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ARS Home » Northeast Area » Geneva, New York » Plant Genetic Resources Unit (PGRU) » Research » Publications at this Location » Publication #352066

Research Project: Management of Genetic Resources and Associated Information for Selected Vegetable Crops

Location: Plant Genetic Resources Unit (PGRU)

Title: Characterization of the USDA germplasm collections for watermelon, melon, cucumber and squash using genotyping-by-sequencing

Author
item FEI, ZHANGJUN - Boyce Thompson Institute
item Ando, Kaori
item BAO, KAN - Boyce Thompson Institute
item Labate, Joanne
item Levi, Amnon
item MAZOUREK, MICHAEL - Cornell University - New York
item McCreight, James - Jim
item PATEL, TAKSHAY - North Carolina State University
item RAMIREZ MADERA, AXEL - University Of Wisconsin
item REDDY, UMESH - West Virginia State University
item REEVES, PAIGE - Cornell University - New York
item WANG, XIN - Boyce Thompson Institute
item WEHNER, TODD - North Carolina State University
item Weng, Yiqun
item WU, SHAN - Boyce Thompson Institute
item GRUMET, REBECCA - Michigan State University

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2018
Publication Date: 7/30/2018
Citation: Fei, Z., Ando, K., Bao, K., Labate, J.A., Levi, A., Mazourek, M., Mccreight, J.D., Patel, T., Ramirez Madera, A., Reddy, U., Reeves, P., Wang, X., Wehner, T., Weng, Y., Wu, S., Grumet, R. 2018. Characterization of the USDA germplasm collections for watermelon, melon, cucumber and squash using genotyping-by-sequencing. American Society of Horticulture Science Meeting. 1.

Interpretive Summary:

Technical Abstract: Germplasm collections are a critically valuable source of genetic diversity for plant breeding efforts. Our ability to make optimal use of such resources for crop improvement is facilitated by genetic characterization. Therefore, one of the objectives of the CucCAP project, “CucCAP: Leveraging applied genomics to improve disease resistance in cucurbit crops”, is to characterize genetic diversity within the U.S. cucurbit plant introduction (PI) collections and develop sequence-informed functional panels for genetic and phenotypic analyses. To this end, we have performed genotyping-by-sequencing (GBS) analysis of the USDA PI collections of the four major cucurbit crops: watermelon (Citrullus lanatus), melon (Cucumis melo), cucumber (Cucumis sativus), and squash (Cucurbita pepo and C. moschata). A total of 1,234 cucumber, 2,077 melon, 1,365 watermelon, 850 C. pepo and 314 C. moschata accessions were genotyped. A total of 1.57, 1.71 and 0.88 billion GBS reads were obtained for cucumber, melon and watermelon, respectively. From these reads, 76.9, 54.2 and 34.6 million unique tags were obtained, of which 593,678, 743,545 and 388,298 tags with at least 10 reads were used for SNP calling for cucumber, melon and watermelon, respectively. A total of 114,338, 89,377 and 62,258 SNPs were called in cucumber, melon and watermelon, respectively, and 23,828, 27,846 and 25,930 SNPs were obtained by applying criteria of missing data rate < 0.5 and minor allele frequency (MAF) > 0.01. The SNPs were well distributed across the genomes with average density of one SNP per 10.6, 14.6, and 15.7 kb for cucumber, melon and watermelon, respectively. Using these SNP data, we have performed population structure and principal component analysis (PCA), and constructed a neighbor-joining trees to infer phylogenetic relationships among the accessions. These analyses are being used to establish functional panels of 300-400 accessions per crop representing ~99% of the genetic diversity along with key disease resistance, fruit quality, horticultural and agronomic traits.