Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits  

作　　者：Qionghou Li Xin Qiao Lanqing Li Chao Gu Hao Yin Kaijie Qi Zhihua Xie Sheng Yang Qifeng Zhao Zewen Wang Yuhang Yang Jiahui Pan Hongxiang Li Jie Wang Chao Wang Loren H.Rieseberg Shaoling Zhang Shutian Tao 

机构地区：[1]National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization,Sanya Institute of Nanjing Agricultural University,College of Horticulture,Nanjing Agricultural University,Nanjing,Jiangsu 210095,China [2]Pomology Institute,Shanxi Agricultural University,Taigu,Shanxi 030801,China [3]Department of Botany and Biodiversity Research Centre,University of British Columbia,Vancouver,BC,Canada

出　　处：《Plant Communications》2024年第10期100-120,共21页植物通讯（英文）

基　　金：funded by the National Key Research and Development Program of China(2022YFF1003100-02);the National Natural Science Foundation of China(32172511);the Jiangsu Agricultural Science and Technology Innovation Fund(CX(22)2025);the Natural Science Foundation of Jiangsu Province(BK20210397);the Seed Industry Promotion Project of Jiangsu(JBGS(2021)022);the Guidance Foundation of the Hainan Institute of Nanjing Agricultural University(NAUSY-MS08);the Project Funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions,the Jiangsu Provincial Key Research and Development Program(BE2023365);the Earmarked Fund for China Agriculture Research System(CARS-28).This study was supported by the High-Performance Computing Platform of the Bioinformatics Center,Nanjing Agricultural University.

摘　　要：Hybrid crops often exhibit increased yield and greater resilience,yet the genomic mechanism(s)underlying hybrid vigor or heterosis remain unclear,hindering our ability to predict the expression of phenotypic traits in hybrid breeding.Here,we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties,‘Yuluxiang’(YLX)and‘Hongxiangsu’(HXS),which share the same maternal parent but differ in their paternal parents.We then used these assemblies to explore the genome-scale landscape of allele-specific expression(ASE)and create a pangenome graph for pear.ASE was observed for close to 6000 genes in both hybrid cultivars.A subset of ASE genes related to aspects of fruit quality such as sugars,organic acids,and cuticular wax were identified,suggesting their important contributions to heterosis.Specifically,Ma1,a gene regulating fruit acidity,is absent in the paternal haplotypes of HXS and YLX.A pangenome graph was built based on our assemblies and seven published pear genomes.Resequencing data for 139 cultivated pear genotypes(including 97 genotypes sequenced here)were subsequently aligned to the pangenome graph,revealing numerous structural variant hotspots and selective sweeps during pear diversification.As predicted,the Ma1 allele was found to be absent in varieties with low organic acid content,and this association was functionally validated by Ma1 overexpression in pear fruit and calli.Overall,these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.

关 键 词：PEAR haplotype-resolved assembly allele-specific expression fruit quality traits pangenome graph 

分 类 号：Q943[生物学—植物学]