Genetic diversity and population structure of cucumber (Cucumis sativus L.).
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.
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Sino-Dutch Joint Lab of Horticultural Genomics, Opening Lab of Genetic Improvement of Agricultural Crops of Ministry of Agriculture, Beijing, China.
Jing
J
Lv
Jianjian
J
Qi
Qiuxiang
Q
Shi
Di
D
Shen
Shengping
S
Zhang
Guangjin
G
Shao
Hang
H
Li
Zhanyong
Z
Sun
Yiqun
Y
Weng
Yi
Y
Shang
Xingfang
X
Gu
Xixiang
X
Li
Xiaoguo
X
Zhu
Jinzhe
J
Zhang
Robbert
R
van Treuren
Willem
W
van Dooijeweert
Zhonghua
Z
Zhang
Sanwen
S
Huang
D002681:China; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D018553:Cucumis sativus / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D005843:Geography; D007194:India; D018895:Microsatellite Repeats / Q000235:genetics*; D009426:Netherlands; D010802:Phylogeny; D011157:Population Dynamics; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014481:United States
D018744:DNA, Plant