期刊
G3-GENES GENOMES GENETICS
卷 4, 期 11, 页码 2219-2230出版社
OXFORD UNIV PRESS INC
DOI: 10.1534/g3.114.012815
关键词
high-density genetic map; genotyping by sequencing; genome-wide recombination rate; linkage disequilibrium; selective sweep; watermelon
资金
- USDA-NIFA [2013-38821-21453]
- NSF-EPSCOR [1003907]
- Gus R. Douglass Institute
- NIH [P20RR016477]
- NIFA [2013-38821-21453, 577436] Funding Source: Federal RePORTER
- Office Of The Director
- Office of Integrative Activities [1003907] Funding Source: National Science Foundation
We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima's D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.
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