title: Insertions/Deletions-Associated Nucleotide Polymorphism inArabidopsis thaliana.
abstract: 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.e., 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 inArabidopsis. 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.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China.
authors.forename: Changjiang
authors.initials: C
authors.lastname: Guo
authors.affiliation: Provincial Key Laboratory of Agrobiology, Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences Nanjing, China.
authors.forename: Jianchang
authors.initials: J
authors.lastname: Du
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China.
authors.forename: Long
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China.
authors.forename: Sihai
authors.initials: S
authors.lastname: Yang
authors.affiliation: Department of Genetics, University of Georgia Athens, GA, USA.
authors.forename: Rodney
authors.initials: R
authors.lastname: Mauricio
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University Nanjing, China.
authors.forename: Dacheng
authors.initials: D
authors.lastname: Tian
authors.affiliation: State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University Nanjing, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Gu
keywords: deletion; insertion; nucleotide dimorphism; nucleotide polymorphism; structural variation