title: High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon.
abstract: 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.
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000 ureddy@wvstateu.edu.
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
authors.affiliation: U.S. Vegetable Laboratory, USDA-ARS, 2875 Savannah Highway, Charleston, South Carolina 29414.
authors.forename: Amnon
authors.initials: A
authors.lastname: Levi
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Venkata Lakshmi
authors.initials: VL
authors.lastname: Abburi
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Yan R
authors.initials: YR
authors.lastname: Tomason
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Gopinath
authors.initials: G
authors.lastname: Vajja
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Rishi
authors.initials: R
authors.lastname: Reddy
authors.affiliation: Gus R. Douglass Institute, Department of Biology, West Virginia State University, Institute, West Virginia 25112-1000.
authors.forename: Lavanya
authors.initials: L
authors.lastname: Abburi
authors.affiliation: Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina 27695-7609.
authors.forename: Todd C
authors.initials: TC
authors.lastname: Wehner
authors.affiliation: Institute of Evolution, Haifa University, Haifa 31905, Israel.
authors.forename: Yefim
authors.initials: Y
authors.lastname: Ronin
authors.affiliation: Institute of Evolution, Haifa University, Haifa 31905, Israel.
authors.forename: Abraham
authors.initials: A
authors.lastname: Karol
mesh_terms: D029773:Citrullus / Q000235:genetics*; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D012641:Selection, Genetic
keywords: genome-wide recombination rate; genotyping by sequencing; high-density genetic map; linkage disequilibrium; selective sweep; watermelon