一个综合的桃基因组结构变异图谱揭示了与果实性状相关的基因。

An integrated peach genome structural variation map uncovers genes associated with fruit traits.

机构信息

Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.

College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan, China.

出版信息

Genome Biol. 2020 Oct 6;21(1):258. doi: 10.1186/s13059-020-02169-y.

BACKGROUND

Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.

RESULTS

Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of PpMYB10.1 is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulates flat shape formation.

CONCLUSIONS

The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

背景

基因组结构变异（SVs）与多种重要农艺物种的关键性状有关；然而，桃的 SV 图谱及其功能影响在很大程度上仍未得到探索。

结果

本研究从 336 个桃基因组中绘制了一张 202233 个 SV 的综合图谱。在桃的驯化和改良过程中，大量的 SV 被选择，共影响了 2268 个基因。利用这些 SVs 对 26 个农艺性状进行全基因组关联研究，确定了一些候选的因果变异。在 Prupe.4G186800 中发现了一个 9bp 的插入，该基因编码一个 NAC 转录因子，与果实早期成熟有关；在 PpMYB10.1 启动子中发现了一个 487bp 的缺失，与石部果肉颜色有关。此外，一个 1.67Mb 的倒位与果实形状高度相关，倒位断点附近的一个基因 PpOFP1 调节扁平形状的形成。