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Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb

  • Genetics and Genomics
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Abstract

Tribulus terrestris is well known for its medicinal importance in curing urino-genital disorders. Amplified fragment length polymorphism (AFLP), selective amplification of microsatellite polymorphic loci (SAMPL), inter-simple sequence repeat (ISSR) and randomly amplified polymorphic DNA (RAPD) markers were used for the first time for the detection of genetic polymorphism in this medicinal herb from samples collected from various geographical regions of India. Six assays each of AFLP and SAMPL markers and 21 each of ISSR and RAPD markers were utilized. AFLP yielded 500 scorable amplified products, of which 82.9% were polymorphic. SAMPL primers amplified 488 bands, 462 being polymorphic (94.7%). The range of amplified bands was 66 [(TC)8G + M-CAG] to 98 [(CA)6AG + M-CAC] and the percentage polymorphism, 89.9 [from (CT)4C (AC)4A + M-CTG] to 100 [from (GACA)4 + M-CTA]. The ISSR primers amplified 239 bands of 0.4–2.5 kb, 73.6% showed polymorphism. The amplified products ranged from 5 to 16 and the percentage polymorphism 40–100. RAPD assays produced 276 bands, of which 163 were polymorphic (59%). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.9 for all the four marker systems. The dendrograms and PCA plots derived from the binary data matrices of the four marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. The relative efficiency of the four molecular marker systems calculated on the basis of multiplex ratio, marker index and average heterozygosity revealed SAMPL to be the best. Distinct DNA fingerprinting profile, unique to every geographical region could be obtained with all the four molecular marker systems. Clustering can be a good indicator for clear separation of genotypes from different regions in well-defined groups that are supported by high bootstrap values.

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References

  • Artyukova EV, Kozyrenko MM, Ilyushko MV, Zhuravlev YN, Reunova GD (2001) Genetic variability of Iris setosa. Russ J Mol Biol 35:134–138

    CAS  Google Scholar 

  • Awasthi AK, Nagaraja GM, Naik GV, Sriramana-Kanginakudru, Thangavelu K, Javaregowda-Nagaraju (2004) Genetic diversity and relationships in mulberry (genus Morus) as revealed by RAPD and ISSR marker assays. BMC Genet. http://www.biomedcentral.com/1471-2156/5/1

  • Bahulikar RA, Stanculescu D, Preston CA, Baldwin IT (2004) ISSR and AFLP analysis of the temporal and spatial population structure of the post-fire annual, Nicotiana attenuata, in SW Utah. BMC Ecol. http://www.biomedcentral.com/1472-6785/4/12. doi:10.1186/1472-6785-4-12

  • Baranger A, Aubert G, Arnau G, Lainé AL, Deniot G, Potier J, Weinachter C, Lejeune-Hénaut I, Lallemand J, Burstin J (2004) Genetic diversity within Pisum sativum using protein and PCR-based markers. Theor Appl Genet 108:1309–1321

    Article  PubMed  CAS  Google Scholar 

  • Das S, Rajagopal J, Bhatia S, Srivastava PS, Lakshmikumaran M (1999) Assessment of genetic variation within Brassica campestris cultivars using amplified fragment length polymorphism and random amplification of polymorphic DNA markers. J Biosci 24:433–440

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Fu YB, Phan AT, Coulman B, Richards KW (2004) Genetic diversity in natural populations and corresponding seed collections of little bluestem as revealed by AFLP markers. Crop Sci 44:2254–2260

    Article  Google Scholar 

  • Garcia AAF, Benchimol LL, Barbosa AMM, Geraldi IO, Souza CL Jr, Souza AP (2004) Comparison of RAPD, RFLP, AFLP and SSR markers for diversity studies in tropical maize inbred lines. Genet Mol Biol 27:579–588

    Article  CAS  Google Scholar 

  • Gustine DL, Voigt PW, Brummer EC, Papadopoulos YA (2002) Genetic variation of RAPD markers for North American white clover collections and cultivars. Crop Sci 42:343–347

    Article  Google Scholar 

  • Han J, Zhang W, Cao H, Chen S, Wang Y (2007) Genetic diversity and biogeography of the traditional Chinese medicine, Gardenia jasminoides, based on AFLP markers. Biochem Syst Ecol 35:138–145

    Article  CAS  Google Scholar 

  • Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

    Google Scholar 

  • Kjølner S, Såstad SM, Taberlet P, Brochmann C (2004) Amplified fragment length polymorphism versus random amplified polymorphic DNA markers: clonal diversity in Saxifraga cernua. Mol Ecol 13:81–86

    Article  PubMed  CAS  Google Scholar 

  • Lim W, Mudge KW, Weston LA (2007) Utilization of RAPD markers to assess genetic diversity of wild populations of North American Ginseng (Panax quinquefolius). Planta Med 73:71–76

    Article  PubMed  CAS  Google Scholar 

  • Liu Y, Wang Y, Huang H (2006) High interpopulation genetic differentiation and unidirectional linear migration patterns in Myricaria laxiflora (Tamaricaceae), an endemic riparian plant in the Three Gorges Valley of the Yangtze River. Am J Bot 93:206–215

    Google Scholar 

  • Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Menkir A, Kling JG, Badu-Apraku B, Ingelbrecht I (2005) Molecular marker-based genetic diversity assessment of Striga-resistant maize inbred lines. Theor Appl Genet 110:1145–1153

    Article  PubMed  CAS  Google Scholar 

  • Na HJ, Um JY, Kim SC, Koh KH, Hwang WJ, Lee KM, Kim CH, Kim HM (2004) Molecular discrimination of medicinal Astragali radix by RAPD analysis. Immunopharmacol Immunotoxicol 26:265–272

    Article  PubMed  CAS  Google Scholar 

  • Negi MS, Sabharwal V, Bhat SR, Lakshmikumaran M (2004) Utility of AFLP markers for the assessment of genetic diversity within Brassica nigra germplasm. Plant Breed 123:13–16

    Article  CAS  Google Scholar 

  • Odat N, Jetschke G, Hellwig FH (2004) Genetic diversity of Ranunculus acris L. (Ranunculaceae) populations in relation to species diversity and habitat type in grassland communities. Mol Ecol 13:1251–1257

    Article  PubMed  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) marker for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Rohlf FJ (2001) NTSYS-pc numerical taxonomy and multivariate analysis system. Version 5.1. Exeter Publishing Ltd, Setauket

    Google Scholar 

  • Roldan-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in rye grasses (Lolium spp.). Mol Breed 6:125–134

    Article  CAS  Google Scholar 

  • Roy A, Bandyopadhyay A, Mahapatra AK, Ghosh SK, Singh NK, Bansal KC, Koundal KR, Mohapatra T (2006) Evaluation of genetic diversity in jute (Corchorus species) using STMS, ISSR and RAPD markers. Plant Breed 125:292–297

    Article  CAS  Google Scholar 

  • Ru Z, Zhou C, Weifeng L, Baorong L (2006) Estimating genetic diversity and sampling strategy for a wild soybean (Glycine soja) population based on different molecular markers. Chin Sci Bull 51:1219–1227

    Article  CAS  Google Scholar 

  • Sambrook J, Maccallum P, Russell D (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Press, New York, 2344 p

  • Selvi A, Nair NV, Noyer JL, Singh NK, Balasundaram N, Bansal KC, Koundal KR, Mohapatra T (2006) AFLP analysis of phenetic organization and genetic diversity in the sugarcane complex, Saccharum and Erianthus. Genet Resour Crop Evol 53:831–842

    Article  CAS  Google Scholar 

  • Shan F, Clarke HC, Plummer JA, Yan G, Siddique KHM (2005) Geographical patterns of genetic variation in the world collections of wild annual Cicer characterized by amplified fragment length polymorphisms. Theor Appl Genet 110:381–391

    Article  PubMed  CAS  Google Scholar 

  • Sica M, Gamba G, Stefania Montieri S, Gaudio L, Aceto S (2005) ISSR markers show differentiation among Italian populations of Asparagus acutifolius. BMC Genet. http://www.biomedcentral.com/1471-2156/6/17

  • Singh A, Chaudhury A, Srivastava PS, Lakshmikumaran M (2002) Comparison of AFLP and SAMPL markers for assessment of intra-population genetic variation in Azadirachta indica A. Juss. Plant Sci 162:17–25

    Article  CAS  Google Scholar 

  • Singh AK, Sharma RK, Singh NK, Bansal KC, Koundal KR, Mohapatra T (2006) Genetic diversity in ber (Ziziphus spp.) as revealed by AFLP markers. J Hortic Sci Biotechnol 81:205–210

    CAS  Google Scholar 

  • Souframanien J, Gopalakrishna T (2004) A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers. Theor Appl Genet 109:1687–1693

    Article  PubMed  CAS  Google Scholar 

  • Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    Article  PubMed  CAS  Google Scholar 

  • Teulat B, Aldam C, Trehin R, Lepbrun P, Barker JHA, Arnold GM, Karp A, Baudouin L, Rognan F (2000) An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence tagged microsatellites (SSRs) and AFLPs. Theor Appl Genet 100:764–771

    Article  CAS  Google Scholar 

  • Tosti N, Negri V (2002) Efficiency of three PCR-based markers in assessing genetic variation among cowpea (Vigna unguiculata ssp. unguiculata) landraces. Genome 45:268–275

    Article  PubMed  CAS  Google Scholar 

  • Wang X, Li Y, Li H, Zhang Y, Zhao L, Yu Y (2003) RAPD analysis of genuineness on source of Bupleurum chinense. Zhong Yao Cai 26:855–856

    PubMed  Google Scholar 

  • Wu YQ, Taliaferro CM, Bai GH, Martin DL, Anderson JA, Anderson MP, Edwards RM (2006) Genetic analyses of Chinese Cynodon accessions by flow cytometry and AFLP markers. Crop Sci 46:917–926

    Article  Google Scholar 

  • Yap IV, Nelson R (1995) WinBoot: a program for performing bootstrap analysis of binary data to determine the confidence limits of UPGMA-based dendrograms. IRRI discussion paper series no.14. IRRI, Los Baños

    Google Scholar 

  • Zhao J, Wang X, Deng B, Lou P, Wu J, Sun R, Xu Z, Vromans J, Koornneef M, Bonnema G (2005) Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor Appl Genet 110:1301–1314

    Article  PubMed  Google Scholar 

  • Zhou M-Q, Zhao K-G, Chen L-Q (2007) Genetic diversity of Calycanthaceae accessions estimated using AFLP markers. Sci Hortic (In press)

Download references

Acknowledgments

MS is grateful to the Department of Biotechnology, Government of India for the award of Junior, and Senior Research Fellowship. The study was supported by a financial grant (number BT/PR 1969/PB/17/096/2000) from the DBT, Governtment of India to SD and PSS.

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  1. Department of Biotechnology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi, 110062, India

    Maryam Sarwat, S. Das & P. S. Srivastava

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  1. Maryam Sarwat
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  2. S. Das
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  3. P. S. Srivastava
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Correspondence to P. S. Srivastava.

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Communicated by P. Puigdomenech.

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Sarwat, M., Das, S. & Srivastava, P.S. Analysis of genetic diversity through AFLP, SAMPL, ISSR and RAPD markers in Tribulus terrestris, a medicinal herb. Plant Cell Rep 27, 519–528 (2008). https://doi.org/10.1007/s00299-007-0478-5

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