Genomic variations and distinct evolutionary rate of rare alleles in Arabidopsis thaliana

BACKGROUND: The variation rate in genomic regions associated with different alleles, impacts to distinct evolutionary patterns involving rare alleles. The rare alleles bias towards genome-wide association studies (GWASs), aim to detect different variants at genomic loci associated with single-nucleotide polymorphisms (SNPs) inclined to produce different haplotypes. Here, we sequenced Arabidopsis thaliana and compared its coding and non-coding genomic regions with its closest outgroup relative, Arabidopsis lyrta, which accounted for the ancestral misinference. The use of genome-wide SNPs interpret the genetic architecture of rare alleles in Arabidopsis thaliana, elucidating a significant departure from a neutral evolutionary model and the pattern of polymorphisms around a selected locus will exclusively influence natural selection. RESULTS: We found 23.4 % of the rare alleles existing randomly in the genome. Notably, in our results significant differences (P < 0.01) were estimated in the relative rates between rare versus intermediate alleles, between fixed versus non-fixed mutations, and between type I versus type II rare-mutations by using the χ(2)-test. However, the rare alleles generating negative values of Tajima’s D suggest that they generated under selective sweeps. Relative to polymorphic sites including SNPs, 67.5 % of the fixed mutations were attributed, indicating major contributors to speciation. Substantially, an evolution occurred in the rare allele that was 1.42-times faster than that in a major haplotype. CONCLUSION: Our results interpret that rare alleles fits a random occurrence model, indicating that rare alleles occur at any locus in a genome and in any accession in a species. Based on the higher relative rate of derived to ancient mutations and higher average D(xy), we conclude that rare alleles evolve faster than the higher frequency alleles. The rapid evolution of rare alleles indicates that they must have been newly generated with fixed mutations, compared with the other alleles. Eventually, PCR and sequencing results, in the flanking regions of rare allele loci confirm that they are of short extension, indicating the absence of a genome-wide pattern for a rare haplotype. The indel-associated model for rare alleles assumes that indel-associated mutations only occur in an indel heterozygote. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-016-0590-7) contains supplementary material, which is available to authorized users.