ARS | Publication request: An Integrated Genetic and Cytogenetic Map of the Cucumber Genome

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 15, 2009
Publication Date: June 15, 2009
Citation: Ren, Y., Zhang, Z., Staub, J.E., Cheng, Z., Li, X., Lu, J., Miao, H., Kang, H., Xie, B., Gu, X. 2009. An Integrated Genetic and Cytogenetic Map of the Cucumber Genome. Genome PloSONE 4:6:e5795 (www.plosone.org).

Interpretive Summary: Cucumber is an important vegetable crop species worldwide. It has been studied to improve its horticultural performance and through plant breeding has resulted in many different marker types. Certain genetic tools related to the evolving field of biotechnology (use of new and novel technologies which incorporate DNA) can be important to plant improvement. Plant improvement can be enhanced by biotechnology by allowing for superior plants to be identified more rapidly with reduced cost inputs (i.e., expensive and extended field testing of plants in the early generations of plant improvement). One biotechnology involves the extraction of DNA from plant cells and characterizing the differences among DNA of different plants to locate their position on chromosomes (i.e., DNA is the substance of genes which are found on chromosomes which are resident in every cell). Once their position on chromosomes is found, information on their position can be used by geneticists and plant breeders to improve plants more rapidly. The location of the genes of cucumber has progressed relatively slowly because of the biology of the crop species. A biotechnology was used to design a study which would allow for the identification of a vast array of genes on cucumber chromosomes. The number of genes identified on the cucumber chromosomes was three times that previously known. The identification of such genes will allow commercial and private plant breeders to use this DNA biotechnology more effectively for plant improvement. This is important for the grower since new and novel cucumber varieties will be available to them more rapidly, thus increasig their global competitiveness.

Technical Abstract: The Cucurbitaceae includes important crops as cucumber, melon, watermelon, and squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originating from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs, spans ~580 cM with a mean marker interval of 0.58 cM, defines ~680 recombination breakpoints, and consists of seven linkage groups. These linkage groups were then correspondingly assigned to the seven chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed that chromosomal inversion occurs between two Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering in the map. Three quarters of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber, and 49%, 28% and 25% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits.