Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana

Abstract

To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the possibility that dimorphic DNA variation exists in the entire nuclear genome of A. thaliana. The ChiA region was divided into two blocks by an intragenic recombination between two parental sequence types, which diverged 7.4 MYA under the assumption that nucleotide mutation rate per site per year is mu = 10(-9). Nucleotide diversity in the entire ChiA region was 0.0104. Tajima's test was significantly negative for both nucleotide and indel variations, which was manifested as an excess of unique polymorphisms. However, the level and pattern of polymorphism in the ChiA region were inconsistent with simple theoretical explanations. The HKA test detected no difference in the levels of intra- and interspecific variations between the ChiA and Adh regions. In the ChiA coding region, no difference in the patterns of synonymous and replacement variation was found in intra- and interspecific comparisons by the MK test. Although it was difficult to determine the exact genetic mechanism acting on the ChA locus, these results suggested that the ChA locus region was under the same genetic mechanism before and after the establishment of A. thaliana as a species.

Evolutionary dynamics of an Arabidopsis insect resistance quantitative trait locus

“…Although excess nonsynonymous polymorphism has been observed in comparisons of several A. thaliana genes with congeneric relatives (e.g., refs. 26, 33, and 34), this reflects locus-specific effects that are not found in most genes (34)(35)(36)(37)(38)(39). Furthermore, MAM2 displays an excess of intermediate-frequency nucleotide polymorphisms, in contrast to most other A. thaliana genes (26,33,34,37,39), including data from Ϸ500 loci sampled throughout the A. thaliana genome (K. Schmid and T.M.-O., unpublished data).…”

Signature of balancing selection in Arabidopsis

“…For observed data, according to Kreitman and Hudson (3), this ratio is calculated for each window as the average pairwise difference between RPS5ϩ and RPS5Ϫ allelic classes in the window divided by divergence between species in the window, divided by the species-wide average ratio of polymorphism to divergence (0.08), based on eight genes in Arabidopsis (Adh, Adh upstream region, ChiA, ChiB, FAH1 and F3H, PgiC, CHI; refs. [21][22][23][24][25][26][27]. For selection predictions, this ratio is the expected coalescence time for two lineages linked to different selected alleles, divided by 2, the expected coalescence time for two random lineages without selection (10), averaged over all sites in the window.…”

National Science Foundation-Sponsored Workshop Report. Draft Plan for Soybean Genomics

“…By comparison, maize (Zea mays) has as much as 10-fold higher levels of nucleotide diversity (Tenaillon et al, 2001;Ching et al, 2002). Similarly, sequence variation in individual Arabidopsis genes (Kawabe and Miyashita, 1999;Purugganan and Suddith, 1999;Kawabe et al, 2000;Kuittinen and Aguade, 2000) has levels of nucleotide diversity 5-to 8-fold higher than that of domesticated soybean. Haplotype analysis of SNP-containing gene and genomic fragments revealed a severe deficiency of haplotypes versus the number that would be anticipated at linkage equilibrium.…”