中国农业科学2025，Vol.58Issue(15)：2933-2947,15.DOI:10.3864/j.issn.0578-1752.2025.15.001
籼稻品种基因组中逆转座子Tos17的鉴定与研究
Identification and Characterization of Retrotransposon Tos17 in the Genomes of Indica Rice
摘要
Abstract
[Objective]Tos17 is a type of retrotransposon in the rice genome.In the japonica variety Nipponbare,a Tos17 located on chromosome 7(Tos17Chr.7)can be activated during tissue culture.This study aims to reveal the genomic features of Tos17 of indica varieties in China and determine whether their Tos17 can be activated in tissue culture like in japonica rice,which may affect biotechnological breeding.[Method]High-quality genome resequencing data of indica varieties or hybrid parents were retrieved from public databases.An in-house program was developed to identify and analyze Tos17 insertion loci,confirmed by IGV visualization and PCR assays.The varieties were classified through hierarchical clustering and principal component analysis,a phylogenetic tree was constructed based on genome-wide single nucleotide polymorphism(SNP)data,and the association between varietal clusters and Tos17 haplotypes was assessed using Mantel test.Transgenic plants were generated by Agrobacterium-mediated transformation of mature embryo-derived callus of indica varieties,and the changes of Tos17 copy number were analyzed in 125 T0 transgenic plants.[Result]23 distinct Tos17 insertion loci were identified in 1 511 indica varieties using the Tos17-finder,a program developed specifically for Tos17 identification.All varieties had a Tos17 on Chr.10(Tos17Chr.10)identical to the one in japonica rice Nipponbare,and there were two high-frequency Tos17 copies on Chr.2,i.e.,Tos17Chr.2-1(79.0%)and Tos17Chr.2-2(83.7%),but only 85(5.6%)varieties carried the Tos17Chr.7 common to japonica rice.There were 4.0 Tos17 copies per variety on average,and while 11 varieties had up to 8 Tos17 copies,35 only had a single Tos17,i.e.,Tos17Chr.10.Twelve Tos17 insertions were located within or 2 kb up-or down-stream of annotated genes,with the remaining 11 in intergenic regions.Phylogenetic analysis based on SNPs classified the 1 511 varieties into three subpopulations,each showing partial correlation with specific Tos17 haplotypes.No new Tos17 insertions were detected in the 125 T0 transgenic seedlings of 5 indica varieties.A molecular marker capable of accurately distinguishing Tos17Chr.7 from other Tos17s was developed.[Conclusion]The genomic features of Tos17 in indica rice varieties differ from those in japonica rice variety Nipponbare.The developed molecular marker can be used to determine readily whether the test materials carry the activatable Tos17Chr.7.关键词
Tos17/籼稻/全基因组重测序/组织培养/转座子基因组学/转座活性Key words
Tos17/indica rice/whole-genome resequencing/tissue culture/transposon genomics/transposition activity引用本文复制引用
罗嘉锐,吴三玲,郭芾,刘振,宋婧含,谭瑗瑗,舒庆尧..籼稻品种基因组中逆转座子Tos17的鉴定与研究[J].中国农业科学,2025,58(15):2933-2947,15.基金项目
科技部"十四五"重点研发计划(2022YFD12007)、江苏省重点研发计划(BE2023336)、海南省自然科学基金高层次人才项目(322RC741)、浙江大学海南研究院专职科研人员启动项目(0201-6602-A12201) （2022YFD12007）
