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Licensed Unlicensed Requires Authentication Published by De Gruyter April 20, 2016

Use of IRAP and REMAP markers to interpret the population structure of Linum usitatissimum from Iran

  • Hossein Abbasi Holasou , Babak Abdollahi Mandoulakani EMAIL logo , Morad Jafari and Iraj Bernousi
From the journal Biologia

Abstract

Flax (Linum usitatissimum L.) is the third largest natural fiber crop in the world. The flax genome shows environmentally induced heritable genomic changes. The activation of transposable elements has been proposed and identified as the mechanism behind this genotypic plasticity. Transposable elements, particularly the retrotransposons, generates genomic diversity by replication which makes them an excellent source of molecular markers. Inter-retrotransposon amplified polymorphism (IRAP) and the retrotransposon-microsatellite amplified polymorphism (REMAP) markers were used to assess the insertional polymorphism of LTR retrotransposons and genetic diversity in 80 genotypes of L. usitatissimum collected from Iran. A total of 77 and 133 loci were amplified using 7 IRAP and 13 REMAP primers, respectively. Percentage of polymorphic loci (PPL) for IRAP and REMAP markers were 53.25% and 58.92%, respectively. Average of expected heterozygosity (He), number of effective alleles (Ne) and Shannon’s information index (I) for IRAP markers were slightly more than those of REMAP markers. A high level of intra-population genetic differentiation was found, which is supported by a moderate level of gene flow among populations. A model-based Bayesian approach and cluster analysis using Minimum Evolution (ME) algorithm distinguished genotypes collected from Alborz region from those collected from Zagros region. Mantel test between genetic and geographical distances of populations revealed low but significant correlation coefficient (r = 0.36, P ≤ 0.05). The results demonstrated that molecular markers developed based on active LTR retrotransposons in flax could be used as relatively reliable tools to analysis population structure in L. usitatissimum.

Acknowledgements

The authors would like to thank the Institute of Biotechnology of the Urmia University (Urmia, Iran) for hosting the lab facilities. Dr A. Hassanzadeh Gorttapeh (Agricultural and Natural Research Center of West Azarbayjan, Urmia, Iran) appreciates for providing the seeds of flax populations.

References

Abdollahi Mandoulakani B., Piri Y., Darvishzadeh R., Bernoosi I. & Jafari M. 2012. Retroelement insertional polymorphism and genetic diversity in Medicago sativa populations revealed by IRAP and REMAP markers. Plant Mol. Biol. Rep. 30: 286–296.10.1007/s11105-011-0338-xSearch in Google Scholar

Abdollahi Mandoulakani B., Rahmanpour S., Shaaf S., Gholamzadeh Khoei S., Rastgou M. & Rafezi R. 2015a. Towards the identification of retrotransposon-based and ISSR molecular markers associated with populations resistant to ZYMV in melon. S. Afr. J. Bot. 100: 141–147.10.1016/j.sajb.2015.05.027Search in Google Scholar

Abdollahi Mandoulakani B., Sadigh P., Azizi H., Piri Y., Nasri Sh. & Arzhangh S. 2015b. Comparative assessment of IRAP, REMAP, ISSR, and SSR markers for evalution of genetic diversity of alfalfa (Medicago sativa L.). J. Agr. Sci. Tech. 17: 999–1010.Search in Google Scholar

Abdollahi Mandoulakani B., Yaniv E., Kalendar R., Raats D., Bariana H.S., Bihamta M.R. & Schulman A.H. 2015c. Development of IRAP- and REMAP- derived SCAR markers for marker-assisted selection of the stripe rust resistance gene Yr15 derived from wild emmer wheat. Theor. Appl. Genet. 128: 211–219.10.1007/s00122-014-2422-8Search in Google Scholar PubMed

Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K., Albright L.M., Coen D.M. & Varki A. 1995. Current Protocols in Molecular Biology. John Wiley, New York.Search in Google Scholar

Barnes D.K., Culbertson J.O. & Lambert J.W. 1960. Inheritance of seed and flower colors in flax. Agron. J. 52: 456–45910.2134/agronj1960.00021962005200080010xSearch in Google Scholar

Biswas M.K., Xu Q. & Deng X. 2010. Utility of RAPD, ISSR, IRAP and REMAP markers for the genetic analysis of Citrus spp. Sci. Hortic. 124: 254–261.10.1016/j.scienta.2009.12.013Search in Google Scholar

Branco C.J.S., Vieira E.A., Malone G., Kopp M.M., Malone E., Bernardes A., Mistura C.C., Carvalho F.I.F. & Oliveira C.A. 2007. IRAP and REMAP assessments of genetic similarity in rice. J. Appl. Genet. 2: 107–113.10.1007/BF03194667Search in Google Scholar PubMed

Chen Y., Schneeberger R.G. & Cullis C.A. 2005. A site-specific insertion sequence in flax genotrophs induced by environment. New Phytol. 167: 171–180.10.1111/j.1469-8137.2005.01398.xSearch in Google Scholar PubMed

Chen Y., Lowenfeld R. & Cullis C.A. 2009. An environmentally induced adaptive (?) insertion event in flax. Int. J. Genet. Mol. Biol. 3: 038–047.Search in Google Scholar

Cloutier S., Ragupathy R. & Niu Z. 2011. SSR-based linkage map of flax (Linum usitassimum L.) and mapping of QTLs underlying fatty acid composition traits. Mol. Breeding. 28: 437–451.10.1007/s11032-010-9494-1Search in Google Scholar

Cullis C.A. 2005. Mechanisms and control of rapid genomic changes in flax. Ann. Bot. 95: 201–206.10.1093/aob/mci013Search in Google Scholar PubMed PubMed Central

Diederichsen A. & Fu Y.B. 2006. Phenotypic and molecular (RAPD) differentiation of four infraspecific groups of cultivated flax (Linum usitatissimum L. subsp. usitatissimum). Genet. Resour. Crop Evol. 53: 77–90.10.1007/s10722-004-0579-8Search in Google Scholar

Diederichsen A. & Hammer K. 1995. Variation of cultivated flax (Linum usitatissimum L. subsp. usitatissimum) and its wild progenitor pale flax (subsp. angustifolium (Huds.) Thell.). Genet. Resour. Crop Evol. 42: 263–272.10.1007/BF02431261Search in Google Scholar

Evanno G., Regnaut S. & Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14: 2611–2620.10.1111/j.1365-294X.2005.02553.xSearch in Google Scholar

Evans G.M., Durrant A. & Rees H. 1966. Associated nuclear changes in the induction of flax genotrophs. Nature. 212: 697–699.10.1038/212697a0Search in Google Scholar

Everaert I., de Riek J., de Loose M., van Waes J. & van Bockstaele E. 2001. Most similar variety grouping for distinctness evaluation of flax and linseed (Linum usitatissimum L.) varieties by means of AFLP and morphological data. Plant Var. Seeds. 14: 69–87.Search in Google Scholar

Fu Y.B. 2006. Redundancy and distinctness in flax germplasm as revealed by RAPD dissimilarity. Plant Genet. Resour. 4: 117–124.10.1079/PGR2005106Search in Google Scholar

Fu Y.B., Diederichsen A., Richards K.W. & Peterson G. 2002. Genetic diversity within a range of cultivars and landraces of flax (Linum usitatissimum L.) as revealed by RAPDs. Genet. Resour. Crop Evol. 49: 167–174.10.1023/A:1014716031095Search in Google Scholar

Gholamzadeh Khoei S., Abdollahi Mandoulakani B. & Bernousi I. 2015. Genetic diversity in Iranian melon populations hybrids assessed by IRAP and REMAP markers. J. Agr .Sci. Tech. 17: 1267–1277.Search in Google Scholar

Gill K.S. 1987. Linseed. Publications and Information Division. Indian Council of Agricultural Research, New Delhi, India.Search in Google Scholar

Gorman N.B., Cullis C.A. & Aldridge N. 1993. Genetic and linkage analysis of isozyme polymorphism in flax. J. Hered. 84: 73–78.10.1093/oxfordjournals.jhered.a111281Search in Google Scholar

Haggans C.J., Hutchins A.M., Olson B.A., Thomas W., Martini M.C. & Slavin J.L. 1999. Effect of flaxseed consumption on urinary estrogen metabolites in postmenopausal women. Nutr. Cancer. 33: 188–195.10.1207/S15327914NC330211Search in Google Scholar

Hilakivi-Clarke L., Clarke R. & Lippman M. 1999. The influence of maternal diet on breast cancer risk among female offspring. Nutrition. 15: 392–401.10.1016/S0899-9007(99)00029-5Search in Google Scholar

Ivanova S., Rashevskaya T. & Makhonina M. 2011. Flaxseed additive application in dairy products production. Procedia Food Sci. 1: 275–280.10.1016/j.profoo.2011.09.043Search in Google Scholar

Kalendar R., Grab T., Regina M., Souniemi A. & Schulman A.H. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet. 98: 704–711.10.1007/s001220051124Search in Google Scholar

Kalendar R., Tanskanen J., Immonen S., Nevo E. & Schulman A.H. 2000. Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc. Natl. Acad. Sci. USA. 97: 6603–6607.10.1073/pnas.110587497Search in Google Scholar PubMed PubMed Central

Laurentin H. 2009. Data analysis for molecular characterization of plant genetic resources. Genet. Resour. Crop Evol. 56: 277–292.10.1007/s10722-008-9397-8Search in Google Scholar

Lowe A., Harris S. & Ashton P. 2004. Ecological Genetics: Design, Analysis and Application. Blackwell Science Ltd, Oxford, (UK), 326 pp.Search in Google Scholar

Melnikova N.V., Kudryavtseva A.V., Zelenin A.V., Lakunina V.A., Yurkevich O.Y., Speranskaya A.N., Dmitriev A.A., Krinitsina A.A., Belenikim M.S., Uroshlev L.A., Snezhkina A.V., Sadritdinova A.F., Koroban N.V., Amosova A.V., Samatadze T.E., Guzenko E.V., Lemesh V.A., Savilova A.M., Rachinskaia O.A., Kishlyan N.V., Rozhmina T.A., Bolsheva N.L. & Muravenko O.V. 2014. Retrotransposon-based molecular markers for analysis of genetic diversity within the genus Linum. BioMed Res. Int. 231589.10.1155/2014/231589Search in Google Scholar PubMed PubMed Central

Muravenko O.V., Lemesh V.A., Samatadze T.E., Amosova A.V., Grushetskaya Z.E., Popov K.V., Semenova O.Y.U., Khotyuleva L.V. & Zelenin A.V. 2003. Genome comparisons with chromosomal and molecular markers for three closely related flax species and their hybrids. Russ. J. Genet. 39: 414–421.10.1023/A:1023309831454Search in Google Scholar

Murre M. 1955. Vezelvlas. Uitgeverij Ceres, Meppel, The Netherlands: 112 pp.Search in Google Scholar

Nasri S.H., Abdollahi Mandoulakani B., Darvishzadeh R. & Bernoosi I. 2013. Retrotransposon insertional polymorphism in Iranian bread wheat cultivars and breeding lines revealed by IRAP and REMAP markers. Biochem. Genet. 51: 927–943.10.1007/s10528-013-9618-5Search in Google Scholar PubMed

Paterson A.H., Bowers J.E., Bruggmann R., Dubchak I., Grimwood J., Gundlach H., Haberer G., Hellsten U., Mitors T., Poliakov A., Schmutz J., Spannagl M., Tang H., Wang X., Wicker T., Bharti A.K., Chapman J., Alex Feltus F., Gowik U., Grigoriev I.V., Lyons E., Maher C.A., Martis M., Narechania A., Otillar R.P., Penning B.W., Salamov A.A., Wang Y., Zhang L., Carpita N.C., Freeling M., Gingle A.R., Hash C.T., Keller B., Klein P., Kresovich S., McCann M.C., Ming R., Peterson D.G., Rahman M., Ware D., Westhoff P., Mayer K.F.X., Messing J. & Rokhsar D.S. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551–556.10.1038/nature07723Search in Google Scholar PubMed

Peakall R. & Smouse P.E. 2006. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes. 6: 288–295.10.1111/j.1471-8286.2005.01155.xSearch in Google Scholar

Pritchard J.K., Stephens M. & Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.10.1093/genetics/155.2.945Search in Google Scholar PubMed PubMed Central

Rao N. 2004. Plant genetic resources: Advancing conservation and use through biotechnology. Afr. J. Biotechnol. 3: 136–145.10.5897/AJB2004.000-2025Search in Google Scholar

Rechinger K.H. 1974. Linaceae. In: Rechinger KH (ed.) Flora Iranica. vol, 106. Graz: Akademische Druck-und Verlagsansatalt.Search in Google Scholar

Rohlf F.J. 2000. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, New York.Search in Google Scholar

Sharifinia F. & Assadi M. 2001. Flora of Iran, No. 34: Linaceae. Research Inst, Forests and Rangelands, Ministry of Jahad-e-Sazandegi, Iran (In Persian).Search in Google Scholar

Shimamura M., Yasue H., Ohshima K., Abe H., Kato H., Kishiro T., Goto M., Munechika I. & Okada N. 1997. Molecular evidence from retroposons that whales form a clade within eventoed ungulates. Nature 388: 666–670.10.1038/41759Search in Google Scholar PubMed

Smith J.S.C., Chin E.C.L., Shu H., Smith O.S., Wall S.J., Senior M.L., Mitchell S.E., Kresovich S. & Ziegle J. 1997. An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.) comparisons with data from RFLPS and pedigree. Theor. Appl. Genet. 95: 163–173.10.1007/s001220050544Search in Google Scholar

Smykal P. 2006. Development of an efficient retrotransposonbased fingerprinting method for rapid pea variety identification. J. Appl. Genet. 47: 221–230.10.1007/BF03194627Search in Google Scholar

Smykal P., Hybl M., Corander J., Jarkovsky J., Flavell A.J. & Griga M. 2008. Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor. Appl. Genet. 117: 413–424.10.1007/s00122-008-0785-4Search in Google Scholar

Smykal P., Bacova-Kerteszova N., Kalendar R., Corander J., Schlman A.H. & Pavelek M. 2011. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theor. Appl. Genet. 122: 1385–1397.10.1007/s00122-011-1539-2Search in Google Scholar

Tamura K., Dudley J., Nei M. & Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24: 1596–1599.10.1093/molbev/msm092Search in Google Scholar

Tanksley S.D. & McCouch S.R. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Sci. 277: 1063–1066.10.1126/science.277.5329.1063Search in Google Scholar

Uysal H., Fu Y.B., Kurt O., Peterson G.W., Diederichsen A. & Kusters P. 2010. Genetic diversity of cultivated flax (Linum usitatissimum L.) and its wild progenitor pale flax (Linum bienne Mill.) as revealed by ISSR markers. Genet. Resour. Crop Evol. 57: 1109–1119.10.1007/s10722-010-9551-ySearch in Google Scholar

Vavilov N.I. 1926. Studies on the origin of cultivated plants. Leningrad, Russia: Institute of Applied Botany and Plant Breeding (Leningrad).Search in Google Scholar

Vicient C.M., Kalendar R., Anamthawat-Jonsson K., Suoniemi A. & Schulman A.H. 1999. Structure, functionality, and evolution of the BARE-1 retrotransposon of barley. Genetica. 107: 53–63.10.1007/978-94-011-4156-7_6Search in Google Scholar

Vromans J. 2006. Molecular genetic studies in flax (Linum usitatissimum L.). PhD Thesis, Wageningen University, The Netherlands.Search in Google Scholar

Waugh R., McLean K., Flavell A.J., Pearce S.R., Kumar A., Thomas B.B.T. & Powell W. 1997. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequences-specific amplification polymorphisms (S-SAP). Mol. Genet. Gen. 253: 687–694.10.1007/s004380050372Search in Google Scholar

Wiesnerova D. & Wiesner I. 2004. ISSR-based clustering of cultivated flax germplasm is statistically correlated to thousand seed mass. Mol. Biotechnol. 26: 207–214.10.1385/MB:26:3:207Search in Google Scholar

Zohary D. & Hopf M. 2000. Domestication of plants in the Old World: the origin and spread of cultivated plants in West Asia, Europe and the Nile Valley, 3th ed. Oxford University Press, Oxford.Search in Google Scholar

Zou J., Gong H., Yang T.-J. & Meng J. 2009. Retrotransposons-a major driving force in plant genome evolution and a useful tool for genome analysis. J. Crop Sci. Biotech. 12: 1–8.10.1007/s12892-009-0070-3Search in Google Scholar

Abbreviations
LTR

long terminal repeat

REMAP

retrotransposon-microsatellite amplified polymorphism

SSR

simple sequence repeat

Received: 2015-9-4
Accepted: 2016-2-19
Published Online: 2016-4-20
Published in Print: 2016-3-1

© 2016 Institute of Botany, Slovak Academy of Sciences

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