Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation
文献类型： 外文期刊
作者： Ding, Baopeng 1 ; Hu, Haifei 4 ; Cao, Yunpeng 6 ; Xu, Ruirui 7 ; Lin, Yujing 3 ; Muhammad, Tahir ul Qamar 8 ; Song, Yuqin 3 ; He, Guangqi 9 ; Han, Youzhi 10 ; Guo, Huangping 11 ; Qiao, Jun 1 ; Zhao, Jianguo 1 ; Feng, Xinxin 3 ; Yang, Sheng 11 ; Guo, Xuhu 1 ; Varshney, Rajeev Kumar 13 ; Li, Liulin 3 ;
作者机构： 1.Shanxi Datong Univ, Engn Res Ctr Coal Based Ecol Carbon Sequestrat Te, Minist Educ, Datong 037009, Shanxi, Peoples R China
2.Shanxi Datong Univ, Key Lab Natl Forest Grass Adm Applicat Graphene F, Datong 037009, Shanxi, Peoples R China
3.Shanxi Agr Univ, Coll Hort, Taigu 030801, Shanxi, Peoples R China
4.Guangdong Acad Agr Sci, Rice Res Inst, Guangzhou 510640, Guangdong, Peoples R China
5.Guangdong Acad Agr Sci, Guangdong Key Lab New Technol Rice Breeding, Guangzhou 510640, Guangdong, Peoples R China
6.Chinese Acad Sci, CAS Key Lab Plant Germplasm Enhancement & Special, Wuhan Bot Garden, Wuhan 430074, Hubei, Peoples R China
7.Weifang Univ, Coll Biol & Oceanog, Weifang 261061, Shandong, Peoples R China
8.Govt Coll Univ Faisalabad GCUF, Dept Bioinformat & Biotechnol, Integrat Om & Mol Modeling Lab, Faisalabad 38000, Pakistan
9.Zhejiang Univ, Coll Life Sci, State Key Lab Plant Physiol & Biochem, Hangzhou 310058, Zhejiang, Peoples R China
10.Shanxi Agr Univ, Coll Forestry, Taigu 030801, Shanxi, Peoples R China
11.Shanxi Agr Univ, Pomol Inst, Taigu 030801, Shanxi, Peoples R China
12.Shanxi Datong Univ, Sch Life Sci, Datong 037009, Shanxi, Peoples R China
13.Murdoch Univ, Food Futures Inst, Ctr Crop & Food Innovat, State Agr Biotechnol Ctr, Perth, WA 6000, Australia
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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