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Assessment of genetic diversity and relationships among Coix lacryma-jobi accessions using microsatellite markers

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Biologia Plantarum

Abstract

The present study describes the assessment of genetic diversity and relationships among 79 Job’s tears (Coix lacrymajobi L.) accessions collected from China and Korea using 17 microsatellite markers. A total of 57 alleles were detected with an average of 3.4 alleles per locus. A high frequency of rare alleles (36.3 %) was observed within the collection. Values for observed (HO), expected heterozygosity (HE) and Shannon’s information index (I) within the analysis ranged from 0.00 (GBssrJT183) to 0.81 (GBssrJT130), from 0.01 (GBssrJT170) to 0.65 (GBssrJT130) and from 0.034 (GBssrJt170) to 1.13 (GBssrJT130), respectively. The locus GBJT130 was the most informative marker with the highest values for observed and effective alleles as well as for HO, HE and I. Based on the UPGMA algorithm, the majority of the Chinese accessions grouped in one cluster, whereas all the Korean accessions grouped together in a separate cluster, indicating that Chinese accessions are genetically quite distinct from Korean accessions. No relation between genetic relatedness among Job’s tears accessions and their place of collection was observed. Chinese accessions exhibited greater within population polymorphism (P = 95 %, HE = 0.30, I = 0.52) than the accessions from Korea (P = 68 %, HE = 0.13, I =0.24), indicating their potentiality as a reservoir of novel alleles for crop improvement. However, in general the low diversity within each population indicates a narrow genetic base within our collection.

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Abbreviations

AFLP:

amplified fragment length polymorphism

PCR:

polymerase chain reaction

RAPD:

random amplification of polymorphic DNA

RFLP:

restriction fragment length polymorphism

SSRs:

simple sequence repeats

References

  • Arber, A.: The Gramineae. A Study of Cereal, Bamboo, and Grass. — Wheldon & Wesley, New York 1965.

    Google Scholar 

  • Boys, J., Cherry, M., Dayanandan, S.: Microsatellite analysis reveals genetically distinct populations of red pine (Pinus resinosa, Pinaceae). — Amer. J. Bot. 92: 833–841, 2005.

    Article  CAS  Google Scholar 

  • Budak, H., Pedraza, F., Cregan, P.B., Baenziger, P.S., Dweikat, I.: Development and utilization of SSRs to estimate the degree of genetic relationships in a collection of Pearl millet germplasm. — Crop Sci. 43: 2284–2290, 2003.

    Article  CAS  Google Scholar 

  • Coburn, J.R., Temnykh, S.V., Paul, E.M., McCouch, S.R.: Design and application of microsatellite marker panels for semi automated genotyping of rice (Oryza sativa L.). — Crop Sci. 42: 2092–2099, 2002.

    Article  CAS  Google Scholar 

  • Depeiges, A., Goubely, C., Lenoir, A., Cocherel, S., Picard, G., Raynal, M., Grellet, F., Delseny, M.: Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci. — Theor. appl. Genet. 91: 160–168, 1995.

    Article  CAS  Google Scholar 

  • Dice, L.R.: Measures of the amount of ecologic association between species. — Ecology 26: 297–302, 1945.

    Article  Google Scholar 

  • Dikshit, H.K., Jhang, T., Singh, N.K. Koundal, K.R., Bansal, K.C., Chandra, N., Tickoo, J.L., Sharma, T.R.: Genetic differentiation of Vigna species by RAPD, URP and SSR markers. — Biol. Plant. 51: 451–457, 2007.

    Article  CAS  Google Scholar 

  • Dje, Y., Heuertz, M., Lefebvre, C., Vekemans, X.: Assessment of genetic diversity within and among germplasm accessions in cultivated sorghum using microsatellite markers. — Theor. appl. Genet. 100: 918–925, 2000.

    Article  CAS  Google Scholar 

  • Gao, L.-Z.: Microsatellite variation within and among populations of Oryza officinalis (Poaceae), an endangered wild rice from China. — Mol. Ecol. 14: 4287–4297, 2005.

    Article  PubMed  CAS  Google Scholar 

  • Li, X., Huang, Y., Li, J., Corke, H.: Characterization of genetic variation and relationships among Coix germplasm accessions using RAPD markers. — Genet. Resour. Crop Evolut. 48: 189–194, 2001.

    Article  Google Scholar 

  • Lopes, M.S., Sefc, K.M., Eiras Dias, E., Steinkellner, H., Camara Machado, L.M., Camara Machado, A.: The use of microsatellites for germplasm management in a Portuguese grapevine collection. — Theor. appl. Genet. 99: 733–739, 1999.

    Article  Google Scholar 

  • Ma, K.H., Kim, K.H., Dixit, A., Yu, J.W., Chung, J.W., Lee, J.H., Cho, E.G., Kim, T.S., Park, Y.J.: Newly developed polymorphic microsatellite markers in Job’s tears (Coix lacryma-jobi L.). — Mol. Ecol. Notes 6: 689–691, 2006.

    Article  CAS  Google Scholar 

  • Matus, I.A., Hayes, P.M.: Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. — Genome 45: 1095–1106, 2002.

    Article  PubMed  CAS  Google Scholar 

  • Mohan, M., Nair, S., Krishna, T.G., Yano, M., Rhodes, I.: Genome mapping, molecular markers and marker-assisted selection in crop plants. — Mol. Breed. 3: 87–103, 1997.

    Article  CAS  Google Scholar 

  • Narasimhan, S., Padmesh, P., Nair, G.M.: Assessment of genetic diversity in Coscinium fenestratum. — Biol. Plant. 50: 111–113, 2006.

    Article  CAS  Google Scholar 

  • Orti, G., Pearse, D.E., Avise, J.C.: Phylogenetic assessment of length variation at a microsatellite locus. — Proc. nat. Acad. Sci. USA 94: 10745–10749, 1997.

    Article  PubMed  CAS  Google Scholar 

  • Pritchard, J.K., Stephens, M., Donnelly, P.: Inference of population genetic structure using multilocus genotype data. — Genetics 155: 945–959, 2000.

    PubMed  CAS  Google Scholar 

  • Pritchard, J.K., Wen, W.: Documentation for Structure Software, Ver. 2. — Department of Human Genetics, the University of Chicago, Chicago 2003.

    Google Scholar 

  • Qin, F., Li, J., Li, X., Corke, H.: AFLP and RFLP linkage map in Coix. — Genet. Resour. Crop Evolut. 52: 209–214, 2005.

    Article  Google Scholar 

  • Rohlf, F.J.: NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.0. — Exeter Publishing, Setauket — New York 1998.

    Google Scholar 

  • Roussel, V., Koenig, J., Beckert, M., Balfourier, F.: Molecular diversity in French bread wheat accessions related to temporal trends and breeding programs. — Theor. appl. Genet. 108: 920–930, 2004.

    Article  PubMed  CAS  Google Scholar 

  • Schuelke, M.: An economic method for the fluorescent labeling of PCR fragments. — Natur. Biotechnol. 18: 233–234, 2000.

    Article  CAS  Google Scholar 

  • Yeh, F.C., Yang, R.C., Boyle, T.J.B.: Popgene. Version 1.31. Microsoft Window-based Freeware for Population Genetic Analysis. — University of Alberta and Centre for International Forestry Research, Edmonton 1999.

    Google Scholar 

  • Yifru, T., Hammer, K., Huang, X.Q., Roder, M.S.: Regional patterns of microsatellite diversity in Ethiopian tetraploid wheat accessions. — Plant Breed. 125: 125–130, 2006.

    Article  CAS  Google Scholar 

  • Zhou, H.F., Xie, Z.W., Ge, S.: Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China. — Theor. appl. Genet. 107: 332–339, 2003.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

This study was supported by the BioGreen 21 project (#20080401034058) of the Rural Development Administration (RDA), Republic of Korea.

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Authors and Affiliations

  1. National Agrobiodiversity Center, National Academy of Agricultural Science, Suwon, 441-707, Republic of Korea

    K. -H. Ma, A. Dixit, J. -G. Gwag & T. -S. Kim

  2. College of Life and Environmental Sciences, Konkuk University, Hwa-Yang Dong, Seoul, 143-701, Republic of Korea

    K. -H. Ma, K. -H. Kim & I. -M. Chung

  3. Basmati Export Development Foundation, Roorkee Road, Meerut, 250110, UP, India

    A. Dixit

  4. Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea

    Y. -J. Park

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  1. K. -H. Ma
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  2. K. -H. Kim
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  3. A. Dixit
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  4. I. -M. Chung
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  5. J. -G. Gwag
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  6. T. -S. Kim
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Correspondence to Y. -J. Park.

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Ma, K.H., Kim, K.H., Dixit, A. et al. Assessment of genetic diversity and relationships among Coix lacryma-jobi accessions using microsatellite markers. Biol Plant 54, 272–278 (2010). https://doi.org/10.1007/s10535-010-0047-6

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  • DOI: https://doi.org/10.1007/s10535-010-0047-6

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