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Title: High-resolution genetic map for understanding the effect of genome-wide recombination rate, selection sweep and linkage disequilibrium on nucleotide diversity in watermelon

Author
item REDDY, U - West Virginia State University
item NIMMAKAYALA, P - West Virginia State University
item Levi, Amnon
item ABBURI, V - West Virginia State University
item SAMINATHAN, T - West Virginia State University
item TOMASSON, Y - West Virginia State University
item VAJJA, V - West Virginia State University
item REDDY, R - West Virginia State University
item ABBURI, L - West Virginia State University
item WEHNER, T - North Carolina State University
item RONIN, Y - West Virginia State University

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/11/2014
Publication Date: 11/1/2014
Citation: Reddy, U., Nimmakayala, P., Levi, A., Abburi, V.L., Saminathan, T., Tomasson, Y., Vajja, V.G., Reddy, R., Abburi, L., Wehner, T., Ronin, Y. 2014. High-resolution genetic map for understanding the effect of genome-wide recombination rate, selection sweep and linkage disequilibrium on nucleotide diversity in watermelon. Genes, Genomes, Genetics. 4:2219-2230.

Interpretive Summary: There is limited knowledge about the genome of watermelon or about genes that played an important role in domesticating the sweet red dessert fruit. In this study, ARS scientists collaborated with scientists at West Virginia State University using advanced genomic sequencing technologies to compare gene sequences of feral versus domesticated watermelon varieties collected in Africa. The scientists identified several genomic regions that were selected during the many years of domestication and that may be associated with fruit sweetness and quality traits. The information obtained in this study should be useful for university scientists and students and for seed company breeders interested in studying the genome of watermelon and in improving watermelon nutritional content and fruit quality attributes.

Technical Abstract: Genotyping by sequencing (GBS) technology was used to identify a set of 9,933 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1,087 cM for watermelon. The genome-wide variation of recombination rate (GWRR) across the map was evaluated and a positive correlation between GWRR and genome-wide nucleotide diversity identified. Colinearity between the map and the genome-wide reference sequence for watermelon was studied, using genetic maps in whole resequencing studies of watermelon. Genome-wide genetic diversity, linkage disequilibrium (LD) and selective sweep for wild, semi-wild was evaluated for domesticated accessions of Citrullus lanatus var. lanatus to track domestication signals in cultivated watermelons. Principal component analysis combined with chromosome-wide phylogenetic study based on 1,563 SNPs obtained after LD pruning with minor allele frequency = 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, ancestry proportions that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. Linkage disequilibrium decay was estimated across the genetic and physical distances. These analyses revealed a strong selective sweep on chromosome 3, consisting important genes that may have a role in the domestication of sweet watermelon.