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Title: A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery

Author
item LAMBEL, S - Hm-Clause
item LANINI, B - Hm-Clause
item VIVODA, E - Hm-Clause
item FAUVE, J - Hm-Clause
item Wechter, William - Pat
item Harris-Shultz, Karen
item Massey, Laura
item Levi, Amnon

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2014
Publication Date: 8/8/2014
Citation: Lambel, S., Lanini, B., Vivoda, E., Fauve, J., Wechter, W.P., Harris-Shultz, K.R., Massey, L.M., Levi, A. 2014. A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery. Theoretical and Applied Genetics. 127:2105-2115.

Interpretive Summary: Watermelon is an important vegetable crop in the United States and throughout the world. Fusarium wilt is the major soil borne disease of watermelon, causing serious damage and great losses to the growers of this important specialty crop. There is a continuous need to develop watermelon cultivars resistant to this disease. However, there is limited knowledge on genetic improvement strategies that could be used to enhance disease resistance in this important crop. In this study, USDA scientists collaborated with scientists and plant breeders at a private seed company in using next generation sequencing technology to identify gene sequences that might confer resistance to Fusarium wilt. In these cooperative studies, the researchers identified several gene sequences closely associated with resistance to Fusarium wilt expressed in certain watermelon stocks. The DNA markers and knowledge gained in this study should be useful for researchers and plant breeders interested in developing breeding methods aimed at improving disease resistance in watermelon cultivars.

Technical Abstract: Fusarium wilt is a major soil-borne disease of watermelon caused by the fungus Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F. Sm.) W.C. Snyder & H.N. Hans (Fon). In this study, a genetic population of 186 F3 families (24 plants in each family) exhibited continuous distribution for Fon race 1 response. Using a “selective genotyping” approach, DNA was isolated from 91 F2 plants whose F3 progeny exhibited the highest resistance (30 F2 plants) versus highest susceptibility (32 F2 plants), or moderate resistance to Fon race 1 (29 F2 plants). Genotyping-by-sequencing (GBS) technology was used on these 91 selected F2 samples to produce 266 single nucleotide polymorphism (SNP) markers, representing the 11 chromosomes of watermelon. A major QTL associated with resistance to Fon race 1 was identified with a peak LOD of 33.31 and 1-LOD confidence interval from 2.3 - 8.4 cM on chromosome 1 of the watermelon genetic map. This QTL was designated “Chr1.1 Fon1” and is positioned in a genomic region where several disease-resistance candidate genes, known as pathogenesis-related (PR) proteins, including a glucan endo-1, 3-beta-glucosidase and two acidic class III chitinase genes were identified. Additional independent, but minor QTLs were identified on chromosome 1 (LOD 4.16), chromosome 3 (LOD 4.36), chromosome 4 (LOD 4.52), chromosome 9 (LOD 6.8), and chromosome 10 (LOD 5.03 and 4.26). The results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers used in breeding programs of watermelon.