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Genetic variation among Iranian Medicago polymorpha L. populations based on SSR markers

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Abstract

Burr medic (Medicago polymorpha L.), a native of the Mediterranean Basin, has become a worldwide weed. Pasture cultivars have been selected, especially in Australia. The species is extremely variable, and there is little agreement on its infraspecific classification. Towards a better understanding of its variation pattern, present study examined population genetic structure and genetic diversity in Iran, employing co-dominant SSR markers. Seventy-one randomly collected plants from 14 geographical populations were sampled. Six primer pairs generated 21 polymorphic bands. The average polymorphic information content was high (0.923). Genetic diversity parameters were determined in these populations. STRUCTURE analysis and K-Means clustering identified two and three gene pools in the country. Mantel test results revealed isolation by distance among the studied populations. The cluster analysis showed correlation between genetic and geographical distance. AMOVA revealed a significant genetic difference among populations and showed that 46% of total genetic variation was due to among population diversity. These data may be useful for future breeding and conservation of this important and potentially agricultural plant.

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References

  • Abdelkefi A, Boussaid M, Biborchi A, Haddioui A, Salhi-Hanachi A, Marrakchi M (1996) Genetic diversity inventory and valuation of spontaneous species belonging to Medicago genus in Tunisia. CIHEAM 18:143–150

    Google Scholar 

  • Aitken Y (1981) Temperate herbage grasses and legumes. In: Handbook of flowering. Halevy, CRC, Boca Raton, Florida

  • Badri M, Arraouadi S, Huguet T, Aouani ME (2010) Comparative effects of water deficit on Medicago laciniata and M. truncatula lines sampled from sympatric populations. J Plant Breed Crop Sci 2:192–204

    Google Scholar 

  • Badri M, Cheikh NB, Mahjoub A, Abdelly C (2016) Morpho-phenological diversity among natural populations of Medicago polymorpha of different Tunisian ecological areas. Watsonia 15(25):1330–1338

    CAS  Google Scholar 

  • Badri M, Zitoun A, Soula S, Ilahi H, Huguet T, Aouani ME (2008) Low levels of quantitative and molecular genetic differentiation among natural populations of Medicago ciliaris Kroch. (Fabaceae) of different Tunisian eco-geographical origin. Conserv Genet 9:1509–1520

    CAS  Google Scholar 

  • Bagavathiannan MV, Julier B, Barre P, Gulden RH, Van Acker RC (2010) Genetic diversity of feral alfalfa (Medicago sativa L.) populations occurring in Manitoba, Canada and comparison with alfalfa cultivars: an analysis using SSR markers and phenotypic traits. Euphytica 173:419–432

    Google Scholar 

  • Baquerizo-Audiot E, Desplanque B, Prosperi JM, Santoni S (2001) Characterization of microsatellite loci in the diploid legume Medicago truncatula (barrel medic). Mol Ecol Notes 1:1–3

    CAS  Google Scholar 

  • Boissier E (1872) Medicago in Flora Oriental. -Rep. 1975, by Asher A, and Co. B. V., Amsterdam, 2: 90–105

  • Cholastova T, Knotova D (2012) Using morphological and microsatellite (SSR) markers to assess the genetic diversity in Alfalfa (Medicago sativa L.). Int J Biol Biomol Agric Food Biotechnol Eng 6(9):782–787

    Google Scholar 

  • De Kort H, Vandepitte K, Honnay O (2012) A meta-analysis of the effects of plant traits and geographical scale on the magnitude of adaptive differentiation as measured by the difference between QST and FST. Evol Ecol 27:6

    Google Scholar 

  • Diwan N, Bouton JH, Kochert G (2000) Cregan Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa. Theor Appl Genet 101:165–172

    CAS  Google Scholar 

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

    Google Scholar 

  • Earl DA, VonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res 4:359–361

    Google Scholar 

  • Ellwood SR, Souza NKD, Kamphuis LG, Burgess TI, Nair RM, Oliver RP (2006) SSR analysis of the Medicago truncatula SARDI core collection reveals substantial diversity and unusual genotype dispersal throughout the Mediterranean basin. Theor Appl Genet 112:977–983

    CAS  PubMed  Google Scholar 

  • Escudero A, Iriondo JM, Torres ME (2003) Spatial analysis of genetic diversity as a tool for plant conservation. Biol Conserv 113:351–365

    Google Scholar 

  • Esfandani-Bozchaloyi S, Sheidai M, Keshavarzi M, Noormohammadi Z (2017) Genetic diversity and morphological variability in Geranium purpureum Vill. (Geraniaceae) of Iran. Genetika 49(2):543–557

    Google Scholar 

  • Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108(3):414–422

    CAS  PubMed  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detectig the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620

    CAS  PubMed  Google Scholar 

  • Falahati-Anbaran M, Habashi AA, Esfahany M, Mohammadi SA, Ghareyazie B (1997) Population genetic structure based on SSR markers in alfalfa (Medicago sativa L.) from various regions contiguous to the centres of origin of the species. J Genet 86(1):59–63

    Google Scholar 

  • Flajoulot S, Ronfort J, Baudouin P, Barre P, Huguet T, Huyghe C, Julier B (2005) Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers. Theor Appl Genet 111(7):1420–1429

    CAS  PubMed  Google Scholar 

  • Freeland JR (2020) Molecular ecology, 3rd edn. Wiley-Blackwell, London, p 363

    Google Scholar 

  • Hammer Ø, Harper DAT, Ryan PD (2012) PAST: paleontological statistics software package for education and data analysis. Palaeontol Electron 4:9 p. http://palaeo-electron.org/2001-1/past/issue1-01.htm. Accessed 15 May 2020

  • Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding and germplasm resources. Sinauer Associates, Sunderland, pp 43–63

    Google Scholar 

  • Hendry AP (2002) QST >=≠>FST? Trends Ecol Evol 17:502

    Google Scholar 

  • Heyn CC (1963) The annual species of Medicago. Scripta Hierosolymitana 12. Publications of the Hebrew University, Jerusalem p 154

  • Heyn CC (1984) Medicago in Flora Iranica. In: Rechinger KH (ed) Akademische Druch–U. Verlagsanstalt Graz, pp 253–271

  • Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23(2):254–267

    CAS  PubMed  Google Scholar 

  • Jafari N, Behroozi R, Bagheri A, Moshtaghi N (2013) Determination of Genetic diversity of cultivated chickpea (Cicer arietinum L.) using Medicago truncatula EST–SSRs. JPMB pp 1–16

  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806

    CAS  PubMed  Google Scholar 

  • Jolivet C, Bernasconi G (2007) Molecular and quantitative genetic differentiation in European populations of Silene latifolia (Caryophyllaceae). Ann Bot 100:119–127

    PubMed  PubMed Central  Google Scholar 

  • Juan A, Crespo MB, Cowan RS, Lexer C, Fay MF (2004) Patterns of variability and gene flow in Medicago citrina, an endangered endemic of islands in the western Mediterranean, as revealed by amplified fragment length polymorphism (AFLP). Mol Ecol 13:2679–2690

    CAS  PubMed  Google Scholar 

  • Julier B, Flajoulot S, Barre P, Cardinet G, Santoni S, Huguet T, Huyghe C (2003) Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol. 3:1471–1490

    Google Scholar 

  • Keivani M, Ramezanpour SS, Soltanloo H, Choukan R, Naghavi M, Ranjbar M (2010) Genetic diversity assessment of alfalfa (Medicago sativa L.) populations using AFLP markers. Aust. J. Crop Sci. 4(7):491–497

    CAS  Google Scholar 

  • Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R, Remm M (2018) Primer3–masker: integrating masking of template sequence with primer design software. Bioinform 34:1937–1938

    CAS  Google Scholar 

  • Liu ZP, Liu GS, Yang QC (2007) A novel statistical method for assessing SSR variation in autotetraploid alfalfa (Medicago sativa L.). Genet Mol Biol 30(2):385–391

    Google Scholar 

  • Loi A, Howieson JG, Cocks PS, Caredda S (1993) The adaptation of Medicago polymorpha to a range of edaphic and environmental conditions: effect of temperature on growth, and acidity stress on nodulation and nod gene induction. Aust J Agric Res 33:25–30

    Google Scholar 

  • Loi A, Porqeuddu C, Veronesi F, Cocks PS (1995) Distribution, diversity and potential agronomic value of Medicago polymorpha in Sardinia. J Agric Res 124:419–426

    Google Scholar 

  • Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinform 27:2957–2963

    CAS  Google Scholar 

  • Mandoulakani AB, Sadigh P, Azizi H, Piri Y, Nasri S (2015) Comparative assessment of IRAP, REMAP, ISSR, and SSR markers for evaluation of genetic diversity of alfalfa (Medicago sativa L.). J Agric Sci Technol 17:999–1010

    Google Scholar 

  • Mehregan I, Rahiminejad MR, Azizian D, Hemmat M, Moussavi M (2001) Introduction to taxonomy of the genus Medicago in Iran. In: Proceedings of 10th biological conferences of Iran, pp 469–472

  • Mehregan I, Rahiminejad MR, Azizian D (2002) A taxonomic revision of the genus Medicago L. (Fabaceae) in Iran. Iran J Bot 9(2):207–221

    Google Scholar 

  • Mehregan I, Moussavi M, Nasrabadi N (2003) The genus Medicago in Iran: biodiversity and variation centres. Rostaniha (Bot J Iran) 4(1):5–18

    Google Scholar 

  • Min X, Zhang Z, Liu Y, Wei X, Liu Z, Wang Y, Liu W (2017) Genome-wide development of MicroRNA-based SSR markers in Medicago truncatula with their transferability analysis and utilization in related legume species. Int J Mol Sci 18:2440. https://doi.org/10.3390/ijms18112440

    Article  CAS  PubMed Central  Google Scholar 

  • Mohammadzadeh F, Monirifar H, Saba J, Valizadeh M (2011) Genetic variation among Iranian alfalfa (Medicago sativa L.) populations based on RAPD markers. BJPT 18(2):93–104

    Google Scholar 

  • Moussavi M (1977) Identification of Medicago species in Tehran. MAJ, Iran, p 45p

    Google Scholar 

  • Parsa A (1948) Medicago in Flora de L’Iran. Pubication du Ministere de L’Education, Museaum LHistoire Naturelle de Tehran, Iran, pp 171–181

  • Peakall R, Smouse PE (2006) GENAIEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539

    CAS  PubMed  PubMed Central  Google Scholar 

  • Perez MF, Franco FF, Bombonato JR, Bonatelli IA, Khan G, Romeiro-Brito M, Fegies AC, Ribeiro PM, Silva GAR, Moraes EM (2018) Assessing population structure in the face of isolation by distance: Are we neglecting the problem? Divers Distrib 24(12):1883–1889

    Google Scholar 

  • Podani J (2000) Introduction to the exploration of multi-variate data [English translation]. Backhuyes Publishers, Leide, p 407

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ronfort J, Bataillon T, Santoni S, Delalande M, David J, Prosperi JM (2006) Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collections for studying naturally occurring variation in Medicago truncatula. BMC Plant Biol 6(28):1471–2229

    Google Scholar 

  • Salhi Hannachi A, Boussaid M, Marrakchi M (1998) Genetic variability organisation and gene flow in natural populations of Medicago polymorpha L. prospected in Tunisia. GSE 30:121–135

    Google Scholar 

  • Small E (2011) Alfalfa and relatives: Evolution and classification of Medicago. NRC Research Press, Canada

    Google Scholar 

  • Small E, Jomphe M (1989) A synopsis of the genus Medicago (Leguminosae). Can J Bot 67:3260–3294

    Google Scholar 

  • Small E, Brookes B, Crawford EJ (1990) Intercontinental differentiation in Medicago rigidula. Can J Bot 68(12):2607–2613

    Google Scholar 

  • Steele KP, Ickert-Bond SM, Zarre S, Wojciechowski MF (2010) Phylogeny and character evolution in Medicago (Leguminosae): evidence from analyses of plastic TRNK/MATK and nuclear GA3OX1 sequences. Am J Bot 97(7):1142–1155

    CAS  PubMed  Google Scholar 

  • Takezaki N, Nei M, Tamura K (2009) POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752

    PubMed  PubMed Central  Google Scholar 

  • Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395–420

    Google Scholar 

  • Yan J, Chu HJ, Wang HC, Li JQ, Sang T (2009) Population genetic structure of two Medicago species shaped by distinct life form, mating system and seed dispersal. Ann Bot 103(6):825–834

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang T, Fang L, Zhang X, Hu J, Bao S, Hao J, Li L, He Y, Jiang J, Wang F, Tian S, Zong X (2015) High-throughput development of SSR markers from Pea (Pisum sativum L.) based on next generation sequencing of a purified Chinese commercial variety. PLoS ONE 10:e0139775

    Google Scholar 

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Acknowledgements

The authors would to thank Ali Ghaderi for his helps in field works, and two anonymous reviewers for their valuable comments on an earlier version of the manuscript. Ethical standards.

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Authors and Affiliations

  1. Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran

    Samane-Sadat Emami-Tabatabaei & Iraj Mehregan

  2. Department of Botany, Research Institute of Forests and Rangelands, Agricultural Research Education and Extension Organization (AREEO), P. O. Box 13185-116, Tehran, Iran

    Mostafa Assadi

  3. Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada

    Ernest Small

  4. Department of Biology, Borujerd Branch, Islamic Azad University, Borujerd, Iran

    Mohammad Mehdi Dehshiri

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  1. Samane-Sadat Emami-Tabatabaei
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  2. Ernest Small
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Correspondence to Iraj Mehregan.

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Emami-Tabatabaei, SS., Small, E., Assadi, M. et al. Genetic variation among Iranian Medicago polymorpha L. populations based on SSR markers. Genet Resour Crop Evol 68, 1411–1424 (2021). https://doi.org/10.1007/s10722-020-01071-7

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  • DOI: https://doi.org/10.1007/s10722-020-01071-7

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