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Location: Vegetable Research

Title: A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome

item Ren, Y
item Zhao, H
item Kou, Q
item Guo, S
item Zhang, H
item Hou, W
item Zou, X
item Sun, H
item Gong, G
item Levi, Amnon
item Xu, Y

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2011
Publication Date: 1/11/2012
Citation: Ren, Y., Zhao, H., Kou, Q., Guo, S., Zhang, H., Hou, W., Zou, X., Sun, H., Gong, G., Levi, A., Xu, Y. 2012. A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome. PLoS One. 2012. 7:e29453.

Interpretive Summary: Watermelon is an important crop in the United States and throughout the world. Due to many years of selection for specific, desirable horticultural qualities, today watermelon cultivars are genetically similar and susceptible to a large number of diseases and pests. The watermelon industry, including seed companies and growers, expend great efforts to develop high quality seedless watermelon cultivars with enhanced resistance to diseases and pests. However, there is limited information about the genetics of watermelon and about genes that may confer resistance to diseases or pests in this important crop, and as a consequence, progress is slow. In this study, scientists at the USDA, ARS, U.S. Vegetable Laboratory (Charleston, SC), collaborated with a team of scientists in China on developing an extensive genetic linkage map for watermelon. These scientists were able to map a large number of gene sequences on this map. This genetic map will be a valuable tool for researchers and plant breeders focused on identifying the genes controlling valuable horticultural traits, including disease resistance or fruit quality characteristics, and in incorporating them into elite watermelon cultivars.

Technical Abstract: As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high-density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the Chinese elite line 97103 (C. lanatus var. lanatus) and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contain resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of 11 linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers representing the 234 scaffolds. These markers were also useful in orienting the position of 152 (228.3 Mb) of the 234 scaffolds on the linkage map. The map spans ~800 cM with a mean marker interval of 0.8 cM. Using a fluorescent in situ hybridization (FISH) technology, we have conducted a cytogenetic study to identify and depict the watermelon chromosomes that correspond to the 11 linkage groups constructed in this genetic mapping study. Of 86 single copy BAC clones that were aligned to corresponding scaffolds by paired-ends sequences, 11 unique-signal BAC clones were selected as FISH probes to assign the 11 linkage groups to corresponding pseudo-chromosomes. The high-density genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of gene sequences associated with disease resistance or watermelon fruit qualities.