title: A genome-wide scan of selective sweeps and association mapping of fruit traits using microsatellite markers in watermelon.
abstract: Our genetic diversity study uses microsatellites of known map position to estimate genome level population structure and linkage disequilibrium, and to identify genomic regions that have undergone selection during watermelon domestication and improvement. Thirty regions that showed evidence of selective sweep were scanned for the presence of candidate genes using the watermelon genome browser (www.icugi.org). We localized selective sweeps in intergenic regions, close to the promoters, and within the exons and introns of various genes. This study provided an evidence of convergent evolution for the presence of diverse ecotypes with special reference to American and European ecotypes. Our search for location of linked markers in the whole-genome draft sequence revealed that BVWS00358, a GA repeat microsatellite, is the GAGA type transcription factor located in the 5' untranslated regions of a structure and insertion element that expresses a Cys2His2 Zinc finger motif, with presumed biological processes related to chitin response and transcriptional regulation. In addition, BVWS01708, an ATT repeat microsatellite, located in the promoter of a DTW domain-containing protein (Cla002761); and 2 other simple sequence repeats that association mapping link to fruit length and rind thickness.
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Umesh K
authors.initials: UK
authors.lastname: Reddy
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Lavanya
authors.initials: L
authors.lastname: Abburi
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Venkata Lakshmi
authors.initials: VL
authors.lastname: Abburi
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Thangasamy
authors.initials: T
authors.lastname: Saminathan
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Robert
authors.initials: R
authors.lastname: Cantrell
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Venkata Gopinath
authors.initials: VG
authors.lastname: Vajja
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Rishi
authors.initials: R
authors.lastname: Reddy
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Yan R
authors.initials: YR
authors.lastname: Tomason
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Amnon
authors.initials: A
authors.lastname: Levi
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Todd C
authors.initials: TC
authors.lastname: Wehner
authors.affiliation: From the Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV 25112-1000 (Reddy, Abburi, Saminathan, Cantrell, Vajja, Reddy, Tomason, and Nimmakayala); the U.S. Vegetable Laboratory, USDA, ARS, 2875 Savannah Highway, Charleston, SC 29414 (Levi); and the Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609 (Wehner).
authors.forename: Padma
authors.initials: P
authors.lastname: Nimmakayala
mesh_terms: D005075:Biological Evolution; D002874:Chromosome Mapping; D029773:Citrullus / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D060146:Ecotype; D005638:Fruit / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D012641:Selection, Genetic
chemical_list: D018744:DNA, Plant
keywords: domestication; heterozygosity; linkage disequilibrium; population structure; recombination rate