生物
转座因子
遗传学
基因组
全基因组关联研究
数量性状位点
反向重复
单核苷酸多态性
人口
作者
Raúl Castanera,Pol Vendrell-Mir,Amélie Bardil,Marie-Christine Carpentier,Olivier Panaud,Josep M. Casacuberta
出处
期刊:Plant Journal
[Wiley]
日期:2021-04-18
卷期号:107 (1): 118-135
被引量:4
摘要
Transposable elements (TEs) are a rich source of genetic variability. Among TEs, miniature inverted-repeat TEs (MITEs) are of particular interest as they are present in high copy numbers in plant genomes and are closely associated with genes. MITEs are deletion derivatives of class II transposons, and can be mobilized by the transposases encoded by the latter through a typical cut-and-paste mechanism. However, MITEs are typically present at much higher copy numbers than class II transposons. We present here an analysis of 103 109 transposon insertion polymorphisms (TIPs) in 738 Oryza sativa genomes representing the main rice population groups. We show that an important fraction of MITE insertions has been fixed in rice concomitantly with its domestication. However, another fraction of MITE insertions is present at low frequencies. We performed MITE TIP-genome-wide association studies (TIP-GWAS) to study the impact of these elements on agronomically important traits and found that these elements uncover more trait associations than single nucleotide polymorphisms (SNPs) on important phenotypes such as grain width. Finally, using SNP-GWAS and TIP-GWAS we provide evidence of the replicative amplification of MITEs.
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