High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon

作者：Reddy Umesh K^*; Nimmakayala Padma; Levi Amnon; Abburi Venkata Lakshmi; Saminathan Thangasamy; Tomason Yan R; Vajja Gopinath; Reddy Rishi; Abburi Lavanya; Wehner Todd C; Ronin Yefim; Karol Abraham

来源：Genes Genomes Genetics, 2014, 4(11): 2219-2230.

DOI：10.1534/g3.114.012815

• high-density genetic map
• genotyping by sequencing
• genome-wide recombination rate
• linkage disequilibrium
• selective sweep
• watermelon

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%26apos;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.

• 出版日期2014-11-1