 1980; Pickersgill, 1991; Bosland and Votava, 1999; Chiou and Hastorf, 2014). Chile peppers (Capsicum spp.) are represented by at least 32 species, of which Capsicum annuum, Capsicum baccatum L. var. Pendulum (Willd.) Eshbaugh, Capsicum chinense Jacq., Capsicum frutescens L., and Capsicum pubescens Ruiz & Pavon represent domesticated taxa (Heiser and Smith, 1953; Eshbaugh, 1980; Pickersgill, 1991; Bosland and Votava, 1999; Chiou and Hastorf, 2014). C. baccatum, with yellow spotted white flowers, is thought to have domesticated in lowland Bolivia or coastal Peru, whereas entirely white-flowered C. annuum was domesticated in Mexico (Eshbaugh, 1980; Andrews, 1984; Pickersgill, 1997; AguilarMeléndez et al, 2009b; Chiou and Hastorf, 2014). Because C. annuum and C. baccatum are sexually incompatible, the question cannot be resolved by crossing these genetically isolated domesticated peppers. The use of C. baccatum and C. annuum species in interspecific breeding programs has been limited because of post-fertilization barriers
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