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Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms
- Source :
- Frontiers in Plant Science, Vol 7 (2016), Frontiers in Plant Science
- Publication Year :
- 2016
- Publisher :
- Frontiers Media S.A., 2016.
-
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.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Linkage disequilibrium
genome-wide association mapping
Single-nucleotide polymorphism
Plant Science
Biology
lcsh:Plant culture
01 natural sciences
Fixation index
Nucleotide diversity
03 medical and health sciences
genotyping by sequencing
lcsh:SB1-1110
Capsicum baccatum
Original Research
2. Zero hunger
Genetics
Haplotype
food and beverages
population structure
biology.organism_classification
peduncle length
haplotyping
Minor allele frequency
030104 developmental biology
Chromosome 4
linkage disequilibrium
010606 plant biology & botany
Subjects
Details
- Language :
- English
- ISSN :
- 1664462X
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- Frontiers in Plant Science
- Accession number :
- edsair.doi.dedup.....c1ab0f50b96a3063b67a40e2f18705f1
- Full Text :
- https://doi.org/10.3389/fpls.2016.01646