Banner
Current IssueEditorial BoardOnline First ArticlesArchive
Current IssueEditorial BoardOnline First ArticlesArchive

volume 35 issue 4 (december 2012) : 285 - 293

GENETIC DIVERSITY ASSESSMENT IN CHICKPEA GENOTYPES USING STMS

K
K.P. Suthar
R
R. Bhatnagar
Y
Y.M. Shukla*
V
V.P. Suthar
S
S.D. Kadam
N
N.J. Patel
1B. A. College of Agriculture, Anand Agricultural University, Anand- 388 110, India

  • Submitted|

  • First Online |

  • doi

Cite article:- Suthar K.P., Bhatnagar R., Shukla* Y.M., Suthar V.P., Kadam S.D., Patel N.J. (2025). GENETIC DIVERSITY ASSESSMENT IN CHICKPEA GENOTYPES USING STMS. Legume Research. 35(4): 285 - 293. doi: .

ABSTRACT

Sequence Tagged Microsatellite Markers (STMS) were employed to assess the genetic diversity in chickpea (Cicer arietinum L.), the third most important grain legume crop in the world. STMS analysis with eleven microsatellites markers of 24 chickpea genotypes amplified total 49 alleles. The average numbers of alleles per locus was 4.45, whereas effective numbers of alleles was 3.23. The eleven primer pairs amplified single loci producing a minimum of 3 (NCPGR51) and maximum of 6 (NCPGR41, NCPGR90) alleles. The mean Polymorphic Information Content (PIC) value from all tested microsatellite was 0.68. Highest PIC value (0.77) was observed for two primers viz. NCPGR21 and NCPGR90 but the primer NCPGR90 showed highest Shannon’s information index (1.61), hence it was found more informative. The Unweighted Pair Group Method with Arithmetic Averages (UPGMA) based dendrogram showed two major clusters and distinguished all the genotypes. The highest genetic diversity was observed between KAK-2 and Dahod Yellow. The microsatellites could successfully detect intraspecific genetic diversity in chickpea. The divergent genotypes may be further used in breeding programmes.

REFERENCES

  1. Abbo S., Berger, J. and Turner N.C. (2003) Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct Plant Biol., 30: 1081-1087.
  2. Agrawal,P. K. and Srivastava A. (2010) Assessment of genetic diversity among chickpea cultivars of India using RAPD markers. Indian J Genet Plant Breed., 70 : 320-332.
  3. Ahmad F. and Slinkard A. E. (1992) Genetic relationships in the genus Cicer L. as revealed by polyacrylamide gel electrophoresis of seed storage proteins. Theor Appl Genet., 84: 688–692.
  4. Akkaya, M.S., Bhagwat A. A. and Cregan P. B. (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics, 132: 1131–1139.
  5. Bharadwaj, C., Chauhan, S.K., Rajguru, G., Srivastava, R., Satyavathi, C.T., Yadav, S., Rizvi, A.H., Kumar, J. and
  6. Solank, R.K. (2010) Diversity analysis of chickpea (Cicer arietinum) cultivars using STMS markers. Indian J Agric Sci., 80 : 947–51.
  7. Choudhary, M.A., Vandenberg, V. and Warkentin, T. (2002) Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea (Cicer arietinum L.). Euphytica., 127:317–325.
  8. Choudhary, S., Sethy, N.K., Shokeen, B. and Bhatia, S. (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes., 6: 93–95.
  9. Collard, B.C.Y., Pang, E.C.K., Ades, P. K. and Taylor, P. W.J. (2003) Preliminary investigation of QTL associated with seedling resistance to Ascochyta blight from Cicer echinospermum, a wild relative of chickpea. Theor Appl Genet., 107: 719–729.
  10. Croser, J.S., Ahmad, F., Clarke, H.J. and Siddique, K.H.M. (2003) Utilisation of wild Cicer in chickpea improvement— progress, constraints and prospects. Aust J Agri Res., 54: 429–444.
  11. Fakrudin, B., Shashidhar, H.E., Kulkarni, R.S. and Hittalmani, S. (2004) Genetic diversity assessment of finger millet, Eleusine coracana (Gaertn.) germplasm through RAPD analysis. PGR News lett. 138: 50-54.
  12. FAO (2010) http:z/faostat.fao.org/faostat/collections?subset=agriculture. Last updated February 2010.
  13. Flandez-Galvez, H., Ford, R., Pang, E.C. and Taylor, P.W. (2003) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theor Appl. Genet., 106: 1447–1456.
  14. Gemechu, K., Endashaw, B., Muhammad, I., Kifle, D., Emana, G., and Fassil, A., (2012) Genetic diversity and population structure of ethiopian chickpea (Cicer arietinum L.) germplasm accessions from different geographical origins as revealed by microsatellite markers. Plant Mol Biol Rep., 30 : 654-665.
  15. Gupta, P.K. and Varshney, R.K. (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.
  16. Gupta, S., Chakraborti, D., Sengupta, A., Basu, D. and Das, S. (2011) Primary metabolism of chickpea is the initial target of wound inducing early sensed Fusarium oxysporum f. sp. ciceri Race I, Plos one. 5 (2): e9030-37. DOI:10.1371/ journal.pone.0009030.
  17. Huttel, B., Winter, P., Weising, K., Choumane, W., Weigand, F. and Kahl, G. (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome, 42: 210–217.
  18. Innan, H., Terauchi, R. and Miyashita, N.T. (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics, 146: 1441–1452.
  19. Lichtenzveig, J., Scheuring, C., Dodge, J., Abbo, S. and Zhang, H.B. (2005) 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., 110: 492–510.
  20. Mahmood, Z., Athar, M., Khan, M.A., Ali, M., Saima, S. and Dasti, A.A. (2011) Analysis of genetic diversity in chickpea (Cicer arietinum L.) cultivars using Random Amplified Polymorphic DNA (RAPD) markers. Afr J Biotechnol., 10(2): 140-145.
  21. Rao, L.S., UshaRani, P., Deshmukh, P.S., Kumar, P.A. and Panguluri, S.K. (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genet Resour Crop Evol., 54: 1235–1244.
  22. Rogers, S.O. and Bendich, A.J. (1988) Extraction of DNA from plant tissues. Plant Mol Boil Man., A6: 1-10.
  23. Rohf, F.J., (2004) NTSYS-pc Numerical Taxonomy and Multivariant Analysis System version 2.02, Exeter software, Applied biostatics, New York.
  24. Sant, V.J., Patankar, A.G., Sarode, N.D., Mhase, L.B., Sainani, M.N., Deshmukh, R.B., Ranjekar, P.K. and Gupta, V.S. (1999) Potential of DNA markers in detecting divergence and in analysing heterosis in Indian elite chickpea cultivars. Theor Appl Genet., 98: 1217-1225.
  25. Sethy, N.K., Shokeen, B. and Bhatia, S. (2003) Isolation and characterization of sequence tagged-microsatellite markers in chickpea (Cicer arietinum L.). Mol Ecol Notes., 3: 428–430.
  26. Sethy, N.K., Shokeen, B., Edwards, K.J. and Bhatia, S. (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.) Theor Appl Genet., 112: 1416–1428.
  27. Sharma, P.C., Huttel, B., Winter, P., Kahl, G., Gardner, R.C. and Weising, K. (1995) The potential of microsatellites for hybridization and polymerase chain reaction-based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species. Electrophoresis., 16: 1755–1761.
  28. Singh, R., Kumar, R. and Kumari, N. (2012) Genetic diversity analysis of chickpea using STMS marker. Progressive Agriculture., 12(1): 35-45.
  29. Staub, J.E. and Crubaugh, L. (1995) Selection for multiple lateral determinate cucumber genotypes. Cucurbit Gen Coop Rep., 18: 5-6.
  30. Sudupak, M.A., Akkaya, M.S. and Kence, A. (2002) Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers. Theor Appl Genet., 105: 1220–1228.
  31. Talebi, R., Naji, A.M. and Fayaz, F. (2008) Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism. Plant Soil Environ., 54: 447- 452.
  32. Tara Satyavathi, C., Bhat, K.V., Bharadwaj, C., Tiwari, S.P. and Chaudhary, V. (2005). AFLP based DNA profiling and genetic diversity assessment of Indian soybean [Glycine max (L.) Merrill] varieties. Genet Resour Crop Ev., 53: 1069–79.
  33. Tayyar, R.I. and Wainess, J.G. (1996) Genetic relationships among annual species of Cicer (Fabaceae) using isozyme variation. Theor Appl Genet., 92: 245-254.
  34. Udupa, S.M. and Baum, M. (2001) High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Mol Gen Genom., 265: 1097–1103.
  35. Udupa, S.M., Sharma, A., Sharma, R.P. and Pai, R.A. (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J Plant Biochem Biotech., 2: 83–86.
  36. Winter, P. and Kahl, G. (1995) Molecular marker technologies for plant improvement. World J Microbiol Biotechnol., 11: 438–448.
  37. Winter, P., Pfaff, T., Udupa, S.M., Huttel, B, Sharma, PC, Sahi, S, Arreguin-Espinoza, R, Weigand, F, Muehlbauer, F.J. and Kahl, G. (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet., 262: 90–101.
  38. Yeh, F.C. and Boyle, T.J.B. (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belgian J Bot., 129:157-162.
Published In
Legume Research
Article Metrics
Metrics Icon
0
Views
0
Citations
Reviewed By
Share Article
Download Article
In this Article
    Contact us
    Follow us

    volume 35 issue 4 (december 2012) : 285 - 293

    GENETIC DIVERSITY ASSESSMENT IN CHICKPEA GENOTYPES USING STMS

    K
    K.P. Suthar
    R
    R. Bhatnagar
    Y
    Y.M. Shukla*
    V
    V.P. Suthar
    S
    S.D. Kadam
    N
    N.J. Patel
    1B. A. College of Agriculture, Anand Agricultural University, Anand- 388 110, India

    • Submitted|

    • First Online |

    • doi

    Cite article:- Suthar K.P., Bhatnagar R., Shukla* Y.M., Suthar V.P., Kadam S.D., Patel N.J. (2025). GENETIC DIVERSITY ASSESSMENT IN CHICKPEA GENOTYPES USING STMS. Legume Research. 35(4): 285 - 293. doi: .

    ABSTRACT

    Sequence Tagged Microsatellite Markers (STMS) were employed to assess the genetic diversity in chickpea (Cicer arietinum L.), the third most important grain legume crop in the world. STMS analysis with eleven microsatellites markers of 24 chickpea genotypes amplified total 49 alleles. The average numbers of alleles per locus was 4.45, whereas effective numbers of alleles was 3.23. The eleven primer pairs amplified single loci producing a minimum of 3 (NCPGR51) and maximum of 6 (NCPGR41, NCPGR90) alleles. The mean Polymorphic Information Content (PIC) value from all tested microsatellite was 0.68. Highest PIC value (0.77) was observed for two primers viz. NCPGR21 and NCPGR90 but the primer NCPGR90 showed highest Shannon’s information index (1.61), hence it was found more informative. The Unweighted Pair Group Method with Arithmetic Averages (UPGMA) based dendrogram showed two major clusters and distinguished all the genotypes. The highest genetic diversity was observed between KAK-2 and Dahod Yellow. The microsatellites could successfully detect intraspecific genetic diversity in chickpea. The divergent genotypes may be further used in breeding programmes.

    REFERENCES

    1. Abbo S., Berger, J. and Turner N.C. (2003) Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct Plant Biol., 30: 1081-1087.
    2. Agrawal,P. K. and Srivastava A. (2010) Assessment of genetic diversity among chickpea cultivars of India using RAPD markers. Indian J Genet Plant Breed., 70 : 320-332.
    3. Ahmad F. and Slinkard A. E. (1992) Genetic relationships in the genus Cicer L. as revealed by polyacrylamide gel electrophoresis of seed storage proteins. Theor Appl Genet., 84: 688–692.
    4. Akkaya, M.S., Bhagwat A. A. and Cregan P. B. (1992) Length polymorphisms of simple sequence repeat DNA in soybean. Genetics, 132: 1131–1139.
    5. Bharadwaj, C., Chauhan, S.K., Rajguru, G., Srivastava, R., Satyavathi, C.T., Yadav, S., Rizvi, A.H., Kumar, J. and
    6. Solank, R.K. (2010) Diversity analysis of chickpea (Cicer arietinum) cultivars using STMS markers. Indian J Agric Sci., 80 : 947–51.
    7. Choudhary, M.A., Vandenberg, V. and Warkentin, T. (2002) Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea (Cicer arietinum L.). Euphytica., 127:317–325.
    8. Choudhary, S., Sethy, N.K., Shokeen, B. and Bhatia, S. (2006) Development of sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Mol Ecol Notes., 6: 93–95.
    9. Collard, B.C.Y., Pang, E.C.K., Ades, P. K. and Taylor, P. W.J. (2003) Preliminary investigation of QTL associated with seedling resistance to Ascochyta blight from Cicer echinospermum, a wild relative of chickpea. Theor Appl Genet., 107: 719–729.
    10. Croser, J.S., Ahmad, F., Clarke, H.J. and Siddique, K.H.M. (2003) Utilisation of wild Cicer in chickpea improvement— progress, constraints and prospects. Aust J Agri Res., 54: 429–444.
    11. Fakrudin, B., Shashidhar, H.E., Kulkarni, R.S. and Hittalmani, S. (2004) Genetic diversity assessment of finger millet, Eleusine coracana (Gaertn.) germplasm through RAPD analysis. PGR News lett. 138: 50-54.
    12. FAO (2010) http:z/faostat.fao.org/faostat/collections?subset=agriculture. Last updated February 2010.
    13. Flandez-Galvez, H., Ford, R., Pang, E.C. and Taylor, P.W. (2003) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite site and resistance gene analog markers. Theor Appl. Genet., 106: 1447–1456.
    14. Gemechu, K., Endashaw, B., Muhammad, I., Kifle, D., Emana, G., and Fassil, A., (2012) Genetic diversity and population structure of ethiopian chickpea (Cicer arietinum L.) germplasm accessions from different geographical origins as revealed by microsatellite markers. Plant Mol Biol Rep., 30 : 654-665.
    15. Gupta, P.K. and Varshney, R.K. (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163–185.
    16. Gupta, S., Chakraborti, D., Sengupta, A., Basu, D. and Das, S. (2011) Primary metabolism of chickpea is the initial target of wound inducing early sensed Fusarium oxysporum f. sp. ciceri Race I, Plos one. 5 (2): e9030-37. DOI:10.1371/ journal.pone.0009030.
    17. Huttel, B., Winter, P., Weising, K., Choumane, W., Weigand, F. and Kahl, G. (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome, 42: 210–217.
    18. Innan, H., Terauchi, R. and Miyashita, N.T. (1997) Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics, 146: 1441–1452.
    19. Lichtenzveig, J., Scheuring, C., Dodge, J., Abbo, S. and Zhang, H.B. (2005) 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., 110: 492–510.
    20. Mahmood, Z., Athar, M., Khan, M.A., Ali, M., Saima, S. and Dasti, A.A. (2011) Analysis of genetic diversity in chickpea (Cicer arietinum L.) cultivars using Random Amplified Polymorphic DNA (RAPD) markers. Afr J Biotechnol., 10(2): 140-145.
    21. Rao, L.S., UshaRani, P., Deshmukh, P.S., Kumar, P.A. and Panguluri, S.K. (2007) RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky. Genet Resour Crop Evol., 54: 1235–1244.
    22. Rogers, S.O. and Bendich, A.J. (1988) Extraction of DNA from plant tissues. Plant Mol Boil Man., A6: 1-10.
    23. Rohf, F.J., (2004) NTSYS-pc Numerical Taxonomy and Multivariant Analysis System version 2.02, Exeter software, Applied biostatics, New York.
    24. Sant, V.J., Patankar, A.G., Sarode, N.D., Mhase, L.B., Sainani, M.N., Deshmukh, R.B., Ranjekar, P.K. and Gupta, V.S. (1999) Potential of DNA markers in detecting divergence and in analysing heterosis in Indian elite chickpea cultivars. Theor Appl Genet., 98: 1217-1225.
    25. Sethy, N.K., Shokeen, B. and Bhatia, S. (2003) Isolation and characterization of sequence tagged-microsatellite markers in chickpea (Cicer arietinum L.). Mol Ecol Notes., 3: 428–430.
    26. Sethy, N.K., Shokeen, B., Edwards, K.J. and Bhatia, S. (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.) Theor Appl Genet., 112: 1416–1428.
    27. Sharma, P.C., Huttel, B., Winter, P., Kahl, G., Gardner, R.C. and Weising, K. (1995) The potential of microsatellites for hybridization and polymerase chain reaction-based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species. Electrophoresis., 16: 1755–1761.
    28. Singh, R., Kumar, R. and Kumari, N. (2012) Genetic diversity analysis of chickpea using STMS marker. Progressive Agriculture., 12(1): 35-45.
    29. Staub, J.E. and Crubaugh, L. (1995) Selection for multiple lateral determinate cucumber genotypes. Cucurbit Gen Coop Rep., 18: 5-6.
    30. Sudupak, M.A., Akkaya, M.S. and Kence, A. (2002) Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers. Theor Appl Genet., 105: 1220–1228.
    31. Talebi, R., Naji, A.M. and Fayaz, F. (2008) Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism. Plant Soil Environ., 54: 447- 452.
    32. Tara Satyavathi, C., Bhat, K.V., Bharadwaj, C., Tiwari, S.P. and Chaudhary, V. (2005). AFLP based DNA profiling and genetic diversity assessment of Indian soybean [Glycine max (L.) Merrill] varieties. Genet Resour Crop Ev., 53: 1069–79.
    33. Tayyar, R.I. and Wainess, J.G. (1996) Genetic relationships among annual species of Cicer (Fabaceae) using isozyme variation. Theor Appl Genet., 92: 245-254.
    34. Udupa, S.M. and Baum, M. (2001) High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Mol Gen Genom., 265: 1097–1103.
    35. Udupa, S.M., Sharma, A., Sharma, R.P. and Pai, R.A. (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J Plant Biochem Biotech., 2: 83–86.
    36. Winter, P. and Kahl, G. (1995) Molecular marker technologies for plant improvement. World J Microbiol Biotechnol., 11: 438–448.
    37. Winter, P., Pfaff, T., Udupa, S.M., Huttel, B, Sharma, PC, Sahi, S, Arreguin-Espinoza, R, Weigand, F, Muehlbauer, F.J. and Kahl, G. (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet., 262: 90–101.
    38. Yeh, F.C. and Boyle, T.J.B. (1997) Population genetic analysis of codominant and dominant markers and quantitative traits. Belgian J Bot., 129:157-162.
    In this Article
      Contact us
      Follow us
      Published In
      Legume Research

      Editorial Board

      View all (0)