An Integrated Peach Genome Structural Variation Map Uncovers Genes Associated with Fruit Traits
Recently, Prof. Wang Lirong’s team from Zhengzhou Fruit Research Institute (ZFRI) has published their new findings in peach genome structure variation in the journal of Genome Biology. 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.
In this study, the researchers presented an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs were selected during peach domestication and improvement, affecting a total of 2,268 genes. Genome-wide association studies of 26 agronomic traits using these SVs were conducted and a number of candidate causal variants were identified. A 9 bp insertion in Prupe.4G186800, which encodes a NAC transcription factor, was shown to be associated with early fruit maturity, and a 487 bp deletion in the promoter of PpMYB10.1 was found to be associated with flesh color around the stone. In addition, a 1.67 Mb inversion was highly associated with fruit shape, and a gene adjacent to the inversion breakpoint, PpOFP1, regulated flat shape formation.
This study is the fourth important achievement of the “1000 Peach Genome Project” after their findings in 2014, 2016 and 2019. The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.
This study was supported by the grants from the National Natural Science Foundation of China (31972392), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2020-ZFRI-01), National Horticulture Germplasm Resources Center.
Link of research paper in Genome Biology:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02169-y
Identification and functional characterization of the candidate fruit shape gene
By Guojian (ytguojian@163.com)
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