Microsatellite Polymorphism in Natural Populations of the Wild Plant Arabidopsis Thaliana

Overview

Journal Genetics

Publisher Oxford University Press

Specialty Genetics

Date 1997 Aug 1

PMID 9258686

Citations 45

Authors

H Innan

R Terauchi

N T Miyashita

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

Global and Local Ancestry and its Importance: A Review.

Goli R, Chishi K, Ganguly I, Singh S, Dixit S, Rathi P Curr Genomics. 2024; 25(4):237-260.

PMID: 39156729 PMC: 11327809. DOI: 10.2174/0113892029298909240426094055.

Development of genome-specific SSR markers for the identification of introgressed segments of in the background.

Singh K, Kumari P, Raipuria R, Rai P 3 Biotech. 2022; 12(12):332.

PMID: 36325472 PMC: 9618473. DOI: 10.1007/s13205-022-03402-0.

Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment of genetic diversity of National Genebank of India and synteny with other related cucurbits.

Bonthala B, Abdin M, Arya L, Pandey C, Sharma V, Yadav P J Appl Genet. 2022; 63(2):237-263.

PMID: 35106708 DOI: 10.1007/s13353-022-00684-1.

Asymmetric gene flow between traditional and hybrid rice varieties (Oryza sativa) indicated by nuclear simple sequence repeats and implications for germplasm conservation.

Rong J, Xia H, Zhu Y, Wang Y, Lu B New Phytol. 2021; 163(2):439-445.

PMID: 33873619 DOI: 10.1111/j.1469-8137.2004.01100.x.

Phenotypic plasticity is the major determinant of changes in phenotypic integration in Arabidopsis.

Pigliucci M, Hayden K New Phytol. 2021; 152(3):419-430.

PMID: 33862986 DOI: 10.1046/j.0028-646X.2001.00275.x.

References

Clark A . Neutrality tests of highly polymorphic restriction-fragment-length polymorphisms. Am J Hum Genet. 1987; 41(5):948-56. PMC: 1684334. View

Powell W, Morgante M, McDevitt R, Vendramin G, Rafalski J . Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci U S A. 1995; 92(17):7759-63. PMC: 41225. DOI: 10.1073/pnas.92.17.7759. View

Weber J . Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics. 1990; 7(4):524-30. DOI: 10.1016/0888-7543(90)90195-z. View

Condit R, Hubbell S . Abundance and DNA sequence of two-base repeat regions in tropical tree genomes. Genome. 1991; 34(1):66-71. DOI: 10.1139/g91-011. View

Chakraborty R, Fornage M, Gueguen R, Boerwinkle E . Population genetics of hypervariable loci: analysis of PCR based VNTR polymorphism within a population. EXS. 1991; 58:127-43. DOI: 10.1007/978-3-0348-7312-3_10. View

Estoup A, Tailliez C, Cornuet J, Solignac M . Size homoplasy and mutational processes of interrupted microsatellites in two bee species, Apis mellifera and Bombus terrestris (Apidae). Mol Biol Evol. 1995; 12(6):1074-84. DOI: 10.1093/oxfordjournals.molbev.a040282. View

Estoup A, Garnery L, Solignac M, Cornuet J . Microsatellite variation in honey bee (Apis mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics. 1995; 140(2):679-95. PMC: 1206644. DOI: 10.1093/genetics/140.2.679. View

Michalakis Y, Veuille M . Length variation of CAG/CAA trinucleotide repeats in natural populations of Drosophila melanogaster and its relation to the recombination rate. Genetics. 1996; 143(4):1713-25. PMC: 1207433. DOI: 10.1093/genetics/143.4.1713. View

Innan H, Tajima F, Terauchi R, Miyashita N . Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana. Genetics. 1996; 143(4):1761-70. PMC: 1207437. DOI: 10.1093/genetics/143.4.1761. View

10.

van Treuren R, Kuittinen H, Karkkainen K, Savolainen O . Evolution of microsatellites in Arabis petraea and Arabis lyrata, outcrossing relatives of Arabidopsis thaliana. Mol Biol Evol. 1997; 14(3):220-9. DOI: 10.1093/oxfordjournals.molbev.a025758. View

11.

Kimura M, Crow J . THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION. Genetics. 1964; 49:725-38. PMC: 1210609. DOI: 10.1093/genetics/49.4.725. View

12.

Deka R, Chakroborty R, Ferrell R . A population genetic study of six VNTR loci in three ethnically defined populations. Genomics. 1991; 11(1):83-92. DOI: 10.1016/0888-7543(91)90104-m. View

13.

Hudson T, Engelstein M, Lee M, Ho E, Rubenfield M, ADAMS C . Isolation and chromosomal assignment of 100 highly informative human simple sequence repeat polymorphisms. Genomics. 1992; 13(3):622-9. DOI: 10.1016/0888-7543(92)90133-d. View

14.

Dallas J . Estimation of microsatellite mutation rates in recombinant inbred strains of mouse. Mamm Genome. 1992; 3(8):452-6. DOI: 10.1007/BF00356155. View

15.

Zhao X, Kochert G . Phylogenetic distribution and genetic mapping of a (GGC)n microsatellite from rice (Oryza sativa L.). Plant Mol Biol. 1993; 21(4):607-14. DOI: 10.1007/BF00014544. View

16.

Valdes A, Slatkin M, Freimer N . Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics. 1993; 133(3):737-49. PMC: 1205356. DOI: 10.1093/genetics/133.3.737. View

17.

Lagercrantz U, Ellegren H, Andersson L . The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 1993; 21(5):1111-5. PMC: 309270. DOI: 10.1093/nar/21.5.1111. View

18.

Silver L . Bouncing off microsatellites. Nat Genet. 1992; 2(1):8-9. DOI: 10.1038/ng0992-8. View

19.

Weber J, Wong C . Mutation of human short tandem repeats. Hum Mol Genet. 1993; 2(8):1123-8. DOI: 10.1093/hmg/2.8.1123. View

20.

Morgante M, Olivieri A . PCR-amplified microsatellites as markers in plant genetics. Plant J. 1993; 3(1):175-82. View