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

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

机构地区：[1]Engineering Research Center of Coal-Based Ecological Carbon Sequestration Technology of the Ministry of Education and Key Laboratory of National Forest and Grass Administration for the Application of Graphene in Forestry,Shanxi Datong University,Datong,Shanxi 037009,China [2]College of Horticulture,Shanxi Agricultural University,Taigu,Shanxi 030801,China [3]Rice Research Institute&Guangdong Key Laboratory of New Technology in Rice Breeding,Guangdong Academy of Agricultural Sciences,Guangzhou,Guangdong 510640,China [4]CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture,Wuhan Botanical Garden,Chinese Academy of Sciences,Wuhan,Hubei 430074,China [5]College of Biology and Oceanography,Weifang University,Weifang,Shandong 261061,China [6]Integrative Omics and Molecular Modeling Laboratory,Department of Bioinformatics and Biotechnology,Government College University Faisalabad(GCUF),Faisalabad 38000,Pakistan [7]State Key Laboratory of Plant Physiology and Biochemistry,College of Life Sciences,Zhejiang University,Hangzhou,Zhejiang 310058,China [8]College of Forestry,Shanxi Agricultural University,Taigu,Shanxi 030801,China [9]Pomology Institute,Shanxi Agricultural University,Taigu,Shanxi 030801,China [10]School of Life Sciences,Shanxi Datong University,Datong,Shanxi 037009,China [11]Centre for Crop&Food Innovation,State Agricultural Biotechnology Centre,Food Futures Institute,Murdoch University,Western Australia,Perth 6000,Australia

出　　处：《Horticultural Plant Journal》2024年第6期1274-1290,共17页园艺学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant No.32102364);the General Program of Shandong Natural Science Foundation(Grant No.ZR2022MC064);the Shanxi Province Postdoctoral Research Activity Fund(Grant No.K462101001);the Doctoral Research Initiation Fund of Shanxi Datong University(Grant No.2023-B-15);the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.2023CYJSTX07);the Shanxi Province Excellent Doctoral Work Award Project(Grant No.606-02010609)。

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 21224 gene PAVs(Presence-absence variation)and 1158812 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 overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

关 键 词：PEAR Phased diploid genome Pangenome PAV Fruit quality 

分 类 号：S661.2[农业科学—果树学]