Indian Journal of Agricultural Research

  • Chief EditorV. Geethalakshmi

  • Print ISSN 0367-8245

  • Online ISSN 0976-058X

  • NAAS Rating 5.60

  • SJR 0.293

Frequency :
Bi-monthly (February, April, June, August, October and December)
Indexing Services :
BIOSIS Preview, ISI Citation Index, Biological Abstracts, Elsevier (Scopus and Embase), AGRICOLA, Google Scholar, CrossRef, CAB Abstracting Journals, Chemical Abstracts, Indian Science Abstracts, EBSCO Indexing Services, Index Copernicus
Submit

Research Article

Indian Journal of Agricultural Research, volume 54 issue 2 (april 2020) : 129-138

Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

Bouri Amina, Mediouni Mohammed Rida, Ameur Ameur Abdelkader, Udupa Sripada, Gaouar Souheil Bechir Semir
1Laboratory of Physiology, Physiopathology and Biochemistry of Nutrition (PPABIONUT), Faculty of Natural and  Life  Sciences, Earth and Universe, Abou-Bekr  Belkaïd University. 22, Rue Abi Ayad Abdelkrim, Fg Pasteur B.P 119, Tlemcen 13000, Algeria.
Cite article:- Amina Bouri, Rida Mohammed Mediouni, Abdelkader Ameur Ameur, Sripada Udupa, Semir Bechir Souheil Gaouar (2020). Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR). Indian Journal of Agricultural Research. 54(2): 129-138. doi: 10.18805/IJARe.A-487.

ABSTRACT

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P < 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

REFERENCES

  1. Ajibade SR, Weeden NF, Chite SM. (2000). Inter simple sequence repeat analysis of genetic relationships in the genus Vigna. Euphytica. 111: 47–55. 
  2. Arumuganathan K, Earle ED. (1991). Nuclear DNA content of some important plant species. Plant Mol Biol Report. 9: 208–    218. doi: 10.1007/BF02672069. 
  3. Babayeva S.M, Nasibova J.A, Akparov Z.I, Shikhaliyeva K.B, Mammadova A.D, Izzatullayeva V.I, Abbasov M.A. (2018). Application of DNA markers in determination of fusarium resistance and genetic diversity in chickpea. Legume Research-An International Journal. (41): 537-542. DOI: 10.18805/LR-407.
  4. Bampidis, V. A., Christodoulou, V., Nistor, E., Skapetas, B., Nistor, G. H. (2009). The use of chickpeas (Cicer arietinum) in poultry diets: a review. Lucrãri ºtiinþifice Zootehnieºi Biotehnologii, 42 (1): 323-330. 
  5. Bart S, Melchinger AE, Lubberstedt T. (2002). Genetic diversi in Arabidopsis thaliana L. Heynh investigated by cleave amplified polymorphic sequence (CAPS) and inter-simpsequence repeat (ISSR) markers. Mol Ecol 11: 495–505.
  6. Bejiga, G.; van der Maesen, L. J. G. (2006). Cicer arietinum L. Record from Protabase. Brink, M. and Belay, G. (Editors). PROTA (Plant Resources of Tropical Africa / Ressources végétales de l’Afrique tropicale), Wageningen, Netherlands
  7. Bharadwaj C., Chauhan S. K., Yadav S., Satyavathi T. C., Singh R., Kumar J. et al. (2011) Molecular marker based linkage map of chickpea (Cicer arietinum L.) developed from desi × kabuli cross. Indian J. Agric. Sci. 81 : 116–118.
  8. Ghaffari P, Talebi R, Keshavarz F. (2014). Genetic diversity and geographical differentiation of Iranian landrace, cultivars and exotic chickpea lines as revealed by morphological andmicrosatellite markers. Physiol Mol Biol Plant. 20(2): 225–233.
  9. Hajibarat, Z., Saidi, A., Hajibarat, Z. and Talebi, R. (2015). Characterization of genetic diversity in chickpea using SSRmarkers, Start Codon Targeted Polymorphism (SCoT) and Conserved DNA-Derived Polymorphism (CDDP). Physiol Mol Biol Plants. 21(3):365–373.
  10. Hajibarat, Z., Saidi, A., Hajibarat, Z. and Talebi, R. (2014). Genetic diversity and population structure analysis of landrace and improved chickpea (Cicer arietinum) genotypes using morphological and microsatellite markers. Environmental and Experimental Biology. (12): 161–166.
  11. Hüttel B, Winter P, Weising K, Choumane W, Weigand F. (1999). Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome (42): 210–217. ICRISAT. (2017). Chickpea (Cicer arietinum L.). ICRISAT, Morocco.
  12. Keneni, G., Bekele, E., Imtiaz, M. (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.
  13. Khan, R., Khan, H., Farhatullah. (2010). Evaluation of microsatellite markers to discriminate induced mutation lines, hybrid lines and cultigens in chickpea (Cicer arietinum L.). Aust. J. Crop Sci. (4): 301 – 308.
  14. Liu K, Muse SV. (2005). Power Marker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 1: 21(9): 2128-9. Epub 2005 Feb 10. MADR.2018. Ministère de l’Agriculture et Développement Rural
  15. Nayak SN, Zhu H, Varghese N, Datta S, Choi H-K, Horres R, Jüngling R, Singh J, Kavi Kishore PB, Sivaramakrishnan S, Hoisington DA, Kahl G, Winter P, Cook DR, Varshney RK. (2010). Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. Theor Appl Genet. 120: 1415.
  16. Nei M.and Saitou N. (1987).The neighbor-joining method: a new method for reconstructing phylogenetic trees. 4(4): 406-25.
  17. Peakall, R. and Smouse, P. (2006). Genetic analysis in excel. Population genetic software for teaching and research. Mol. Ecol. Notes. 6: 288–295.
  18. Raina SN, Rani V, Kojima T, Ogihara Y, Singh KP, Devarumath RM. (2001). RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species. Genome. 44: 763–772.
  19. Saeed A, Hovsepyan H, Darvishzadeh R, Imtiaz M, Panguluri S.K, Nazaryan R.(2011). Genetic diversity of Iranian accessions, improved lines of chickpea (Cicer arietinum L.) and their wild relatives by using simple sequence repeats. Plant Mol. Biol. Rep. (29): 848–858.
  20. Saghai-Maroof, M.A, Soliman, K.M, Jorgensen, R.A, Et Allard, R. W. (1984). Ribosomal DNA spacer-length polymorphism Mendelian inheritance, chromosomal location and population dynamics. PNAS, 8
  21. Sefera, T, Abebie, B, Gaur, P. M. (2011). Characterization and genetic diversity analysis of selected chickpea cultivars of nine countries using simple sequence repeat (SSR) markers. Crop Pasture Sci. (62): 177–187.
  22. Sethy NK, Choudhary S, Shokeen B, Bhatia S. (2006) a. Identification of microsatellite markers from Cicer reticulatum; molecular variation and phylogenetic analysis. Theor Appl Genet. (112): 347–357.
  23. Sethy NK, Shokeen B, Edwards KJ, Bhatia S.(2006) b. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet. 114: 1416-1428.
  24. Syed Gul Abbas Shah Sani, Peter L. Chang, Asif Zuhair, Noelia Carrasquilla-Garcia, et al. (2017). Genetic diversity, population structure and genetic correlation with climatic variation in chickpea landraces from Pakistan. Plant Genome 11: 170067 doi: 10.3835/plant genome 2017.08.0067 
  25. Srivastava A.K., Chaturvedi S.K, Singh N.P. (2016). Genetic base of Indian chickpea (Cicer arietinum L.) varieties revealed by pedigree analysis. Legume Research-An International Journal. (40): 22-26. DOI: 10.18805/lr.v0iOF.3550 
  26. Syeda Asma Koinain, Hegde V.S, Bharadwaj C.(2015). Genetic diversity analysis among selected short duration chickpea cultivars and breeding lines based on STMS marker. Legume Research-An International Journal. 39: 851-859. DOI: 10.18805/lr.v0iOF.11299.
  27. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol. 28(10): 2731-9. doi: 10.1093/molbev/msr121. Epub 2011 May 4.
  28. Taylor, W. J, Ford, R. (2007). Chickpea. In: Genome Mapping and Molecular Breeding in Plants. [Chittarajan, K.] 3(6): 109-122.
  29. Tayyar, R, Federici, C. V. and Waines, G. J. (1996). Natural out crossing in chickpea (Cicer arietinum L.). Crop Sci. 36: 203–205.
  30. Torutaeva E, Asanaliev A, Prieto-Linde M, Zborowska A, Ortiz R, Bryngelsson T and Gustavsson L G. (2014). Evaluation of microsatellite-based genetic diversity, protein and mineral content in chickpea accessions grown in Kyrgyzstan. Hereditas. 151: 81–90.
  31. Udita Basu, Rishi Srivastava, Deepak Bajaj, Virevol Thakro, Anurag Daware, et al. (2018). Genome-wide generation and genotyping of informative SNPs to scan molecular signatures for seed yield in chickpea. Scientific reports (2018) 8: 13240. DOI:10.1038/s41598-018-29926-1
  32. Udupa S. M., Robertson L. D., Weigand F., Baum M. and Kahl G. (1999). Allelic variation at (TAA) n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Theor. Appl. Genet. 97: 299–307.
  33. Upadhyaya H.D., Dwivedi S.L., Baum M., Varshney R.K., Udupa S.M., Gowda C.L.L., (2008). Genetic structure, diversity and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol. 8: 106. doi:10.1186/1471-2229-8-106.
  34. Varshney RK, Song C, Saxena RK, Azam S, Yu S, Sharpe AG. (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. Epub January 27. Available from: http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.249.html. 
  35. Yeh, F. C. and Boyle, T. J. B. (1997). Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot. 129: 157.
  36. Winter P, Pfaff T, Udupa SM, Sharma PC, Sahi S et al. (1999). Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet. 262: 90–101.
Reviewed By

Download Article
In this Article
    Contact us
    Follow us

    Editorial Board

    View all (0)