scholarly journals Intragenic Recombination in the Adh Locws of the Wild Plant Arabidopsis thaliana

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1761-1770 ◽  
Author(s):  
Hideki Innan ◽  
Fumio Tajima ◽  
Ryohei Terauchi ◽  
Naohiko T Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Dna Polymorphism ◽  
Geographic Origin ◽  
Wild Plant ◽  
Intragenic Recombination ◽  
Nucleotide Variation ◽  
Nucleotide Mutation ◽  
Sequence Types ◽  
Plant Arabidopsis Thaliana

Abstract Nucleotide variation in the Adh region of the wild plant Arabidopsis thaliana was analyzed in 17 ecotypes sampled worldwide to investigate DNA polymorphism in natural plant populations. The investigated 2.4kb Adh region was divided into four blocks by intragenic recombinations between two parental sequence types that diverged 6.3 million years (Myr) ago, if the nucleotide mutation rate μ = 10−9 is assumed. Within each block, dimorphism of segregating variations was observed with intermediate frequencies, which caused a substantial amount of nucleotide variation in A. thaliana at the species level. The first recombination introduced the divergent variation that resulted in dimorphism in this plant species ~3.3 Myr ago, and three subsequent intragenic recombinations have occurred sporadically in ~1.1-Myr intervals. It was shown that there was only a limited number (six) of sequence types in this species and that no clear association was observed between sequence type and geographic origin. Taken together, these results suggest that A. thaliana has spread over the world only recently. It can be concluded that recombination played an important role in the evolutionary history of A. thaliana, especially through the generation of DNA polymorphism in the natural populations of this plant species.

scholarly journals DNA polymorphism at the ACAULIS5 locus of the wild plant Arabidopsis thaliana

2003 ◽  
Vol 78 (1) ◽  
pp. 11-21 ◽  
Author(s):  
Kentaro Yoshida ◽  
Taku Kamiya ◽  
Akira Kawabe ◽  
Naohiko T. Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Polymorphism ◽  
Wild Plant ◽  
Plant Arabidopsis Thaliana

scholarly journals Nucleotide polymorphism at the Atmyb2 locus of the wild plant Arabidopsis thaliana

2002 ◽  
Vol 80 (2) ◽  
pp. 89-98 ◽  
Author(s):  
TAKU KAMIYA ◽  
AKIRA KAWABE ◽  
NAOHIKO T. MIYASHITA
Keyword(s):  
Arabidopsis Thaliana ◽  
Regulatory Gene ◽  
Purifying Selection ◽  
Wild Plant ◽  
Dna Variation ◽  
Mutation Theory ◽  
Neutral Mutation Theory ◽  
Species Specific ◽  
Plant Arabidopsis Thaliana ◽  
Myb Domain

DNA variation was studied in a 2.2 kb region of the regulatory gene Atmyb2 using 20 ecotypes of Arabidopsis thaliana and one accession each of Arabis gemmifera and Arabidopsis himalaica. Nucleotide diversity (π) in the region was 0.0027, which was lower than for other loci in A. thaliana. The MYB domain of the Atmyb2 gene (π = 0.0036) had a larger variation than the non-MYB region (π = 0.0013). Tajima's test and Fu and Li's test did not give a significant result. In contrast to the low level of polymorphism, the degree of divergence of the Atmyb2 region was higher between A. thaliana and A. gemmifera (K = 0.0730) than for other loci. The MYB domain (K = 0.0436) had smaller divergence than the non-MYB region (K = 0.0939). The HKA test detected significant discordance in the ratio of polymorphism to divergence in some comparisons. The pattern of low polymorphism and high divergence, which is mainly observed in the non-MYB region of the gene, is inconsistent with the neutral mutation theory. Strong purifying selection after establishment of A. thaliana and a species-specific adaptive process could be invoked to account for this pattern of polymorphism and divergence of Atmyb2.

scholarly journals Microsatellite Polymorphism in Natural Populations of the Wild Plant Arabidopsis thaliana

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1441-1452 ◽  
Author(s):  
Hideki Innan ◽  
Ryohei Terauchi ◽  
Naohiko T Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Repetitive Sequences ◽  
Geographic Origin ◽  
Natural Populations ◽  
Wild Plant ◽  
Sign Test ◽  
Repeat Number ◽  
Average Gene

Variation in repeat number at 20 microsatellite loci of Arabidopsis thaliana was studied in a worldwide sample of 42 ecotypes to investigate the pattern and level of polymorphism in repetitive sequences in natural plant populations. There is a substantial amount of variation at microsatellite loci despite the selfing nature of this plant species. The average gene diversity was 0.794 and the average number of alleles per locus was 10.6. The distribution of alleles was centered around the mean of repeat number at most loci, but could not be regarded as normal. There was a significantly positive correlation between the number of repeats and the amount of variation. For most loci, the observed number of alleles was between the expected values of the infinite allele and stepwise mutation models. The two models were rejected by the sign test. Linkage disequilibrium was detected in 12.1% of the pairwise comparisons between loci. In phylogenetic tree, there was no association between ecotype and geographic origin. This result is consistent with the recent expansion of A. thaliana throughout the world.

Heterogeneous Selection at Specific Loci in Natural Environments in Arabidopsis thaliana

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 321-329 ◽  
Author(s):  
Cynthia Weinig ◽  
Lisa A Dorn ◽  
Nolan C Kane ◽  
Zachary M German ◽  
Solveig S Halldorsdottir ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Natural Selection ◽  
Rhode Island ◽  
Plant Species ◽  
Allelic Variation ◽  
Balancing Selection ◽  
Wild Plant ◽  
Natural Environments ◽  
Fitness Effects

Abstract Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.

scholarly journals DNA Variation in the Wild Plant Arabidopsis thaliana Revealed by Amplified Fragment Length Polymorphism Analysis

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1723-1731 ◽  
Author(s):  
Naohiko T Miyashita ◽  
Akira Kawabe ◽  
Hideki Innan
Keyword(s):  
Arabidopsis Thaliana ◽  
Frequency Distribution ◽  
Geographic Origin ◽  
Pairwise Distance ◽  
Wild Plant ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Entire Genome ◽  
Dna Variation ◽  
In The Wild

Abstract To investigate the level and pattern of DNA variation of Arabidopsis thaliana at the entire genome level, AFLP analysis was conducted for 38 ecotypes distributed throughout the world. Ten pairs of selective primers were used to detect a total of 472 bands, of which 374 (79.2%) were polymorphic. The frequency distribution of polymorphic bands was skewed toward an excess of singleton variation. On the basis of AFLP variation, nucleotide diversity for the entire genome was estimated to be 0.0106, which was within the range reported previously for specific nuclear genes. The frequency distribution of pairwise distance was bimodal because of an ecotype (Fl-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs was tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype Fl-3. This result indicates that the effect of recombination could not be ignored in this selfing species. A neighbor-joining tree was constructed on the basis of the AFLP variation. This tree has a star-like topology and shows no clear association between ecotype and geographic origin, suggesting a recent spread of this plant species and limited migration between its habitats.

scholarly journals DNA Variation in the Basic Chitinase Locus (ChiB) Region of the Wild Plant Arabidopsis thaliana

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1445-1453 ◽  
Author(s):  
Akira Kawabe ◽  
Naohiko T Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Nucleotide Diversity ◽  
Wild Plant ◽  
Entire Region ◽  
Evolutionary Mechanisms ◽  
Dna Variation ◽  
Linkage Disequilibria ◽  
Before And After ◽  
Genetic Mechanisms ◽  
Plant Arabidopsis Thaliana

Abstract Nucleotide variation in a 2.2-kbp region of basic chitinase (ChiB) locus in 17 ecotypes of Arabidopsis thaliana was compared with previously investigated regions to investigate genetic mechanisms acting on DNA polymorphism. In the ChiB region, dimorphic DNA variation was detected, as in the Adh and ChiA regions. Nucleotide diversity (π) of the entire region was 0.0091, which was similar to those of the two other regions. About half of polymorphic sites (37/87) in the ChiB region were observed in only two ecotypes. Tajima's D was negative but not significantly, while Fu and Li's D* was positive. Neither McDonald-Kreitman nor Hudson, Kreitman, Aguadé tests showed a significant result, indicating that these loci were under similar evolutionary mechanisms before and after speciation. Linkage disequilibria were observed within the three regions because of dimorphic polymorphisms. Interlocus linkage disequilibrium was not detected between the Adh and the two chitinase regions, but was observed between the ChiA and ChiB regions. This could be due to epistatic interaction between the two chitinase loci, which are located on different chromosomes.

scholarly journals DNA Polymorphism at the Cytosolic Phosphoglucose Isomerase (PgiC) Locus of the Wild Plant Arabidopsis thaliana

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1339-1347 ◽  
Author(s):  
Akira Kawabe ◽  
Kyoko Yamane ◽  
Naohiko T Miyashita
Keyword(s):  
Arabidopsis Thaliana ◽  
Dna Polymorphism ◽  
Allozyme Variation ◽  
Phosphoglucose Isomerase ◽  
Wild Plant ◽  
Nucleotide Polymorphisms ◽  
Test Statistic ◽  
Dna Variation ◽  
Outgroup Species ◽  
Expanding Population

Abstract DNA variation in a 4.7-kb region of the cytosolic phosphoglucose isomerase (PgiC) locus was investigated for 21 ecotypes of Arabidopsis thaliana. The estimated nucleotide diversity was 0.0038, which was one-third of those in previously investigated loci. Since most of the nucleotide variations (93%) were singleton and doubleton, Tajima's test statistic was significantly negative. About 50% of nucleotide polymorphisms in exons were replacement, which caused significance in McDonald and Kreitman's test when compared with Arabis gemmifera and Cardaminopsis petraea. These results indicated that DNA polymorphism at the PgiC locus was not under neutrality. There were two divergent sequence types in the PgiC region, which were associated with allozyme variation. The Fast allozyme was shown to have originated from the Slow allozyme, since two outgroup species had the Slow form. A phylogenetic tree of ecotypes with the Fast allozyme had the shape of a star phylogeny. Mismatch distribution of the Fast allozyme ecotypes resembled that expected under an expanding population model. These results suggest positive selection for the Fast allozyme of the PGIC in A. thaliana.

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