Cotton transposon-related variome reveals roles of transposon-related variations in modern cotton cultivation.
J Adv Res
; 2024 May 27.
Article
em En
| MEDLINE
| ID: mdl-38810909
ABSTRACT
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 transposon-related 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.
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Bases de dados:
MEDLINE
Idioma:
En
Revista:
J Adv Res
Ano de publicação:
2024
Tipo de documento:
Article