Development of Microsatellite Markers and Analysis of Intraspecific Genetic Variability in Chickpea (Cicer Arietinum L.)

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2006 Mar 15

PMID 16534564

Citations 40

Authors

Niroj Kumar Sethy

Bhumika Shokeen

Keith J Edwards

Sabhyata Bhatia

Affiliations

Soon will be listed here.

Abstract

Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08-0.91) and 0.74 (0.23-0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution.

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References

Kruglyak S, Durrett R, Schug M, Aquadro C . Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proc Natl Acad Sci U S A. 1998; 95(18):10774-8. PMC: 27971. DOI: 10.1073/pnas.95.18.10774. View

Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang H . Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet. 2005; 110(3):492-510. DOI: 10.1007/s00122-004-1857-8. View

Amos W, Sawcer S, Feakes R, Rubinsztein D . Microsatellites show mutational bias and heterozygote instability. Nat Genet. 1996; 13(4):390-1. DOI: 10.1038/ng0896-390. View

Richards R, Sutherland G . Simple repeat DNA is not replicated simply. Nat Genet. 1994; 6(2):114-6. DOI: 10.1038/ng0294-114. View

Udupa S, Baum M . High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Mol Genet Genomics. 2001; 265(6):1097-103. DOI: 10.1007/s004380100508. View

Sibly R, Meade A, Boxall N, Wilkinson M, Corne D, Whittaker J . The structure of interrupted human AC microsatellites. Mol Biol Evol. 2003; 20(3):453-9. DOI: 10.1093/molbev/msg056. View

Ahmad F, Gaur P, Slinkard A . Isozyme polymorphism and phylogenetic interpretations in the genus Cicer L. Theor Appl Genet. 2013; 83(5):620-7. DOI: 10.1007/BF00226907. View

Schlotterer C . Evolutionary dynamics of microsatellite DNA. Chromosoma. 2000; 109(6):365-71. DOI: 10.1007/s004120000089. View

Zhu Y, Queller D, Strassmann J . A phylogenetic perspective on sequence evolution in microsatellite loci. J Mol Evol. 2000; 50(4):324-38. DOI: 10.1007/s002399910036. View

10.

Winter P, Kahl G . Molecular marker technologies for plant improvement. World J Microbiol Biotechnol. 2014; 11(4):438-48. DOI: 10.1007/BF00364619. View

11.

Udupa S, Robertson L, Weigand F, Baum M, Kahl G . Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet. 1999; 261(2):354-63. DOI: 10.1007/s004380050976. View

12.

Jin L, Macaubas C, Hallmayer J, Kimura A, Mignot E . Mutation rate varies among alleles at a microsatellite locus: phylogenetic evidence. Proc Natl Acad Sci U S A. 1996; 93(26):15285-8. PMC: 26396. DOI: 10.1073/pnas.93.26.15285. View

13.

Winter P, Pfaff T, Udupa S, Huttel B, Sharma P, Sahi S . Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet. 1999; 262(1):90-101. DOI: 10.1007/s004380051063. View

14.

Matsuoka Y, Mitchell S, Kresovich S, Goodman M, Doebley J . Microsatellites in Zea - variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet. 2003; 104(2-3):436-450. DOI: 10.1007/s001220100694. View

15.

Messier W, Li S, Stewart C . The birth of microsatellites. Nature. 1996; 381(6582):483. DOI: 10.1038/381483a0. View

16.

Symonds V, Lloyd A . An analysis of microsatellite loci in Arabidopsis thaliana: mutational dynamics and application. Genetics. 2003; 165(3):1475-88. PMC: 1462854. DOI: 10.1093/genetics/165.3.1475. View

17.

Harr B, Schlotterer C . Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation. Genetics. 2000; 155(3):1213-20. PMC: 1461152. DOI: 10.1093/genetics/155.3.1213. View

18.

Abbo S, Shtienberg D, Lichtenzveig J, Lev-Yadun S, Gopher A . The chickpea, summer cropping, and a new model for pulse domestication in the ancient near east. Q Rev Biol. 2004; 78(4):435-48. DOI: 10.1086/378927. View

19.

Iruela M, Rubio J, Cubero J, Gil J, Millan T . Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theor Appl Genet. 2003; 104(4):643-651. DOI: 10.1007/s001220100751. View

20.

Riaz S, Dangl G, Edwards K, Meredith C . A microsatellite marker based framework linkage map of Vitis vinifera L. Theor Appl Genet. 2003; 108(5):864-72. DOI: 10.1007/s00122-003-1488-5. View