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Plant Cell. 2015 Jun;27(6):1595-604. doi: 10.1105/tpc.114.135848. Epub 2015 May 22.

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

Author information

1
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China.
2
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853.
3
Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
4
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
5
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Shandong Academy of Agricultural Sciences, Jinan 250100, China.
6
Shanghai Jiaotong University, Shanghai 200240, China.
7
Department of Computer Science, University of Hong Kong, Hong Kong 999077, China.
8
Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
9
Deparment of Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research Centre, 6700AA Wageningen, The Netherlands.
10
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853 USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853.
11
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing 100081, China Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China huangsanwen@caas.cn.

Abstract

Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.

PMID:
26002866
PMCID:
PMC4498199
DOI:
10.1105/tpc.114.135848
[Indexed for MEDLINE]
Free PMC Article

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