Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

Authors: NIMMAKAYALA, PADMA - West Virginia State University; ABBURI, VENKATA - West Virginia State University; SAMINATHAN, THANGASAMY - West Virginia State University; ALAPARTHI, SURESH - West Virginia State University; ALMEIDA, ALDO - West Virginia State University; DAVENPORT, BRITTANY - West Virginia State University; DAVIDSON, JOSHUA - West Virginia State University; VAJJA, GOPINATH - West Virginia State University; REDDY, CVCM - West Virginia State University; TOMASON, YAN - West Virginia State University; NADIMI, MARJAN - West Virginia State University; HANKINS, GERALD - West Virginia State University; CHOI, DOIL - Seoul National University; Stommel, John; REDDY, UMESH - West Virginia State University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/18/2016
Publication Date: 11/3/2016
Citation: Nimmakayala, P., Abburi, V.L., Saminathan, T., Alaparthi, S.B., Almeida, A., Davenport, B., Davidson, J., Vajja, G., Reddy, C., Tomason, Y., Nadimi, M., Hankins, G., Choi, D., Stommel, J.R., Reddy, U. 2016. Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms. Frontiers in Plant Science. 7:1646.

Interpretive Summary: Five domesticated species of pepper have been recognized. Domestication of these cultivated forms of the crop originated in ancestral groups from the native geographic range of peppers across Central America and South America. Migration of modern day forms of these species and changes in plant and fruit attributes that have occurred during domestication are based largely on physical measurements. We utilized molecular markers to examine the genome of these species and identify differences between cultivated and wild forms of the cultivated pepper Capsicum baccatum, also known as the Aji pepper, and compared our findings to those in Capsicum annuum, the species that includes the popular sweet bell and jalapeno peppers. Our results demonstrated that these two species underwent divergent domestication. Both species likely experienced a loss of diversity with increasing domestication, but Capsicum annum subsequently recovered from this loss of diversity likely via greater selection for diverse attributes and adaptation to diverse ecological niches. Our results revealed molecular markers associated with genes for fruit peduncle (stem) length, a trait associated with selection for larger fruit size during crop domestication. These research results will benefit other scientists studying crop domestication and also benefit researchers working to identify genes that can be used to improve the efficiency of developing improved pepper varieties.

Technical 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 show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide diversity (p) 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 p 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 of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 genome-wide SNPs significantly associated. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future genome-wide association study of economically important traits in C. baccatum peppers.