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Application of EST-SSR marker in detection of genetic variation among purslane (Portulaca oleracea L.) accessions

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Abstract

Express sequence tag (EST)-simple sequence repeat (SSR) was employed to assess the genetic diversity in elite germplasm collections of purslane (Portulaca oleracea L.) which is a saline and drought tolerant annual herb containing high amount of vitamins, minerals, and antioxidant properties. The 10 primers gave a total of ninety five bands among which 95 were polymorphic (100 %). The genetic diversity as estimated by Shannon’s information index was 1.85, revealing a high level of genetic diversity in the germplasm. The average numbers of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC), and Nei’s information index were 9.5, 5.14, 0.81, 0.33, 0.77, and 0.79, respectively. The UPGMA dendrogram based on Nei’s genetic distance grouped the whole germplasm into eight distinct clusters. The analysis of molecular variance (AMOVA) revealed that 71.87 % of total variation occurred within population while 28.13 % from among populations. Considering all these criteria and results from marker-assisted diversity analysis, accessions that are far apart based on their genetic coefficient (like Ac11 and Ac17; Ac4 and Ac42; Ac16 and Ac31; Ac38 and Ac17; Ac21 and Ac31; Ac30 and Ac10) could be selected as parents for further breeding programs.

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References

  • Alam MA, Juraimi AS, Rafii MY, Hamid AA, Aslani F, Hasan MM, Zainudin MAM, Uddin MK (2014a) Evaluation of antioxidant compounds, antioxidant activities and mineral composition of 13 collected purslane (Portulaca oleracea L.) accessions. Biomed Res Int 2014:1–10

  • Alam MA, Juraimi AS, Rafii MY, Hamid AA, Aslani F (2014b) Screening of Purslane (Portulaca oleracea L.) accessions for high salt tolerance. Sci World J 2014:1–12

  • Alam MA, Juraimi AS, Rafii MY, Hamid AA, Aslani F, Alam MZ (2014c) Effects of salinity on phenolic compounds and antioxidant activities of 13 collected purslane (Portulaca oleracea L.) germplasms. Food Chem 169:439–447

  • Alam MA, Juraimi AS, Rafii MY, Hamid AA, Aslani F (2014d) Collection and identification of different Purslane (Portulaca oleracea L.) accessions available in Western Peninsular Malaysia. Life Sci J 11:431–437

  • Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186

    Article  CAS  PubMed  Google Scholar 

  • Arolu IW, Rafii MY, Hanafi MM, Mahmud TMM, Latif MA (2012) Molecular characterization of Jatropha curcas germplasm using inter simple sequence repeat (ISSR) markers in Peninsular Malaysia. Aust J Crop Sci 6:1666–1673

  • Blair MW, González LF, Kimani PM, Butare L (2010) Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa. Theor App Genet 121:237–248

    Article  CAS  Google Scholar 

  • Brown SM, Kresovich S (1996) The use of molecular markers in plant germplasm conservation. In: Paterson AH (ed) Genome mapping in plants, Clandes, New York, pp 85–93

  • Danin A, Baker I, Baker HG (1978) Cytogeography and taxonomy of the Portulaca oleracea L. polyploid complex. Israel J Bot 27:177–211

    Google Scholar 

  • Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008

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

  • Du QZ, Zhang DQ, Li BL (2012) Development of 15 novel microsatellite markers from cellulose synthase genes in Populus tomentosa (Salicaceae). Am J Bot 99:46–48

    Article  Google Scholar 

  • Dweck AC (2001) Purslane (Portulaca oleracea): the global panacea. Pers Care Mag 2:7–15

  • Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50

    PubMed Central  CAS  Google Scholar 

  • Fu N, Wang P, Liu X, Shen H (2014) Use of EST-SSR markers for evaluating genetic diversity and fingerprinting Celery (Apium graveolens L.) cultivars. Molecules 19:1939–1955

    Article  PubMed  Google Scholar 

  • Hu J, Wang L, Li J (2011) Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol Plant 55:577–580

  • Hwang J, Kang J, Son B, Kim K, Park Y (2011) Genetic diversity in watermelon cultivars and related species based on AFLPs and EST-SSRs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39:285–292

  • Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 44:223–270

    Google Scholar 

  • Jena SN, Srivastava A, Rai KM, Ranjan A, Singh SK, Nisar T, Srivastava M, Bag SK, Mantri S, Asif MH (2012) Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). Theor Appl Genet 124:565–576

    Article  CAS  PubMed  Google Scholar 

  • Joshi SP, Gupta VS, Aggarwal RK, Ranjekar PK, Brar DS (2000) Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genus Oryza. Theor Appl Genet 100:1311–1320

    Article  CAS  Google Scholar 

  • Kong Q, Zhang G, Chen W, Zhang Z, Zou X (2012) Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae). Am J Bot 2012:59–61

    Article  Google Scholar 

  • Kumar H, Kaur G, Banga S (2012) Molecular characterization and assessment of genetic diversity in sesame (Sesamum indicum L.) germplasm collection using ISSR markers. J Crop Improv 26:540–557

    Article  CAS  Google Scholar 

  • Li G, Quiros CF (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. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  • Li G, Ra WH, Park JW, Kwon SW, Lee JH, Park CB, Park YJ (2011) Developing EST-SSR markers to study molecular diversity in Liriope and Ophiopogon. Biochem Systemat Ecol 39:241–252

  • Lokhande VH, Nikam TD, Patade VY, Surasanna P (2009) Morphological and molecular diversity analysis among the Indian clones of Sesuvium portulacastrum L. Genet Res Crop Evol 56:705–717

    Article  CAS  Google Scholar 

  • Mujaju C, Sehic J, Nybom H (2013) Assessment of EST-SSR markers for evaluating genetic diversity in Watermelon accessions from Zimbabwe. Am J Plant Sci 4:1448–1456

    Article  Google Scholar 

  • Parsons JB, Newbury HT, Jackson MT, Ford-Lloyd BV (1997) Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types. Mole Breed 3:115–125

    Article  CAS  Google Scholar 

  • Ramu P, Billot C, Rami JF, Senthilvel S, Upadhyaya HD, Reddy LA, Hash CT (2013) Assessment of genetic diversity in the sorghum reference set using EST-SSR markers. Theor Appl Genet 126:2051–2064

    Article  CAS  PubMed  Google Scholar 

  • Rao NK (2004) Plant genetic resources: advancing conservation and use through biotechnology. Afr J Biotechnol 3:136–145

    Google Scholar 

  • Ren S, Weeda S, Akande O, Guo Y, Rutto L, Mebrahtu T (2011) Drought tolerance and AFLP-based genetic diversity in purslane (Portulaca oleracea L.). J Biotech Res 3:51–61

    CAS  Google Scholar 

  • Rohlf FJ (2002) NTSYS-pc: numerical taxonomy system ver.2.1. Exeter Publishing Ltd., New York

    Google Scholar 

  • Samy J, Sugumaran M, Lee KLW (2004) Herbs of Malaysia: an introduction to the medicinal, culinary, aromatic and cosmetic use of herbs. Times, Kuala Lumpur

    Google Scholar 

  • Schulman AH (2007) Molecular markers to assess genetic diversity. Euphytica 158:313–321

    Article  CAS  Google Scholar 

  • Simopoulos AP, Norman HA, Gillaspy JE (1995) Purslane in human nutrition and its potential for world agriculture. World Rev Nutr Diet 77:47–74

    CAS  PubMed  Google Scholar 

  • Simopoulos AP, Tan DX, Mancheste LC, Reiter RJ (2005) Purslane: a plant source of omega-3 fatty acids and melatonin. J Pineal Res 39:331–332

    Article  CAS  PubMed  Google Scholar 

  • Tatikonda L, Wani SP, Kannan S, Beerelli N, Sreedevi TK, Hoisington DA, Devi D, Varshney RK (2009) AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant. Plant Sci 176:505–513

    Article  CAS  Google Scholar 

  • Uddin MK, Juraimi AS, Anwar F, Hossain MA, Alam MA (2012) Effect of salinity on proximate mineral composition of purslane (Portulca oleracea L.). Aust J Crop Sci 6:1732–1736

  • Uddin MK, Juraimi AS, Hossain MS, Nahar MAU, Ali ME, Rahman MM (2014) Purslane weed (Portulaca oleracea): A prospective plant source of nutrition, omega-3 fatty acid, and antioxidant attributes. Sci World J 2014:1–6

    Article  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genetic microsatellite markers in plants: features and applications. Trends in Biotechnol 23:48–55

    Article  CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans T, Van de Lee T et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wen M, Wang H, Xia Z, Zou M, Cheng LuC, Wang W (2010a) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Res Notes 42:1–8

  • Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W (2010b) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Notes 3:42–50

    Article  PubMed Central  PubMed  Google Scholar 

  • Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535

  • Yan G, Aryamanesh N, Wang S (2009) Purslane – A potential vegetable crop. Rural Industries Research and Development Corporation, Australia, pp 1–26 RIRDC Publication No. 09/088

    Google Scholar 

  • Yazici I, Turkan I, Sekmen AH, Demiral T (2007) Salinity tolerance of purslane (Portulaca oleracea L.) is achieved by enhanced antioxidative system, lower level of lipid peroxidation and proline accumulation. Environ Exp Bot 61:49–57

    Article  CAS  Google Scholar 

  • Yeh FC, Yang R, Boyle TJ, Ye Z, Xiyan JM (2000) PopGene32, Microsoft Windowsbased Freeware for Population Genetic Analysis, Version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton

    Google Scholar 

  • Zai-quan C, Fu-you Y, Ding-qing L, Teng-qiong Y, Jian F, Hui-jun Y, Qiao-fang Z, Dun-yu Z, Wei-jiao L, Xing-qi H (2012) Genetic diversity of wild rice species in Yunnan province of China. Rice Sci 19:21–28

  • Zhang G, Xu S, Mao W, Hu Q, Gong Y (2013) Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers. J Zhejiang Univ Sci B (Biomed & Biotechnol) 14:279–288

  • Zietkiewiez E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183

    Article  Google Scholar 

Download references

Acknowledgments

The authors sincerely acknowledge UPM Research University Grant (01-02-12-1695RU) for financial support of the project and IGRF (International Graduate Research Fellowship, UPM) for PhD Fellowship.

Conflict of interests

The authors declare that there is no conflict of interests regarding the publication of this article.

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Authors and Affiliations

  1. Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, DE, Malaysia

    Md. Amirul Alam, Abdul Shukor Juraimi & M. Y. Rafii

  2. Institutes of Tropical Agriculture, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, DE, Malaysia

    M. Y. Rafii & Ibrahim Wasiu Arolu

  3. Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, DE, Malaysia

    Azizah Abdul Hamid

  4. Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh

    M. A. Latif

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  1. Md. Amirul Alam
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  2. Abdul Shukor Juraimi
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  3. M. Y. Rafii
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  4. Azizah Abdul Hamid
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  5. Ibrahim Wasiu Arolu
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  6. M. A. Latif
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Correspondence to Md. Amirul Alam.

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Alam, M.A., Juraimi, A.S., Rafii, M.Y. et al. Application of EST-SSR marker in detection of genetic variation among purslane (Portulaca oleracea L.) accessions. Braz. J. Bot 38, 119–129 (2015). https://doi.org/10.1007/s40415-014-0103-0

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