Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation

文献类型： 外文期刊

第一作者： Ding, Baopeng

作者： Ding, Baopeng;Qiao, Jun;Zhao, Jianguo;Guo, Xuhu;Ding, Baopeng;Qiao, Jun;Zhao, Jianguo;Guo, Xuhu;Ding, Baopeng;Lin, Yujing;Song, Yuqin;Feng, Xinxin;Li, Liulin;Hu, Haifei;Hu, Haifei;Cao, Yunpeng;Xu, Ruirui;Muhammad, Tahir ul Qamar;He, Guangqi;Han, Youzhi;Guo, Huangping;Yang, Sheng;Guo, Xuhu;Varshney, Rajeev Kumar

作者机构：

关键词： Pear; Phased diploid genome; Pangenome; PAV; Fruit quality

期刊名称：HORTICULTURAL PLANT JOURNAL （ 影响因子：6.2； 五年影响因子：6.1 ）

ISSN： 2095-9885

年卷期： 2024 年 10 卷 6 期

页码：

收录情况： SCI

摘要： The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid 'Yuluxiang' pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm. Using the constructed pangenome, we identified 21 224 gene PAVs (Presence-absence variation) and 1 158 812 SNPs (Single Nucleotide Polymorphism) in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, PAV-based analysis provides additional insights into the pear population structure. In addition, some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in 'Xuehuali' which is vital for pear quality. PsbMGH3.1 may play a role in the IAA pathway, contributing to a distinct low-auxin phenotype observed in plants by heterologously over- expressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

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