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Journal article
Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation
Horticultural plant journal, Vol.10(6), pp.1274-1290
2024
Abstract
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 overexpressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.
Details
- Title
- Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation
- Authors/Creators
- Baopeng Ding - Shanxi Datong UniversityHaifei Hu - Rice Research InstituteYunpeng Cao - Chinese Academy of SciencesRuirui Xu - Weifang UniversityYujing Lin - Shanxi Agricultural UniversityTahir ul Qamar Muhammad - Government College University, FaisalabadYuqin Song - Shanxi Agricultural UniversityGuangqi He - Zhejiang UniversityYouzhi Han - Shanxi Agricultural UniversityHuangping Guo - Shanxi Agricultural UniversityJun Qiao - Shanxi Datong UniversityJianguo Zhao - Shanxi Datong UniversityXinxin Feng - Shanxi Agricultural UniversitySheng Yang - Shanxi Agricultural UniversityXuhu Guo - Shanxi Datong UniversityRajeev Kumar Varshney - Murdoch University, Food Futures InstituteLiulin Li - Shanxi Agricultural University
- Publication Details
- Horticultural plant journal, Vol.10(6), pp.1274-1290
- Publisher
- Elsevier B.V. on behalf of KeAi Communications Co. Ltd.
- Number of pages
- 17
- Grant note
- Shanxi Province Postdoctoral Research Activity Fund: K462101001 Doctoral Research Initiation Fund of Shanxi Datong University: 2023-B-15 Earmarked Fund for Modern Agro-industry Technology Research System: 2023CYJSTX07 Shanxi Province Excellent Doctoral Work Award Project: 606-02010609
This research was 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) , and the Shanxi Province Excellent Doctoral Work Award Project (Grant No. 606-02010609) . We extend our thanks to Engineer Tao Huang from Beijing Biomarker Biotechnology Co., Ltd., as well as Engineer Shaofang He from Wuhan Tanma Technology and Shanxi Editor Technology for his invaluable assistance with genome sequencing and assembly, and to Dr. Renjian Li from the College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China, for his support with molecular docking.r 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) , and the Shanxi Province Excellent Doctoral Work Award Project (Grant No. 606-02010609) . We extend our thanks to Engineer Tao Huang from Beijing Biomarker Biotechnology Co., Ltd., as well as Engineer Shaofang He from Wuhan Tanma Technology and Shanxi Editor Technol-ogy for his invaluable assistance with genome sequencing and assembly, and to Dr. Renjian Li from the College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China, for his support with molecular docking.
- Identifiers
- 991005717664607891
- Copyright
- © 2024 Chinese Society for Horticultural Science (CSHS) and Institute of Vegetables and Flowers (IVF), Chinese Academy of Agricultural Sciences (CAAS).
- Murdoch Affiliation
- Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
- Language
- English
- Resource Type
- Journal article
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- Domestic collaboration
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- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1543 Flow Cytometry
- Web Of Science research areas
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