Transposon plays a vital role in cotton genome evolution, contributing to the expansion and divergence of genomes within genus. However, knowledge of transposon activity in modern cotton cultivation is limited. In this study, we aimed to construct transposon-related variome within 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 -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 -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.

中文翻译：

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棉花转座子相关变异揭示了现代棉花种植中转座子相关变异的作用


转座子在棉花基因组进化中发挥着至关重要的作用，有助于属内基因组的扩展和分化。然而，对现代棉花种植中转座子活性的了解是有限的。在本研究中，我们的目的是构建属内转座子相关变异，并揭示转座子相关变异在棉花栽培过程中的作用。此外，我们还尝试为棉花育种鉴定有价值的转座子相关变异。我们利用图形基因组构建来构建图形转座子相关的变异组。基于图形变异组，我们整合了检验、eQTL 分析和孟德尔随机化 (MR)，以识别有价值的转座子活性和精英基因。此外，还构建了卷积神经网络（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了 35,980 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。构建了图形棉花转座子相关变异组，并将现代棉花队列中具有可塑性的 9,614 个转座子相关变异用于 eQTL、表型检验和孟德尔随机化。鉴定出128个基因作为同时提高纤维长度和强度的基因资源。从128个基因中选出4个基因构建精英基因组，其效用已在天然棉花群体和2个具有表型分歧的材料中得到验证。基于eQTL分析结果，我们鉴定了与棉花环境适应和人类驯化相关的转座子相关变异，为它们在棉花适应-驯化合作中的作用提供了证据。 棉花转座子相关变异揭示了转座子相关变异在现代棉花栽培中的作用，为棉花分子育种提供基因组资源。