title: Genome-Wide Divergence and Linkage Disequilibrium Analyses forCapsicum baccatumRevealed by Genome-Anchored Single Nucleotide Polymorphisms.
abstract: Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively forCapsicum annuumandCapsicum baccatumwas 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 cultivatedC. baccatum, indicating a population bottleneck during domestication ofC. baccatum. In contrast,C. annuumchromosomes 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. ForC. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283C. baccatumaccessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST) between domesticatedC. annuumandC. baccatumwas 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis ofC. baccatumvar.pendulumcultivars 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 domesticatedC. baccatumtypes, 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 inC. baccatumpeppers.
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Venkata L
authors.initials: VL
authors.lastname: Abburi
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Aldo
authors.initials: A
authors.lastname: Almeida
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Brittany
authors.initials: B
authors.lastname: Davenport
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Davidson
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: C V Chandra Mohan
authors.initials: CV
authors.lastname: Reddy
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Gerald
authors.initials: G
authors.lastname: Hankins
authors.affiliation: Genetic Resources and Seed Unit, Asian Vegetable Research and Development Center-The World Vegetable Center Tainan, Taiwan.
authors.forename: Andreas
authors.initials: A
authors.lastname: Ebert
authors.affiliation: Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University Seoul, South Korea.
authors.forename: Doil
authors.initials: D
authors.lastname: Choi
authors.affiliation: Genetic Improvement of Fruits and Vegetables Laboratory (United States Department of Agriculture, Agricultural Research Service) Beltsville, MD, USA.
authors.forename: John
authors.initials: J
authors.lastname: Stommel
authors.affiliation: Department of Biology, Gus R. Douglass Institute, West Virginia State University Institute, WV, USA.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
keywords: genome-wide association mapping; genotyping by sequencing; haplotyping; linkage disequilibrium; peduncle length; population structure