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Identification of Highly Polymorphic Molecular Markers and Potential Genotypes for Harnessing Chickpea Breeding Strategies

DOI: 10.18805/LR-4379    | Article Id: LR-4379 | Page : 804-814
Citation :- Identification of Highly Polymorphic Molecular Markers and Potential Genotypes for Harnessing Chickpea Breeding Strategies.Legume Research.2022.(45):804-814
Ashwani Kumar, Ashwani Yadav, Renu Yadav, J.P. Misra, R.S. Yadav, H.D. Upadhyaya, Rajendra Kumar rajendrak64@yahoo.co.in
Address : Department of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut-250110, Uttar Pardesh, India.
Submitted Date : 26-03-2020
Accepted Date : 14-08-2020

Abstract

Background: STMS markers and morphological traits were used to investigate the genetic relationship and allelic diversity in chickpea. In this study, we focused on the selection and more efficient utilization of core germplasm in breeding programs for chickpea crop improvement using STMS and quantitative / morphological traits. 
Methods: Seeds of elite accessions of chickpea were obtained from ICRISAT, Patancheru, Andhra Pradesh, India. 50 STMS markers and 11 quantitative traits were used for exploring the genetic variability and relationship in 35 chickpea accessions. 
Result: A total of 97 alleles were produced out of the 32 polymorphic STMS loci with an average of 3.03 alleles per locus ranging between 2-6 alleles per primer. The PIC value ranged from 0.029 to 0.768 with an average of 0.502. PIC value showed a highly positive correlation (r = 0.718) with number of alleles at the STMS loci. In both molecular and morphological markers / traits-based clustering, out of 35 chickpea accessions only one accession ICC-13892 was isolated at the end of clustering. The results indicated that highly polymorphic microsatellite markers NCPGR 68, NCPGR 50, NCPGR 81, NCPGR 48 and NCPGR 77 along with the accessions ICC-13892 having distant associations with ICC-13816, ICC-15697, ICC-15610, ICC-15868, ICC-15888, ICC-15996 with novel findings should be useful resources for strategies of allele mining, association genetics, mapping and cloning of gene(s) and in applied breeding to broaden the genetic base of chickpea.

Keywords

Allelic diversity Cicer arietinum L. DNA fingerprinting Genetic diversity Polymorphic information content STMS

References

  1. Abe, J., Xu, D.H., Suzuki, Y., Kanazawa, A. and Shimamoto, Y. (2003). Soybean germplasm pools in Asia revealed by nuclear SSRs. Theoretical Applied Genetics. 106: 445-453.
  2. Amurrio, J.M., de Ron, A.M. and Zeven, A.C. (1995). Numerical taxonomy of Iberian pea landraces based on quantitative and qualitative characters. Euphytica. 82: 195-205.
  3. Bhardwaj, J., Kumari, N., Ford, R., Yadav, R., Choi, I. and Kumar, R. (2014). Insilico development and validation of EST derived new SSR markers for drought tolerance in Cicer arietinum L. Indian Journal of Genetics and Plant Breeding. 74(2): 254-256.
  4. Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980). Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics. 32: 314-331.
  5. Bruford, M.W. and Wayne, R.K. (1993). Microsatellites and their application to population genetic studies. Current Opinion in Genetics and Development. 3: 939-943.
  6. Chaudhary, P., Khanna, S.M., Jain, P.K., Bharadwaj, C., Kumar, J., Lakhera, P.C. and Srinivasan, R. (2012). Genetic structure and diversity analysis of the primary gene pool of chickpea using SSR markers. Genetics and Molecular Research. 11(2): 891-905.
  7. Choumane, W., Winter, P., Weigand, F. and Kahl, G. (2000). Conservation and variability of sequence-tagged microsatellite sites (STMS) from chickpea (Cicer arietinum L.) within the genus Cicer. Theoretical Applied Genetics. 101: 269-278.
  8. Doyle, J.J. and Doyle, J.L. (1990). Isolation of plant DNA from fresh tissue. Focus. 12: 13-15.
  9. Federer, T.W. (1956). Augmented (or Hoonuiaku) designs. The Hawaiian Planters’ Record, vol. IV, second issue, pp 191-208.
  10. Gaur, P.M., Jukanti, A.K. and Varshney, R.K. (2012). Impact of genomic technologies on chickpea breeding strategies. Agronomy. 2: 199-221.
  11. Ghaffari, P., Talebi, R. and Keshavarzi, F. (2014). Genetic diversity and geographical differentiation of Iranian landrace, cultivars and exotic chickpea lines as revealed by morphological and microsatellite markers. Physiology and Molecular Biology of Plants. 20(2): 225-233.
  12. Ghafoor, A., Sharif, A., Ahmad, Z., Zahid, M.A. and Rabbani, M.A. (2001). Genetic diversity in Blackgram [Vigna mungo (L.) Hepper]. Field Crops Research. 69: 183-190.
  13. Gil, J., Nadal, S., Luna, D., Moreno, M.T. and Haro, A. (1996). Variability of some physico-chemical characters in Desi and Kabuli chickpea types. Journal of the Science of Food and Agriculture. 71: 179-184. 
  14. He, C., Poysa, V. and Yu, K. (2003). Development and characterization of simple sequence repeat (SSR) markers and their use in determining relationships among Lycopersicon esculentum cultivars. Theoretical Applied Genetics. 106: 363-373.
  15. Hüttel, B., Winter, P., Weising, K., Choumane, W., Weigand, F. and Kahl, G. (1999). Sequence tagged microsatellite markers for chickpea (Cicer arietinum L.). Genome. 42: 210-217.
  16. Iruela, M., Rubio, J., Cubero, J.I., Gil, J. and Millan, T. (2002). Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theoretical Applied Genetics. 104: 643-651.
  17. Katoch, Omika, Chauhan, U.S., Yadav, Renu, Yadav, S.S., Kumar, Ashwani, Yadav, Ashwani, Yadav, Neelam, Upadhyaya, Hari D. and Kumar, Rajendra (2016). Nitrate Reductase based phylogenetic analysis in chickpea. Research Journal of Chemistry and Environment. 20(7): 1-8.
  18. Kumar, Ashwani, Yadav, R. S. and Kumar, Rajendra (2014). Assessment of variability and relationship among some quantitative traits in elite accessions of chickpea (cicer arietinum l.), Progressive Agriculture. 14(1): 63-68.
  19. Kumar, Ashwani, Yadav, R.S. and Kumar, R. (2013). Estimation of genetic parameters and correlation between morphological traits in selected chickpea (Cicer arietinum L.) accessions. Plant Archives. 13(2): 719-723.
  20. Kumar, Rajendra, Yadav, Renu, Soi, Sangeeta, Srinivasan, Yadav, S.S., Yadav, Ashwani, Mishra, J.P., Mittal, Neha, Yadav, Neelam, Kumar, Ashwani, Vaishali, Yadav, Hemant and Upadhyaya, Hari D. (2017). Morpho-molecular charac- terization of landraces/wild genotypes of Cicer for Biotic/ Abiotic stresses. Legume Research-An International Journal. 40(6): 974-984.
  21. Lichtenzveig, J., Scheuring, C., Dodge, J., Abbo, S. and Zhang, H. (2005). Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, (Cicer arietinum L.) Theoretical Applied Genetics. 110: 492-510.
  22. Monika, A., Joshi, Divya Aggarwal and Sanyal, Archana (2018). Cultivar identification and diversity analysis based on morphological descriptors and image analysis in chickpea (Cicer arietinum L.). Legume Research-An International Journal. 41(5): 647-655.
  23. 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.
  24. Naghavi, M.R. and Jahansouz, M.R. (2005). Variation in the agronomic and morphological traits of Iranian chickpea accessions. Journal of Integrative Plant Biology. 47(3): 375-379.
  25. Nkoana, D.K., Gerrano, Abe Shegro and Gwata, E.T. (2019). Agronomic performance and genetic variability of cowpea (Vigna unguiculata) Accessions. Legume Research-An International Journal. 42(6): 757-762.
  26. O’Neill, R., Snowdon, R.J. and Kohler, W. (2003). Population genetics aspects of biodiversity. Progress in Botany. 64: 115-137.
  27. Perry, M.C. and McIntosh, M.S. (1991). Geographical patterns of variation in the USDA soybean germplasm collections. I. Morphological traits. Crop Science. 31: 1350-1355.
  28. Rashmi, Singh, R.K., Vaishali and Kumar, R. (2012). Molecular Diversity Analysis of Selected Drought Resistant Chickpea (Cicer arietinum L) Genotypes. Vegetos, 25(1): 111-116.
  29. Rizvi, H., Babu, B.K. and Agrawal, P.K. (2014). Molecular analysis of kabuli and desi types of Indian chickpea (Cicer arietinum L.) cultivars using STMS markers. Journal of Plant Biochemistry and Biotechnology. 23: 52-60. 
  30. Rohlf, F.J. (1993). NTSYS-pc Numerical Taxonomy and Multivariate Analysis System, Version 2.2, Applied Biostatistics Inc., New York.
  31. Saini, N., Jain, N., Jain, S. and Jain, R.K. (2004). Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP, ISSR and SSR markers. Euphytica. 140: 133-146.
  32. Senior, M.L., Murphy, J.P., Goodman, M.M. and Stuber, C.W. (1998). Utility of SSRs for Determining Genetic Similarities and Relationships in Maize Using an Agarose Gel System. Crop Science. 38: 1088-1098.
  33. Sethy, N.K., Shokeen, B. and Bhatia, S. (2003). Isolation and characterization of sequence tagged microsatellite sites markers in chickpea (Cicer arietinum L.). Molecular Ecology Notes. 3: 428-430.
  34. 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.). Theoretical Applied Genetics. 112: 1416-1428.
  35. Singh, R., Kumari, N., Upadhyaya, H.D., Yadav, R., Vaishali, Chosi Insoo and Kumar, R. (2013). Molecular analysis for genetic structure of biotic and abiotic stress resistant genotypes in chickpea (Cicer arietinum L.). Indian Journal of Biotechnology. 12(4): 537-540.
  36. Singh, R., Singhal, V. and Randhawa, G.J. (2008). Molecular analysis of chickpea (Cicer arietinum L.) cultivars using AFLP and STMS markers. Journal of Plant Biochemistry and Biotechnology. 17: 167-171.
  37. Singh, Rashmi, Singh, Rajesh Kumar, Vaishali and Kumar, Rajendra (2012). Molecular Diversity Analysis of Selected Drought Resistant Chickpea (Cicer arietinum L) Genotypes. Vegetos. 25(1): 111-116.
  38. Singh, Reema, Kumar, Rajendra and Kumari, Nilima (2012). Genetic diversity analysis of chickpeas using STMS markers. Progressive Agriculture. 12(1): 35-40.
  39. Singh, Reema, Kumari, Nilima and Kumar, Rajendra (2011). HPLC based determination of oligosaccharides and diversity analysis in Chickpea (Cicer arietinum L.). Plant Archives. 11(1): 543-551.
  40. Smith, S.E., Guarino, L., Al Doss, A. and Conta, D.M. (1995). Morphological and agronomic affinities among Middle Eastern alfalfas accessions from Oman and Yemen. Crop Science. 35: 1118-1194.
  41. Soi, Sangita, Chauhan, U.S., Yadav, Renu, Kumar, J., Yadav, S.S., Yadav, Hemant and Kumar, Rajendra (2014). STMS based diversity analysis in chickpea (Cicer arietinum L.). New Agriculturist. 25(2): 243-250.
  42. Sultana, T., Ghafoor, A. and Ashraf, M. (2006). Geographic patterns of diversity of cultivated lentil germplasm collected from Pakistan, as assessed by seed protein assays. Acta Biologica Cracoviensia, Series Botanica, Poland. 48(1): 77-84.
  43. Vishnu, B., Jayalakshmi, V. and Sudha Rani, M. (2020). Genetic diversity studies among chickpea (Cicer arietinum L.) genotypes under rainfed and irrigated conditions for yield attributing and traits related to mechanical harvesting. Legume Research-An International Journal. 43(2): 190-194.
  44. Winter, P., Pfaff, T., Udupa, S.M., Hüttel, B., Sharma, P.C., 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. Molecular and General Genetics. 262: 90-101.

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