AUTHOR=Nimmakayala Padma , Abburi Venkata L. , Saminathan Thangasamy , Almeida Aldo , Davenport Brittany , Davidson Joshua , Reddy C. V. Chandra Mohan , Hankins Gerald , Ebert Andreas , Choi Doil , Stommel John , Reddy Umesh K. 

TITLE=Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01646

DOI=10.3389/fpls.2016.01646

ISSN=1664-462X

ABSTRACT=<p>Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for <italic>Capsicum annuum</italic> and <italic>Capsicum baccatum</italic> 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 <italic>C. baccatum</italic>, indicating a population bottleneck during domestication of <italic>C. baccatum</italic>. In contrast, <italic>C. annuum</italic> 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 <italic>C. baccatum</italic>, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 <italic>C. baccatum</italic> accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (<italic>F</italic><sub><italic>ST</italic></sub>) between domesticated <italic>C. annuum</italic> and <italic>C. baccatum</italic> was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of <italic>C. baccatum</italic> var. <italic>pendulum</italic> 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 <italic>C. baccatum</italic> 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 <italic>C. baccatum</italic> peppers.</p>