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Title: Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon

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

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2014
Publication Date: 11/8/2014
Citation: Reddy, U., Abburi, L., Abburi, V., Reddy, R., Saminathan, T., Tomasson, Y., Wehner, T., Levi, A., Wehner, T., Nimmakayala, P. 2014. Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon. Journal of Heredity. 106:166-176.

Interpretive Summary: There is a need to evaluate watermelon varieties collected in different parts of the world and identify valuable gene sequences useful for enhancing watermelon fruit quality. In this study, an USDA, ARS scientist collaborated with a team of scientists at West Virginia State University and North Carolina State University using advanced genomic sequencing technologies to evaluate gene sequences of watermelon varieties collected in different parts of the world. The scientists identified several gene sequences that may affect watermelon fruit quality, including watermelon fruit size, length, width, and rind thickness. The genetic information produced in this study should be useful for seed companies, plant breeders, university scientists, and students interested in elucidating the genome of watermelon and in improving watermelon fruit quality and nutritional content.

Technical Abstract: Watermelon (Citrullus lanatus var. lanatus) contains 88% water, sugars, and several important health-related compounds, including lycopene, citrulline, arginine, and glutathione. The current genetic diversity study uses microsatellites with known map positions to identify genomic regions that underwent selection during watermelon domestication or improvement. It also estimates genome level population structure and linkage disequilbrium (LD) across the linkage groups and perform association mapping for fruit traits of watermelon. Twenty-four regions that underwent selection sweep were scanned for the presence of 11 candidate genes by using the watermelon genome browser. We localized selection sweep in the intergenic regions, very close to the 3‘ untranslated region (UTR) or promoter, or exons and introns of various genes. The main genes were the ripening-related protein, basic helix-loop-helix protein, CYCLIN D1 and cytochrome p450 that involve in protein binding, nucleic acid and ion-binding, transcriptional regulation, and catalytic activities. A total 15 blocks of various sizes were identified across nine chromosomes. Four simple sequence repeat (SSR) markers were linked to fruit length, width and rind thickness through association mapping. Our search for location of the linked markers in the watermelon whole-genome sequence draft revealed that the microsatellite marker BVWS00358, a GA repeat microsatellite, is the GAGA factor located in the 5‘ UTR of C2H2 Zinc finger protein–structure and insertion element (Cla004026), a zinc ion binding motif, whose biological process is chitin response or transcription regulation. In addition, BVWS01708, an ATT repeat type, was located in the promoter of the DTW domain-containing protein (Cla002761).