基于梨泛转录组的抗性与果实品质育种遗传基础解析

doi:10.1016/j.jia.2024.11.026

Journal of Integrative Agriculture ›› 2025, Vol. 24 ›› Issue (5): 1813-1830.DOI: 10.1016/j.jia.2024.11.026

基于梨泛转录组的抗性与果实品质育种遗传基础解析

收稿日期:2024-01-14 修回日期:2024-11-12 接受日期:2024-06-11 出版日期:2025-05-20 发布日期:2025-04-14

Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)

Congrui Sun^{1, 2*}, Runze Wang^{1, 3*}, Jiaming Li^{1, 2}, Xiaolong Li⁴, Bobo Song^{1, 2}, David Edwards^5#, Jun Wu^{1, 2#}

¹College of Horticulture, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
²Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
³School of Horticulture, Anhui Agricultural University, Hefei 230036, China
⁴Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetables of Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
⁵Centre for Applied Bioinformatics and Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia

Received:2024-01-14 Revised:2024-11-12 Accepted:2024-06-11 Online:2025-05-20 Published:2025-04-14
About author:#Correspondence Jun Wu, E-mail: wujun@njau.edu.cn; David Edwards, E-mail: dave.edwards@uwa.edu.au * These authors contributed equally to this study.
Supported by:
This work was supported by the National Science Foundation of China (32230097), the National Key Research and Development Program of China (2022YFD1200503), the earmarked fund for China Agriculture Research System (CARS-28), the earmarked fund for Jiangsu Agricultural Industry Technology System (JATS [2023] 412), and the Natural Science Foundation of Jiangsu Province for Young Scholar, China (BK20221010).

摘要/Abstract

摘要：

砂梨作为梨属植物的重要栽培种，是温带地区的重要果树，其具有丰富的遗传资源，对梨果实品质的改良具有重要意义。目前，包括梨在内的果树物种抗性与果实品质性状之间关系的研究较为有限。而泛转录组能够有效捕捉来自编码区的遗传信息，并反映个体之间基因表达的差异。因此，本研究基于来自不同组织的506个砂梨样本构建了泛转录组，并通过表达存在/缺失变异（ePAVs）解析了改良过程中表型与抗病性之间的内在关系。研究结果表明，砂梨泛转录组包含156,744个转录本，其中新转录本在防御反应生物学过程中显著富集。有趣的是，梨的地方品种中抗病相关基因的表达水平较高，但在改良过程中受到负选择。ePAVs分析表明，具有遗传多样性的砂梨地方品种可以分为两个亚群，并推测它们经历了不同的传播过程。进一步通过共表达网络和相关性分析，发现梨的石细胞形成、果实花青素合成和抗逆性之间相关联，它们由多个模块共同调控，且调控基因的表达具有显著相关性。此外，还鉴定到梨参考基因组中缺失的一些基因，如候选基因HKL1，其可能影响了果实糖含量。研究结果为梨果实复杂性状间的关联分析提供了新见解，并为梨的抗病性和果实品质协同改良提供了数据资源。

Abstract:

Pyrus pyrifolia, commonly known as sand pear, is a key economic fruit tree in temperate regions that possesses highly diverse germplasm resources for pear quality improvement. However, research on the relationship between resistance and fruit quality traits in the breeding of fruit species like pear is limited. Pan-transcriptomes effectively capture genetic information from coding regions and reflect variations in gene expression between individuals. Here, we constructed a pan-transcriptome based on 506 samples from different tissues of sand pear, and explored the intrinsic relationships among phenotypes and the selection for disease resistance during improvement based on expression presence/absence variations (ePAVs). The pan-transcriptome in this study contains 156,744 transcripts, among which the novel transcripts showed significant enrichment in the defense response. Interestingly, disease resistance genes are highly expressed in landraces of pear but have been selected against during the improvement of this perennial tree species. We found that the genetically diverse landraces can be divided into two subgroups and inferred that they have undergone different dispersal processes. Through co-expression network analysis, we confirmed that the formation of stone cells in pears, the synthesis of fruit anthocyanins, and the ability to resist stress are interrelated. They are jointly regulated by several modules, and the expression of regulatory genes has significant correlations with these three processes. Moreover, we identified candidate genes such as HKL1 that may affect sugar content and are missing from the reference genome. This study provides insights into the associations between complex fruit traits, while providing a database resource for pear disease resistance and fruit quality breeding.

Key words: pear , pan-transcriptome , ePAVs , disease resistance , fruit quality , co-expression network

Congrui Sun, Runze Wang, Jiaming Li, Xiaolong Li, Bobo Song, David Edwards, Jun Wu. 基于梨泛转录组的抗性与果实品质育种遗传基础解析[J]. Journal of Integrative Agriculture, 2025, 24(5): 1813-1830.

Congrui Sun, Runze Wang, Jiaming Li, Xiaolong Li, Bobo Song, David Edwards, Jun Wu. Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)[J]. Journal of Integrative Agriculture, 2025, 24(5): 1813-1830.

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基于梨泛转录组的抗性与果实品质育种遗传基础解析

Pan-transcriptome analysis provides insights into resistance and fruit quality breeding of pear (Pyrus pyrifolia)

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