title: Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.
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.
authors.affiliation: 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.
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853.
authors.forename: Linyong
authors.initials: L
authors.lastname: Mao
authors.affiliation: Hunan Vegetable Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
authors.forename: Huiming
authors.initials: H
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Fengjiao
authors.initials: F
authors.lastname: Bu
authors.affiliation: 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.
authors.forename: Guangcun
authors.initials: G
authors.lastname: Li
authors.affiliation: 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.
authors.forename: Jinjing
authors.initials: J
authors.lastname: Sun
authors.affiliation: 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.
authors.forename: Shuai
authors.initials: S
authors.lastname: Li
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853.
authors.forename: Honghe
authors.initials: H
authors.lastname: Sun
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853.
authors.forename: Chen
authors.initials: C
authors.lastname: Jiao
authors.affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853.
authors.forename: Rachel
authors.initials: R
authors.lastname: Blakely
authors.affiliation: Shanghai Jiaotong University, Shanghai 200240, China.
authors.forename: Junsong
authors.initials: J
authors.lastname: Pan
authors.affiliation: Shanghai Jiaotong University, Shanghai 200240, China.
authors.forename: Run
authors.initials: R
authors.lastname: Cai
authors.affiliation: Department of Computer Science, University of Hong Kong, Hong Kong 999077, China.
authors.forename: Ruibang
authors.initials: R
authors.lastname: Luo
authors.affiliation: 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.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Deparment of Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research Centre, 6700AA Wageningen, The Netherlands.
authors.forename: Evert
authors.initials: E
authors.lastname: Jacobsen
authors.affiliation: 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.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: 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.
authors.forename: Sanwen
authors.identifier: http://orcid.org/0000-0002-8547-5309
authors.initials: S
authors.lastname: Huang
mesh_terms: D002874:Chromosome Mapping; D018553:Cucumis sativus / Q000033:anatomy & histology / Q000235:genetics*; D056915:DNA Copy Number Variations / Q000235:genetics*; D035264:Flowers / Q000033:anatomy & histology / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D055106:Genome-Wide Association Study; D010802:Phylogeny