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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 of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

Author
item Wu, Shan - Boyce Thompson Institute
item Wang, Xin - Boyce Thompson Institute
item Reddy, Umesh - West Virginia State University
item Sun, Honghe - Boyce Thompson Institute
item Bao, Kan - Boyce Thompson Institute
item Patel, Takshay - North Carolina State University
item Oritz, Carlos - West Virginia State University
item Abburi, Lakshmi - West Virginia State University
item Nimmakayala, Padma - West Virginia State University
item Branham, Sandra
item Wechter, William - Pat
item Massey, Laura
item Ling, Kai-shu
item Kousik, Chandrasekar - Shaker
item Hammar, Sue - Michigan State University
item Tadmor, Yaakov - Israel Agricultural Research Organization (ARO)
item Portnoy, Vitaly - Israel Agricultural Research Organization (ARO)
item Gur, Amit - Israel Agricultural Research Organization (ARO)
item Katzir, Nurit - Israel Agricultural Research Organization (ARO)
item Guner, Nihat - Sakata Seed America, Inc
item Davis, Angela - Sakata Seed America, Inc
item Hernandez, Alvaro - University Of Illinois
item Wright, Chris - University Of Illinois
item Mcgregor, Cecilia - University Of Georgia
item Jarret, Robert - Bob
item Xu, Yong - National Engineering Center For Vegetables
item Zhang, Xingping - Syngenta
item Wehner, Todd - North Carolina State University
item Grumet, Rebecca - Michigan State University
item Levi, Amnon
item Fei, Zhangjun - Boyce Thompson Institute

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/19/2019
Publication Date: 4/25/2019
Citation: Wu, S., Wang, X., Reddy, U., Sun, H., Bao, K., Patel, T., Oritz, C., Abburi, L., Nimmakayala, P., Branham, S., Wechter, W.P., Massey, L.M., Ling, K., Kousik, C.S., Hammar, S.A., Tadmor, Y., Portnoy, V., Gur, A., Katzir, N., Guner, N., Davis, A., Hernandez, A.G., Wright, C.L., Mcgregor, C., Jarret, R.L., Xu, Y., Zhang, X., Wehner, T.C., Grumet, R., Levi, A., Fei, Z. 2019. Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. Plant Biotechnology J., 10.1111/pbi.13136.
DOI: https://doi.org/10.1111/pbi.13136

Interpretive Summary: Watermelon is an important vegetable fruit crop in the USA and throughout the world. Years of selection for desirable fruit quality traits has narrowed the genetic base in modern watermelon cultivars and diminished their ability to combat a wide range of diseases and pests. In this study, ARS scientists collaborated with scientists at several universities on developing a high-quality genome sequence of the principle American watermelon cultivar ‘Charleston Gray’. In addition, the genomes of 1,365 watermelon plant introduction (PI) lines collected throughout the world and maintained by the USDA, National Plant Germplasm System (NPGS) were sequenced. The genomic analyses here elucidated the genetic diversity among watermelon PIs and facilitated the identification of gene loci associated with important fruit quality and disease resistance traits. The genome sequencing data in this study provide a valuable resource for genetic research and discovery of genes and for breeding and improvement of watermelon.

Technical Abstract: Watermelon (Citrullus lanatus) is a popular vegetable fruit crop. Years of selection for desirable fruit quality traits has resulted in a narrow genetic base in modern dessert watermelon cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here we report a high-quality genome sequence of watermelon cultivar ‘Charleston Gray’, a principal American dessert watermelon that has been used in numerous breeding programs to develop improved cultivars. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’, an East Asian watermelon cultivar, revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1,365 watermelon plant introduction (PI) lines maintained at the United States National Plant Germplasm System using genotyping-by-sequencing (GBS). These PI lines are collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25,000 high-quality single-nucleotide polymorphism (SNP) markers were derived from the GBS data using the high-quality ‘Charleston Gray’ genome as the reference. Comprehensive population genomic analyses using these SNP markers have allowed assessment of genetic diversity within different species and geographic groups, and provided insights into their phylogenetic relationships and the domestication and distribution history of watermelons. The SNP markers also enabled identification of genomic regions associated with important fruit quality traits and disease resistances through genome-wide association studies (GWAS). The high-quality ‘Charleston Gray’ genome and genotyping data of this large collection of watermelon accessions provide a valuable resource for facilitating watermelon research, breeding and improvement.