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Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana

文献类型： 外文期刊

作者： Guo, Changjiang 1 ; Du, Jianchang 2 ; Wang, Long 1 ; Yang, Sihai 1 ; Mauricio, Rodney 3 ; Tian, Dacheng 1 ; Gu, Tingti 1 ;

作者机构： 1.Nanjing Univ, Sch Life Sci, State Key Lab Pharmaceut Biotechnol, Nanjing, Jiangsu, Peoples R China

2.Jiangsu Acad Agr Sci, Prov Key Lab Agrobiol, Inst Biotechnol, Nanjing, Jiangsu, Peoples R China

3.Univ Georgia, Dept Genet, Athens, GA 30602 USA

4.Nanjing Agr Univ, State Key Lab Plant Genet & Germplasm Enhancement, Nanjing, Jiangsu, Peoples R China

5.Nanjing Agr Univ, Coll Hort, Nanjing, Jiangsu, Peoples R China

关键词： structural variation;insertion;deletion;nucleotide polymorphism;nucleotide dimorphism

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2016 年 7 卷

页码：

收录情况： SCI

摘要： Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.a, a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.

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