ARS | Publication request: Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 2, 2012
Publication Date: July 9, 2012
Citation: Weng, Y., Yang, L., Koo, D., Li, Y., Xuejiao, Z., Luan, F., Havey, M.J., Jiang, J. 2012. Chromosome rearrangements during domestication of cucumber as revealed from high-density genetic mapping and draft genome assembly . Plant Journal. 71:895-906.

Interpretive Summary: Cucumber, Cucumis sativus L., is an economically important crop and an ideal system for understanding several important biological processes in plants. Whole genome sequencing is providing exciting opportunities to understanding the chromosome evolution in cucurbits and domestication history of cucumber, which is the only taxa with 2n=2x=14 chromosomes in the genus Cucumis. In this study, a high-density genetic map was developed containing 735 microsatellite marker loci in seven linkage groups with a total map length of 707.8 cM, and near complete physical coverage of the entire cucumber genome as revealed from cytological evidence. This genetic map revealed mis-assemblies in next generation sequencing scaffold assemblies. Integration of genetic and physical maps produced a chromosome-level draft genome assembly for cucumber composed of 193 Mbp, or 53% of the 367 Mbp cucumber genome. These newly developed genetic and genomics resources were used to reveal chromosome differentiation between the wild (C. sativus.var. hardwickii) and cultivated (C. sativus var. sativus) cucumbers. Comparative fluorescence in situ hybridization analysis of pachytene chromosomes revealed significant differences between the two taxa in the amount and distribution of heterochromatin, as well as chromosomal rearrangements including five paracentric and one pericentric inversions. Comparison of marker colinearity in syntenic chromosome regions between cucumber and melon (C. melo, 2n = 2x = 24) suggested that at least three of the six inversions were specific to the cucumber linage. Results supported the subspecies status of these two cucumber taxa, and C. sativus var. hardwickii as the progenitor of cultivated cucumber.

Technical Abstract: Cucumber is an economically important vegetable crop, but available genetic and genomics resources for cucumber are limited that hinders progress in cucumber breeding. In this study, we made significant contributions to the cucumber research community by developing a high-density genetic map for cultivated cucumber which 735 molecular markers in seven linkage groups with 707.8cM map length. We used independent cytological analysis to prove that this genetic map has very good coverage of the whole cucumber genome. Using this high quality genetic map, we detected a number of assembly errors in two cucumber draft genomes. We integrated draft genome scaffolds with the genetic map and developed a high-quality chromosome-level cucumber draft genome assembly for cucumber line Gy14. This new assembly is composed of 193.3Mbp, or 53% of the 367Mbp cucumber genome. Using comparative fluorescence in situ hybridization, we revealed, for the first time, significant differentiations - including six large inversions - between the wild and cultivated cucumbers. Available data support the wild cucumber as a progenitor species from which cultivated cucumber was domesticated.