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Title: DNA Polymorphism Among American Watermelon Cultivars Based on DNA Methylation

item REDDY, U - West Virginia State University
item GIST, R - West Virginia State University
item VAJJA, G - West Virginia State University
item TOMASON, Y - West Virginia State University
item Levi, Amnon
item NIMMAKAYALA, P - West Virginia State University

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2010
Publication Date: 9/24/2010
Citation: Reddy, U.K., Gist, R.A., Vajja, G., Tomason, Y., Levi, A., Nimmakayala, P. 2010. DNA Polymorphism Among American Watermelon Cultivars Based on DNA Methylation. Euphtica. DOI 1007/s10681-010-0259-z.

Interpretive Summary: Watermelon is an important vegetable crop, grown in 44 states in the United States. USDA scientists found that although American watermelon cultivars are widely diverse in their fruit shape, size, color, and quality, they share a narrow genetic base. This narrow genetic base is a result of many years of cultivation and selection for varieties with desirable fruit qualities. As a result, the American watermelon cultivars are susceptible to a large number of diseases and pests, and there is a continuous need to improve them and make them more resistant to diseases and pests. In this study, USDA scientists have collaborated with scientists at West Virginia State University on conducting experiments aiming to elucidate the molecular events that control the genes affecting the quality of watermelon. The knowledge gained in this study should be useful for researchers and plant breeders interested in understanding and the genetic and biological mechanisms that produce the differences among watermelon cultivars, and in utilizing these mechanisms to improve watermelon quality suitable to consumer needs.

Technical Abstract: American watermelon heirlooms are diverse in their growth habits, fruit qualities and responses to biotic and abiotic stress. Wide ranging DNA marker tools resolved a narrow molecular diversity among these collections. The current research explored additional insights such as extent of diversity at the methylation level that can cause epigenetic changes among the watermelon cultivars. DNA profiles were generated using Methylation-Sensitive AFLP Assay (MSA) for 47 watermelon heirlooms. Results indicated that methylation specific diversity (43%) in US watermelon heirlooms is higher than the diversity (19.8%) as estimated by several investigators using conventional DNA markers. Tree topologies of Neighbor-Joining (NJ) phenograms and the clustering pattern of principal component analyses of combined and separate data sets obtained from the methylation specific isoschizomers MspI and HpaII indicated differences in DNA patterns associated with DNA methylation. Our study indicates that the epigenetic variations associated with DNA methylation maybe associated one of the mechanisms contributing to phenotypic variation among the American watermelon cultivars known to have a narrow genetic base.