Liu Shang, Cheng Hailiang, Zhang Youping, He Man, Zuo Dongyun, Wang Qiaolian, Lv Limin, Lin Zhongxv, Liu Ji, Song Guoli
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; Zhengzhou Research Base, Zhengzhou University, Zhengzhou 450001, China.
J Adv Res. 2025 May;71:17-28. doi: 10.1016/j.jare.2024.05.019. Epub 2024 May 27.
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.
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.
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 transposon-related variations.
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.
The cotton transposon-related variome revealed the role of transposon-related variations in modern cotton cultivation, providing genomic resources for cotton molecular breeding.
转座子在棉花基因组进化中起着至关重要的作用，有助于棉属基因组的扩展和分化。然而，现代棉花种植中转座子活性的相关知识有限。
在本研究中，我们旨在构建棉属中转座子相关的变异组，并揭示棉花种植过程中转座子相关变异的作用。此外，我们试图鉴定对棉花育种有价值的转座子相关变异。
我们利用图形基因组构建来建立图形化的转座子相关变异组。基于图形变异组，我们整合了t检验、eQTL分析和孟德尔随机化（MR）来鉴定有价值的转座子活性和优良基因。此外，构建了一个卷积神经网络（CNN）模型来评估转座子相关变异的表观基因组效应。
我们在10个棉花基因组中鉴定出35980个转座子活性，并在21个转座子类别中观察到基因组和表观基因组特征的多样性。构建了图形化的棉花转座子相关变异组，并将现代棉花群体中9614个具有可塑性的转座子相关变异用于eQTL、表型t检验和孟德尔随机化。鉴定出128个基因作为同时改善纤维长度和强度的基因资源。从128个基因中选择4个基因构建优良基因面板，其效用已在一个天然棉花群体和2个具有表型差异的种质中得到验证。基于eQTL分析结果，我们鉴定出参与棉花环境适应和人工驯化的转座子相关变异，为它们在棉花适应-驯化协同作用中的作用提供了证据。
棉花转座子相关变异组揭示了转座子相关变异在现代棉花种植中的作用，为棉花分子育种提供了基因组资源。
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