Highly Polymorphic Microsatellites of Rice Consist of AT Repeats, and a Classification of Closely Related Cultivars with These Microsatellite Loci

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2009 Apr 9

PMID 19352746

Citations 20

Authors

H Akagi

Y Yokozeki

A Inagaki

T Fujimura

Affiliations

Soon will be listed here.

Abstract

Microsatellites consisting of AT repeats are highly polymorphic in rice genomes and can be used to distinguish between even closely related japonica cultivars in Japan. Polymorphisms of 20 microsatellite loci were determined using 59 japonica cultivars, including both domestic and modern Japanese cultivars. Although the polymorphisms of these 20 microsatellite loci indicated that the Japanese cultivars were genetically quite similar, microsatellites consisting of AT repeats showed high gene diversity even among such closely related cultivars. Combinations of these hypervariable microsatellites can be employed to classify individual cultivars, since the microsatellites were stable within each cultivar. An identification system based on these highly polymorphic microsatellites could be used to maintain the purity of rice seeds by eliminating contamination. A parentage diagnosis using 17 polymorphic microsatellite loci clearly demonstrated that plants which carried desired chromosome regions had been selected in breeding programs. Thus, these hypervariable microsatellites consisting of AT repeats should promote the selection of plants which carry desired chromosomes from genetically similar parents. Backcrossing could also help to eliminate unnecessary chromosome regions with microsatellite polymorphisms at an early stage in breeding programs.

Citing Articles

Exploring genetic divergence and marker-trait associations for leaffolder (Guenee) resistance in rice landraces.

Nayak A, Golive P, Sasmal A, Devanna B, Anilkumar C, Mukherjee A 3 Biotech. 2024; 14(3):90.

PMID: 38414829 PMC: 10894780. DOI: 10.1007/s13205-024-03930-x.

Genetic variation of seed oil characteristics in native Korean germplasm of Perilla crop (Perilla frutescens L.) using SSR markers.

Park H, Sa K, Lee S, Lee J Genes Genomics. 2022; 44(10):1159-1170.

PMID: 35900697 DOI: 10.1007/s13258-022-01289-y.

Identifying SSR Markers Related to Seed Fatty Acid Content in Crop ( L.).

Park H, Sa K, Hyun D, Lee S, Lee J Plants (Basel). 2021; 10(7).

PMID: 34371607 PMC: 8309404. DOI: 10.3390/plants10071404.

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Landraces.

Bhuvaneswari S, Gopala Krishnan S, Bollinedi H, Saha S, Ellur R, Vinod K Front Genet. 2020; 11:570731.

PMID: 33193672 PMC: 7593561. DOI: 10.3389/fgene.2020.570731.

Construction of genetic linkage map and identification of QTLs related to agronomic traits in DH population of maize (Zea mays L.) using SSR markers.

Choi J, Sa K, Park D, Lim S, Ryu S, Park J Genes Genomics. 2019; 41(6):667-678.

PMID: 30953340 DOI: 10.1007/s13258-019-00813-x.

References

Akagi H, Yokozeki Y, Inagaki A, Fujimura T . Microsatellite DNA markers for rice chromosomes. Theor Appl Genet. 2013; 93(7):1071-7. DOI: 10.1007/BF00230127. View

Nei M . Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973; 70(12):3321-3. PMC: 427228. DOI: 10.1073/pnas.70.12.3321. View

Senior M, Heun M . Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using a CT primer. Genome. 1993; 36(5):884-9. DOI: 10.1139/g93-116. View

Litt M, Luty J . A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene. Am J Hum Genet. 1989; 44(3):397-401. PMC: 1715430. View

Edwards K, Johnstone C, Thompson C . A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res. 1991; 19(6):1349. PMC: 333874. DOI: 10.1093/nar/19.6.1349. View

Wu K, Tanksley S . Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet. 1993; 241(1-2):225-35. DOI: 10.1007/BF00280220. View

Tautz D . Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res. 1989; 17(16):6463-71. PMC: 318341. DOI: 10.1093/nar/17.16.6463. View

Plaschke J, Ganal M, Roder M . Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet. 2013; 91(6-7):1001-7. DOI: 10.1007/BF00223912. View

Becker J, Heun M . Barley microsatellites: allele variation and mapping. Plant Mol Biol. 1995; 27(4):835-45. DOI: 10.1007/BF00020238. View

10.

Dib C, Faure S, Fizames C, Samson D, Drouot N, Vignal A . A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature. 1996; 380(6570):152-4. DOI: 10.1038/380152a0. View

11.

Akkaya M, Bhagwat A, Cregan P . Length polymorphisms of simple sequence repeat DNA in soybean. Genetics. 1992; 132(4):1131-9. PMC: 1205234. DOI: 10.1093/genetics/132.4.1131. View

12.

Roder M, Plaschke J, Konig S, Borner A, Sorrells M, Tanksley S . Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet. 1995; 246(3):327-33. DOI: 10.1007/BF00288605. View

13.

Akagi H, Nakamura A, Sawada R, Oka M, Fujimura T . Genetic diagnosis of cytoplasmic male sterile cybrid plants of rice. Theor Appl Genet. 2013; 90(7-8):948-51. DOI: 10.1007/BF00222907. View

14.

Yang G, Maroof M, Xu C, Zhang Q, Biyashev R . Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice. Mol Gen Genet. 1994; 245(2):187-94. DOI: 10.1007/BF00283266. View

15.

Weber J, May P . Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 1989; 44(3):388-96. PMC: 1715443. View

16.

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

17.

Wang Z, Weber J, Zhong G, Tanksley S . Survey of plant short tandem DNA repeats. Theor Appl Genet. 2013; 88(1):1-6. DOI: 10.1007/BF00222386. View