The study of genetic relationships between in landrace chickpea collected from north-west of Iran using SCoT molecule marker

Paper Details

Research Paper 01/03/2014
Views (190) Download (8)

The study of genetic relationships between in landrace chickpea collected from north-west of Iran using SCoT molecule marker

Fatemeh Pakseresht, Reza Talebi, Ezat karami, Hooman Shirvani
J. Bio. Env. Sci.4( 3), 12-19, March 2014.
Certificate: JBES 2014 [Generate Certificate]


This study was carried out using 10 SCoT primers, to genetic relationships evaluation for 38 accessions of 4 population’s chickpea of the north-west of Iran. In addition, 95 bands were scored using these primers, that polymorphism were showed for 65 bands. Primer SCoT12 with 14 bands had the highest and primer SCoT35 with 5 bands had the lowest number of bands. The lowest percent of polymorphism belonged to SCoT11 (33%) and the primer of SCoT13 had the highest percent of polymorphism (100%). AMOVA revealed that 12% of the total variance was due to differences between populations and 88% was due to differences within populations. Sanandaj population with the Shannon’s information index (I) and Nei’s gene diversity (He) had the highest variety between reviewed population, and Kurdistan population had the lowest variety. In addition the population of Kurdistan had the highest distance with Qorve and the population of Kurdistan had the highest similarity with Sanandaj. These results were confirmed by cluster analysis and principal coordinate analysis of populations. Cluster analysis and Scatter plot based on first and second axis from principal coordinate analysis for accessions, showed that genetic variation did not agreement with the geographical distribution.


Ahmad F, Khan FS, Awan B. 2010. Genetic diversity of chickpea (Cicer arietinum L.) germplasm in Pakistan as revealed by RAPD analysis. Genetic and Molecular Research 9(3), 1414-1420. http://dx.doi:10.4238/vol9-3gmr862

Anderson JA, Church JE, Autrique SD, Thanksley S, Sorrells ME. 1993. Optimizing parental selection for genetic linkage map. Journal of Genome 36, 181-188.

Arumuganathan K, Earle ED. 1991. Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9(4), 208–218.

Charles MT, Dominique R, Kumar J, Dangi OP. 2002. A preliminary study of the functional properties of chickpea leaves. Annual Meeting of the Canadian Society of Food and Nutrition, Edmonton, Alberta, Canada, 89–96 p.

Chowdhury MA, Vandenberg V, Warkentin T. 2002. Cultivar identification and genetic relationship among selected breeding lines and cultivars in chickpea (Cicer arietinum L.). Euphytica 127(3), 317–325.

Collard  BCY,  Mackill  DJ.  2009.  Start  Codon Targeted (SCoT) polymorphism: a simple novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter 27(1), 86–93.

Coram TE, Mantri  NL, Ford  R, Pang ECK. 2007. Functional genomics in chickpea: an emerging frontier for molecular assisted breeding. Functional Plant Biology 34, 861–873.

De La Rosa R, James C, Tobutt KR. 2002. Isolation and characterization of polymorphic microsatellite in olive (Olea europaea L.) and their transferability to other genera in Oleaceae. Molecular Ecology Notes 2, 265-267.

Gupta PK, Rustgi S. 2004. Molecular markers from the transcribed/expressed region of the genome in higher plants. Functional and Integrative Genomics 4, 139–16.

Hernández P, de la Rosa R, Rallo L, Dorado G. 2001. Development of SCAR markers in olive (Olea europaea) by direct sequencing of RAPD products: applications in olive germplasm evaluation and mapping. Theoretical and Applied Genetics 103, 788–791.

Iruela M, Rubio J, Cubero JI, Gil J, Millan T. 2002. Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers. Theoretical and Applied Genetics 104, 643–651.

McIntosh GH, Topping DL. 2000. Food legumes in human nutrition. In: Knight R (ed) Linking research and marketing opportunities for pulses in the  21st  century.  Kluwer  Academic  Publishers,  pp 655–666.

Millan T, Siddique CHJ, KHM BHK, Gaur PM, Kumar J, Gil J, Kahl G, Winter P. 2006. Chickpea molecular breeding: new tools and concepts. Euphytica 147(1–2), 81–103.

Murry MG, Tompson WF. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acid Research 8, 4321-4325.

Nei NM, Li W. 1979. Mathematical model for studying genetic variation in terms of restriction end nucleases. Proceedings of the National Academy of Sciences 76, 5269–5273, PMCID: PMC413122.

Nguyen TT, Taylor PWJ, Redden RJ, Ford R. 2004. Genetic diversity estimates in Cicer using AFLP analysis. Plant Breeding 123, 173–179.

Powell W, Morgante M, Andre C, Hanafey M, Vogel J, And TS, Rafalski A. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225–238.

Rao LS, Usha Rani P, Deshmukh PS, Kumar PA, Panguluri SK. 2007. RAPD and ISSR fingerprinting in cultivated chickpea (Cicer arietinum L.) and its wild progenitor Cicer reticulatum Ladizinsky.  Genetic  Resources  and  Crop  Evolution 54, 1235–1244.

Ratnaparkhe MB, Gupta VS, Ven Murthy MR, Ranjekar PK. 1995 Genetic fingerprinting of pigeon Cajanus cajan (L.) Millsp and its wild relatives using RAPD markers. Theoretical and Applied Genetics. 91, 893–898.

SaeedA, HovsepyanH, DarvishzadehR, ImtiazM, PanguluriSK, NazaryanR. 2011. Genetic diversity of Iranian accessions improved lines of chickpea (Cicer arietinum) and their wild relatives by using simple sequence repeats. Plant Molecular Biology Reporter.

Sant VJ, Patankar AG, Sarode ND, Mhase LB, Sainani MN, Deshmukh RB, Ranjekar PK, Gupta VS. 1999. Potential of DNA markers in detecting divergence and analysis in heterosis in Indian elite chickpea cultivars. Theoretical and Applied Genetics 98, 1217–1225.

Serret MD, Udupa SM, Weigand F. 1997. Assessment of genetic diversity of cultivated chickpea using microsatellite-derived RFLP markers: implications for origin. Plant Breeding 116, 573–578.

Sethy NK, Shokeen B, Edwards KJ, Bhatia S. 2006.  Development  of  microsatellite  markers  and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theoretical and Applied Genetics 112, 1416–1428.

Shannon CE. 1948. A mathematical theory of communication. Bell System Technical Journal 27, 379-423.

Sudupak A, Akkaya S, Kence A. 2002. Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers. Theoretical and Applied Genetics 105, 1220–1228.

Talebi R, Fayaz F. 2008. Genetic Relationships among Chickpea (Cicer arietinum) EliteLines Based on RAPD and Agronomic Markers. International Journal of Agricultural and Biological Engineering 10, 301-5.

Talebi R, Jelodar NAB, Mardi M., Fayaz F, Furman BJ, Bagheri NA. 2009. Phylogenetic diversity and relationship among annual Cicer species using Random Amplified Polymorphic DNA Markers. General AND Applied Plant Physiology 35(1-2), 3-12.

Tanya P, Taeprayoon P, Hadkam Y, Srinives P. 2011. Genetic diversity among Jatropha and Jatropha-related species based on ISSRmarkers. Plant Molecular Biology Reporter 29, 252–264.