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

Authors

Shan Wu, Boyce Thompson Institute for Plant Research
Xin Wang, Boyce Thompson Institute for Plant Research
Umesh Reddy, West Virginia State University
Honghe Sun, Boyce Thompson Institute for Plant Research
Kan Bao, Boyce Thompson Institute for Plant Research
Lei Gao, Boyce Thompson Institute for Plant Research
Linyong Mao, Boyce Thompson Institute for Plant Research
Takshay Patel, NC State University
Carlos Ortiz, West Virginia State University
Venkata L. Abburi, West Virginia State University
Padma Nimmakayala, West Virginia State University
Sandra Branham, U.S. Department of Agriculture-Agricultural Research Service
Pat Wechter, U.S. Department of Agriculture-Agricultural Research Service
Laura Massey, U.S. Department of Agriculture-Agricultural Research Service
Kai Shu Ling, U.S. Department of Agriculture-Agricultural Research Service
Chandrasekar Kousik, U.S. Department of Agriculture-Agricultural Research Service
Sue A. Hammar, Michigan State University
Yaakov Tadmor, Agricultural Research Organization of Israel
Vitaly Portnoy, Agricultural Research Organization of Israel
Amit Gur, Agricultural Research Organization of Israel
Nurit Katzir, Agricultural Research Organization of Israel
Nihat Guner, Sakata Seed America, Inc.
Angela Davis, Sakata Seed America, Inc.
Alvaro G. Hernandez, University of Illinois Urbana-Champaign
Chris L. Wright, University of Illinois Urbana-Champaign
Cecilia McGregor, College of Agricultural and Environmental Sciences Athens Campus
Robert Jarret, USDA Agricultural Research Service
Xingping Zhang, Syngenta Beijing Innovation Center
Yong Xu, National Engineering Research Center for Vegetables, Beijing
Todd C. Wehner, NC State University
Rebecca Grumet, Michigan State University
Amnon Levi, U.S. Department of Agriculture-Agricultural Research Service
Zhangjun Fei, Boyce Thompson Institute for Plant Research

Document Type

Article

Publication Date

12-1-2019

Abstract

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern 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, to complement the existing reference genome from ‘97103’, an East Asian cultivar. Comparative analyses between genomes of ‘Charleston Gray’ and ‘97103’ revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping-by-sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high-quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the ‘Charleston Gray’ genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome-wide association studies. The high-quality ‘Charleston Gray’ genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.

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