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 breakinduced 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.

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

“…Using a read-depth approach, 1059 CNVs (minimum length 1 kb) were identified across all lines, impacting ;500 protein coding genes (<2%) and 2.2 Mb (;1.6%) of the assembled genome. In a recent study including a panel of 115 cucumber accessions, fewer structural variants were discovered than in Arabidopsis (Zhang et al, 2015). A similar analysis of 50 rice accessions, including 10 wild species, detected 1327 gene loss events (2.4%) and 865 gene-associated duplications (Xu et al, 2012).…”

Cataloging Plant Genome Structural Variations

“…CNV is defined as unbalanced changes in the genome structure and cover deletions (which is the same as copy number of zero) as well as duplications of > 50 bp in size (Girirajan et al, 2011). Based on the data from the genomic hybridization (CGH) array and NGS technologies, a couple of plant CNVs (Table 11.1) were identified at genome-wide level (DeBolt, 2010;Swanson-Wagner et al, 2010;Zheng et al, 2011;Muñoz-Amatriaín et al, 2013;Ping Yu et al, 2013;Boocock et al, 2015;Zhang et al, 2015;Zhou et al, 2015;Bai et al, 2016;Cardone et al, 2016;Hardigan et al, 2016).…”

“…Comparison between the gynoecious and monoecious cucumber genomes led to the discovery of a 30.2-kb duplicated segment that was significantly associated with gynoecy. This particular CNV event is the underlying genetic cause for the variation at the Female locus that has led to the development of gynoecy in cucumber (Zhang et al, 2015).…”

“…(Zhang et al, 2015). (B) Boron-toxicity symptoms in leaf blades of boron-intolerant (Clipper) and boron-tolerant (Sahara) barley plants.…”

“…(E) Rice grain length diversity is associated with copy number variations in GL7 locus . Images were based on the respective studies (Sutton et al, 2007;Shomura et al, 2008;Uchiyama et al, 2013;Wang et al, 2015;Zhang et al, 2015), and reproduced with permission.…”