中国水稻科学2026，Vol.40Issue(5)：598-606,9.DOI:10.16819/j.1001-7216.2026.250213
泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用
A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima
摘要
Abstract
[Objective]Transposable elements(TEs)are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice.However,due to the highly repetitive nature of TE sequences,their identification typically requires high-quality genome sequences.Currently,the limited genomic resources for African cultivated rice(Oryza glaberrima,Og)hinder systematic investigations into TE diversity and its contributions to the Og domestication process.[Method]We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions(11 Og and 10 Oryza barthii[Ob]).We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.[Result]The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb,with 61.7%of the TE variations larger than 1 kb.The total number of TE variations in the Ob accessions was greater than that in the Og accessions.A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process,which were significantly enriched in biological processes related to basic metabolism.Notably,30 genes with known functions were involved in the independent domestication of Og.[Conclusion]This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process.The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.关键词
非洲栽培稻/短舌野生稻/转座子/泛基因组/驯化Key words
Oryza glaberrima/Oryza barthii/transposable element/pan-genome/domestication引用本文复制引用
李笑霞,张天驰,贺文闯,贺慧英,盘楠,刘祎凡,钱前,商连光..泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用[J].中国水稻科学,2026,40(5):598-606,9.基金项目
国家重点研发计划资助项目(2024YFF1000400). （2024YFF1000400）
