Construction Of High-density SSR Genetic Map Of Cucumber And Its Applications

The Cucurbitaceae includes important vergetable and fruity crops as cucumber, melon, watermelon, and pumpkin. It is the fourth important plant family following the Gramineae, Leguminosae, and Solanaceous crops. However, limited genetic and genomic resources are available for them. Cucumber has a narrow genetic base, which limited the development of polymorphic molecular markers and impeded the construction of genetic map as well as its applications. Here, we constructed a saturated genetic and cytogenetic map of the cucumber genome by using the whole genome shotgun sequence data from International Cucumber Genome Project, and this map showed the utility for Cucurbitaceae crops. The major results are listed as follows:⑴A total of 23,800 SSR loci were identified from 3×shot-gun sequencing, of which 13,157 were unique in the cucumber genome. We selected 1,940 SSRs with the longest repeat motifs for polymorphism screening between parental lines (GY 14,PI 183967). As a result, 68% (1322) showed polymorphism between GY 14 and PI 183967, it was higher than that of previously reported markers (20%-30%).⑵A high-density SSR genetic map containing 995 SSR markers in seven linkage groups was constructed. This map spans in total 573 cM, approximately one SSR marker each 0.68cM. Only four marker clusters were found on this map. By FISH it was found that the cluster on the short arm of chromosome 5 was caused by paracentric inversion between parents.⑶Using FISH technology, we anchored the linkage groups onto the corresponding seven chromosomes of cucumber, and confirmed the orders of markers on the genetic map.⑷To detect the utilities of newly developed 995 SSR markers in breeding, 11 inbred lines of cucumber were used for evaluating their potential in marker-assisted selection. As a result, approximately 65% (760) of 995 SSRs showed different alelles among the 11 lines, 53% of them showed 2-4 alelles. The PIC values ranged from 0.17 to 0.84, with an average value of 0.5. These indicate that the markers could likely be used for cucumber breeding.⑸Of the 995 markers, 487 (50%), 258 (26%) and 221 (22%) were conserved in melon, watermelon and pumpkin respectively, about 193 (40%), 120 (47%) and 121 (55%) showed polymorphism between two lines of the three crops separately.⑹A comparative genetic map between cucumber and melon was constructed using the markers of chromosome 3 in cucumber. A high level of collinearity between melon and cucumber could be observed. Interestingly, chromosome 3 of cucumber was divided into two individual linkage groups in melon, and recombination suppression of chromosome 3 in cucumber was revealed.This saturated SSR genetic map will play an important role in cucumber molecular breeding, gene cloning, physical mapping, QTL analysis and comparative genomics research in cucurbits.