NEW YORK (GenomeWeb News) – In a paper appearing online today in PLoS ONE, researchers from China and the US reported that they have come up with an integrated genetic and cytogenetic map of cucumber.
Researchers from the Chinese Academy of Agricultural Sciences, the China Agricultural University, and the US Department of Agriculture's Agricultural Research Service used whole genome shotgun sequencing to come up with nearly 1,000 polymorphic simple sequence repeat markers in cucumber. Using these markers, along with cytogenetic data, they then created a high-density linkage map that's expected to form the foundation for future genetic and genomic studies in cucumbers and related plants.
"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," senior author Sanwen Huang, a researcher at the Chinese Academy of Agricultural Sciences' Institute of Vegetables and Flowers, and his co-authors wrote.
Cucumbers belong to the family Cucurbitaceae, which contains about 800 species. Among them: other commercially important plants such as melon, watermelon, squash, and pumpkin.
Previous research suggests the cucumber genome — which is an estimated 367 million bases in size — is contained on seven different chromosomes. Although low density genetic linkage maps have been developed for cucumber over the years, Huang and his team noted that genetic resources are few and far between in the cucumber family.
To create a high-density linkage map of the cucumber genome, the researchers started by using whole genome Sanger shotgun sequencing to get about three times coverage of the cucumber genome. Based on their sequencing effort, the researchers selected 995 simple sequence repeat, or SSR, markers belonging to seven different linkage groups.
The team subsequently integrated data from these polymorphic SSR markers with results from fluorescence in situ hybridization to assign these linkage groups to seven cucumber chromosomes. They also identified 678 recombination breakpoints in the cucumber genome.
Using FISH, the team detected an inversion on chromosome 5 that differed between the cultivated cucumber variety C. sativus var. sativus and the C. sativus var. hardwickii variety, which is believed to represent the feral form of cucumber.
The researchers also detected roughly three times as many polymorphisms as expected between the North American strain Gy14 and the PI 183967, a C. sativus var. hardwickii strain from India.
"This result demonstrated the power of whole genome sequences in enhancing genetic analysis of an under-investigated crop with a narrow genetic base," the authors wrote. "In turn, the saturated genetic map will help anchor DNA sequence assemblies onto chromosomes to generate a map-based genome sequence of cucumber."
When the researchers compared SSR markers in eleven inbred cucumber lines and two lines each of melon, watermelon, and squash, they found that about 65 percent of the markers were polymorphic in the cucumber lines, suggesting they may by useful for following desirable cucumber traits and perhaps guiding crop improvement.
The researchers suggested that the newly identified SSR markers may also prove beneficial in other crops as well. Nearly half of the cucumber SSR markers — 49 percent — appear to be conserved in melon. About 26 percent of the 995 cucumber SSRs were conserved in watermelon and 22 percent were conserved in pumpkin.