Genetic diversity and population structure of cucumber (Cucumis sativus L.)

Authors: LU, J - Chinese Academy Of Agricultural Sciences; QI, J - Chinese Academy Of Agricultural Sciences; SHI, Q - Chinese Academy Of Agricultural Sciences; SHEN, D - Chinese Academy Of Agricultural Sciences; ZHANG, S - Chinese Academy Of Agricultural Sciences; SHAO, G - Chinese Academy Of Agricultural Sciences; LI, H - Renmin University Of China; SUN, Z - East-West Seed International, Ltd; Weng, Yiqun; SHANG, Y - Chinese Academy Of Agricultural Sciences; VAN TREUREN, R - Wageningen University; VAN DOOIJEWEERT, W - Wageningen University; ZHANG, Z - Chinese Academy Of Agricultural Sciences; HUANG, S - Chinese Academy Of Agricultural Sciences

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/6/2012
Publication Date: 10/12/2012
Citation: Lu, J., Qi, J.J., Shi, Q.X., Shen, D., Zhang, S.P., Shao, G.I., Li, H., Sun, Z.Y., Weng, Y., Shang, Y., Van Treuren, R., Van Dooijeweert, W., Zhang, Z.H., Huang, S.W. 2012. Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS One. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0046919.

Interpretive Summary: Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.

Technical Abstract: Understanding genetic variation in germplasm collection is essential for the conservation and their efficient use in plant breeding. Cucumber is an important vegetable crop worldwide. Previous studies revealed a low genetic diversity in cucumber, but detailed insights into the crop’s genetic structure and diversity are largely missing. In this study, we fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna of Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.