Cotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation

文献类型： 外文期刊

第一作者： Liu, Shang

作者： Liu, Shang;Cheng, Hailiang;Zhang, Youping;He, Man;Zuo, Dongyun;Wang, Qiaolian;Lv, Limin;Liu, Ji;Song, Guoli;Liu, Shang;Lin, Zhongxv;Cheng, Hailiang;Song, Guoli

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关键词： Cotton; Transposon-related variation; Graphical genome; mendelian randomization (MR); Cotton cultivation; Fiber quality

期刊名称：JOURNAL OF ADVANCED RESEARCH （ 影响因子：13.0； 五年影响因子：11.6 ）

ISSN： 2090-1232

年卷期： 2025 年 71 卷

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收录情况： SCI

摘要： Introduction: Transposon plays a vital role in cotton genome evolution, contributing to the expansion and divergence of genomes within the Gossypium genus. However, knowledge of transposon activity in modern cotton cultivation is limited. Objectives: In this study, we aimed to construct transposon-related variome within Gossypium genus and reveal role of transposon-related variations during cotton cultivation. In addition, we try to identify valuable transposon-related variations for cotton breeding. Methods: We utilized graphical genome construction to build up the graphical transposon-related variome. Based on the graphical variome, we integrated t-test, eQTL analysis and Mendelian Randomization (MR) to identify valuable transposon activities and elite genes. In addition, a convolutional neural network (CNN) model was constructed to evaluate epigenomic effects of transposonrelated variations. Results: We identified 35,980 transposon activities among 10 cotton genomes, and the diversity of genomic and epigenomic features was observed among 21 transposon categories. The graphical cotton transposon-related variome was constructed, and 9,614 transposon-related variations with plasticity in the modern cotton cohort were used for eQTL, phenotypic t-test and Mendelian Randomization. 128 genes were identified as gene resources improving fiber length and strength simultaneously. 4 genes were selected from 128 genes to construct the elite gene panel whose utility has been validated in a natural cotton cohort and 2 accessions with phenotypic divergence. Based on the eQTL analysis results, we identified transposon-related variations involved in cotton's environmental adaption and human domestication, providing evidence of their role in cotton's adaption-domestication cooperation. Conclusions: The cotton transposon-related variome revealed the role of transposon-related variations in modern cotton cultivation, providing genomic resources for cotton molecular breeding. (c) 2024 The Authors. Published by Elsevier B.V. on behalf of Cairo University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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