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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #354794

Research Project: Genetics and Breeding of Lettuce, Spinach, Melon, and Related Species to Improve Production and Consumer-related Traits

Location: Crop Improvement and Protection Research

Title: Exploring genetic diversity in the U.S. national melon collection

item Ando, Kaori
item WANG, XIN - Cornell University
item REDDY, UMESH - West Virginia State University
item FEI, ZHANGJUN - Cornell University
item McCreight, James - Jim

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 10/11/2018
Publication Date: 11/12/2018
Citation: Ando, K., Wang, X., Reddy, U., Fei, Z., McCreight, J.D. 2018. Exploring genetic diversity in the U.S. national melon collection. Cucurbitaceae 2018, November 12-15, 2018, Davis, California.

Interpretive Summary:

Technical Abstract: It is essential to maintain, as well as to incorporate genetic diversity into breeding programs for the improvement of quality, nutrients, yield, and biotic and abiotic stress tolerances. The U.S. National Plant Germplasm System (NPGS) maintains more than 2K Cucumis melo L. accessions from >70 countries. The NPGS melon collection has a paucity of systematically collected phenotypic data, and few of them have been classified to the horticultural Group level. These accessions and additional heirloom cultivars not in the NPGS collection were genotyped by the Genotyping by Sequence (GBS) method to understand the genetic diversity, population structure, and phylogenetic relationships within the U.S. melon collection. Over 27K single nucleotide polymorphism (SNP) markers with missing rate less than 0.5 and minimum allele frequency greater than 0.01 were obtained. Eleven sub-populations were identified via population structure analysis. We then developed a core panel subset (n=384) based on genome-wide SNPs, origin and known phenotypic properties, which captured 98.96% of the allelic diversity of the base population. The core panel was evaluated in a non-replicated field test in Imperial Valley, CA for 10 phenotypic traits (leaf shape, sex expression, and fruit traits including exocarp, flesh and cavity color, shape, weight, and soluble solids). Each member of the core panel was classified for horticultural Group based on phenotypic data, and we examined the relationship between genotypic data and horticultural Group classification. The core panel data were subjected to genome-wide association study in order to identify marker-trait associations for the key phenotypic traits. Overall, characterization of the genetic diversity and structure of the entire U.S. melon collection based on the high-density SNP markers derived from GBS and establishment of a melon core panel provide a valuable resource for melon genetic improvement.