Use Of Promoter-Anchored Rapd Analysis For Divergence Assessment In Soybean As Against Conventionally Used Issr Assay
DOI:
https://doi.org/10.48165/Keywords:
Diversity, ISSR, PAAP-RAPD markers, soybeanAbstract
The present study was aimed to compare the genetic diversity among 24 soybean genotypes as revealed by Promoter-anchored amplified polymorphism based on RAPD (PAAP-RAPD) primer-combinations analysis and Inter Simple Sequence Repeat (ISSR) analysis. All the 16 PAAP-RAPD primer-combinations, derived from 4 Promoter-based primers (TA1/G1/CA1/GC1) and 4 RAPD primers (OPE 1/5/7/9) showed amplification, of which 8 were polymorphic. They produced 63 loci, of which 52 were polymorphic. All 20 ISSR primers used were polymorphic generating 115 alleles of which 95 were polymorphic. The similarity coefficient based on ISSR and PAAP-RAPD analysis ranged from 0.67 to 0.93 and 0.41 to 1.00, respectively. The PAAP-RAPD consensus tree revealed 17 clusters; while ISSR revealed all genotypes as separate clusters. In 2D scatter plot, these were broadly classified into 5 major groups. Group-Ia had lowest divergence (MAUS71, KDS 344, KDS387, NRC94, KDS722, Bragg and KDS743) while Group-Ib had low divergence (Birsa Soya1, KDS749, KDS726, KDS739 and JS335). Moderate divergence was observed in Group II (JS9305 and RKS 18) and Group III (Himso 1684, Dsb22 and MACS450). Group IV (KDS741, VLS65, Rpp3 PI462312 variant, EC241778 and PI462312) had highest divergence. Only two genotypes (KDS753 and DS228) were placed separately in both the analyses. The study revealed that PAAP-RAPD has an advantage that it may specifically target regulatory regions of various candidate genes during molecular tagging for a specific trait.
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References
AOAC. 1986. Official Methods of Analysis. Association of Official Analytical Chemists. Washington, USA.
Alamri, S. 2014. Comparative Analysis of Soybean (Glycine max) Accessions Using ISSR and RAPD Markers. M.Sc. (Biology) thesis. Laurentian University, Sudbury, Ontario, Canada. Anonymous 2012. FAO STAT data base. Rome, Italy (http//www.faostat.fao.org).
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Baloch, F.S., Kurt, C. and Arioglu, H. 2010. Assaying of diversity among soybean and peanut genotypes at DNA level. Turkish Journal of Agriculture and Forestry, 34: 285-301. Collard, B.C.Y. and Mackill, D.J. 2009 Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, 27: 86-93.
Cox, T.S. 1985. Relationship between coefficient of parentage and similarity indices in the soybean. Crop Science, 25: 529-532.
Desmarais, E., Lanneluc, I. and Lagnel, J. 1998. Direct amplification of length polymorphisms (DALP), or how to get and characterize new genetic markers in many species. Nucleic Acids Research, 26: 1458-1465.
Gizlice, Z., Carter Jr. T.E., and Burton, J.W. 1994. Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Science, 34: 1143-1151.
Gupta, P.K., and Rustgi, S. 2004. Molecular markers from the transcribed/expressed region of the genome in higher plants. Functional and Integrative, Genomics, 4: 139-162. He, H., Wei, S. and Zhang, Y. 2011. Genetic diversity analysis of soybean germplasm in Heilongjiang Province by ISSR marker, Soybean Science, 1: 37-40.
Hu J. and Vick B.B.A. 2003. Target region amplification polymorphism: a novel marker technique for plant genotyping. Plant Molecular Biology Reporter, 21(3): 289-294.
Keim, P., Olson, T.C. and Shoemaker, R.C. 1988. A rapid protocol for isolating soybean DNA. Soybean Genetic Newsletter, 15: 150-152.
Li, G. and Quiros, C.F. 2001. Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics, 103: 455-461.
Nelson, R.L. 1987. Evaluation of USDA Soybean germplasm collection of maturity groups 000 to IV (PI 273-483 to PI 472-107). USDA Technical Bulletin, 17-18.
Pang, M., Percy, R. G., Hughs, E. and Zhang, J. 2009. Promoter anchored amplified polymorphism based on random amplified polymorphic DNA (PAAP-RAPD) in cotton. Euphytica, 167: 281-291.
Patterson, A.H.C. 1996. Genome Mapping in Plants. R.H. Lands Co., Austin, USA. Poczai, P., Varga, I., Laos, M., Cseh, A., Bell, N., Valkonen, J.P. and Hyvönen, J., 20. Advances in plant gene-targeted and functional markers: A review. Plant Methods, 9: 6.
Prevost, A. and Wilkinson, M.J. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics, 98: 107-112. Rohlf, F.J. 1998. NTSYS-PC: Numerical taxonomy and multivariate analysis system, version 2.0 (Exeter Software, New York)
Saxena, P., Singh, K., Bhatt, U. and Khanna, V. 2009. Identification of ISSR marker for the resisance to yellow mosaic virus in soybean (Glycine max (L.) Merrill). Pantnagar Journal of Research, 7(2): 166-170
Tara Satyavathi, C., Bhat, K.V., Bharadwaj, C, Tiwari S.P., Chaudhary V.K. 2006. AFLP based DNA profiling and genetic diversity assessment of Indian soybean [Glycine max (L.) Merrill] varieties. Genetic Resources and Crop Evolution, 53: 1059-1069.
Thormann, C.E. and Osborn, T.C.1992. Use of RAPD and RFLP markers for germplasm evaluation of application of RAPD technology to plant breeding. Plant Breeding, 1: 470-490. Wang, Q., Zhang, B. and Lu Q., 2008. Conserved region amplification polymorphism (CoRAP), a novel marker technique for plant genotyping in Salvia miltiorrhiza. Plant Molecular Biology Reporter, 27: 139-143.
Xie, F. and Yoshihito T. 2005. Phylogenetic analysis of soybean (Glycine max (L.) Merr.) cultivars from different regions through ISSR marker. Soybean Science, 3: 161-165.
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