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Research Project: Genomics and Genetic Improvement of Disease Resistance and Horticultural Characteristics of Watermelon, Broccoli, and Leafy Brassicas

Location: Vegetable Research

Title: Genome-wide diversity for worldwide watermelon collections: Analysis of population structure, haplotype networks, selective sweeps and LD decay to characterize domestication signals

Author
item REDDY, UMESH - West Virginia State University
item PATEL, TAKSHAY - North Carolina State University
item WEHNER, TODD - North Carolina State University
item NIMMAHAYALA, PADMA - West Virginia State University
item Kousik, Chandrasekar - Shaker
item Wechter, William - Pat
item Branham, Sandra
item Ling, Kai-Shu
item Jarret, Robert - Bob
item Levi, Amnon
item ORTIZ, CARLOS - West Virginia State University
item ABBIRO, VEMKATA ALSHMI - West Virginia State University
item BAO, KAN - Boyce Thompson Institute
item WANG, XIN - Boyce Thompson Institute
item RIVERA-BURGOS, LUIS - North Carolina State University
item FEI, ZGANGJUN - Boyce Thompson Institute

Submitted to: Cucurbitaceae Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 7/18/2018
Publication Date: 11/12/2018
Citation: Reddy, U., Patel, T., Wehner, T., Nimmahayala, P., Kousik, C.S., Wechter, W.P., Branham, S., Ling, K., Jarret, R.L., Levi, A., Ortiz, C., Abbiro, V., Bao, K., Wang, X., Rivera-Burgos, L., Fei, Z. 2018. Genome-wide diversity for worldwide watermelon collections: Analysis of population structure, haplotype networks, selective sweeps and LD decay to characterize domestication signals. Cucurbitaceae Proceedings. http://cucurbit2018.ucdavis.edu/wp-content/uploads/2018/10/2018_Cucurbits_Abstracts_Book.pdf (Abstracts Book, Page #87).

Interpretive Summary:

Technical Abstract: Genotyping by sequencing (GBS) technology was employed to differentiate among 1259 watermelon (C. lanatus) and egusi (C. mucasospermus) accessions. Among these accessions, 1052 United States Plant Introductions (PIs) maintained at the USDA, ARS, Plant Genetic Resources Conservation Unit, Griffin, Georgia (https://npgsweb.ars-grin.gov/gringlobal/site.aspx?id=22) were sampled to represent the geographical diversity of these taxa. The GBS analysis produced 64,205 SNPs. A minor allele frequency cutoff of >0.01 and a call rate of >70% retained 17,558 SNPs for use in genetic diversity and population structure analyses. Neighbor joining analysis produced a phylogenetic tree that resolved all genotypes into distinct clusters. Population structure analysis confirmed the clustering patterns produced by the neighbor joining and the principal component (PCA) analyses. A core collection containing 384 accessions was identified and selected. Tajima’s D windows for various chromosomes were used to identify selective sweeps. Linkage disequilibrium (LD) decay was estimated across chromosomes and haplotypes were deduced for various LD blocks and selective sweeps. Haplotype networks were generated for various LD blocks characterized across chromosomes. These networks are analogous to genealogical histories and will be useful in efforts to resolve reticulation histories for the materials analyzed.