Population Genetic and Structure Analyses of Annual Iranian Medicago orbicularis Indicates Advantageous Use of HTS-Generated SSR Markers

Zahra Morshedi1, Mostafa Assadi2, Ernest Small3, Mohammad Mehdi Dehshiri4, Iraj Mehregan1
1Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
2Department of Botany, Agricultural Research Education and Extension Organization (AREEO), Research Institute of Forests and Rangelands, Tehran, Iran
3Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
4Department of Biology, Islamic Azad University, Borujerd Branch, Borujerd, Iran

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Abbate L, Mercati F, Di Noto G, Heuertz M, Carimi F, Fatta Del Bosco S, Schicchi R (2020) Genetic distinctiveness highlights the conservation value of a Sicilian Manna Ash germplasm collection assigned to Fraxinus angustifolia (Oleaceae). Plants (basel) 9(8):1035. https://doi.org/10.3390/plants9081035

Albach DC, Greilhuber J (2004) Genome size variation and evolution in Veronica. Ann Bot (oxford) 94:897–911. https://doi.org/10.1093/aob/mch219

Altman A, Hasegawa PM (2012) Plant biotechnology and agriculture: prospects for the 21st century. Elsevier, Amsterdam and Boston, p 586

Badri M, Ilahi H, Huguet T, Aouani ME (2007) Quantitative and molecular genetic variation in sympatric populations of Medicago laciniata and M. truncatula (Fabaceae): relationships with eco-geographical factors. Genet Res 89(2):107–122. https://doi.org/10.1017/S0016672307008725

Badri M, Zitoun A, Ilahi H, Huguet T, Aouani ME (2008a) Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae). J Genet 87(3):241–255. https://doi.org/10.1007/s12041-008-0038-y

Badri M, Zitoun A, Soula S, Ilahi H, Huguet T, Aouani ME (2008b) 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(6):1509–1520. https://doi.org/10.1007/s10592-007-9483-z

Bagheri Z, Assadi M, Small E, Mehregan I (2022) Cryptic Molecular-Geographical Divergence within Medicago minima revealed by SSR markers. Iran J Sci Technol Trans Sci 46(1):49–60. https://doi.org/10.1007/s40995-021-01236-8

Bayat M, Assadi M, Small E, Mehregan I (2021) Molecular studies of Iranian populations support the morphology-based taxonomic separation of Medicago rigidula and M. rigiduloides. Phytotaxa 518(4):281–299. https://doi.org/10.11646/phytotaxa.518.4.5

Béna G, Lyet A, Huguet T, Olivieri I (2005) Medicago-Sinorhizobium symbiotic specificity evolution and the geographic expansion of Medicago. J Evol Biol 18:1547–1558

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

Botstein D, Whit RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32(3):314–331

Conway MJ, Brandon NJ, Clem RL, Jones RM, Robertson BA, Willcocks JR (2001) Growth and persistence of 17 annual medic (Medicago spp.) accessions on clay soils in Central Queensland. Trop Grassl 35(4):226–234

De Barba M, Miquel C, Lobréaux S, Quenette PY, Swenson JE, Taberlet P (2017) High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA. Mol Ecol Resour 17(3):492–507. https://doi.org/10.1111/1755-0998.12594

Derkaoui M, Caddel JL, Rommann LL (1993) Forage quality in annual Medicago spp. Agric Mediterr 123:86–91

Djedid IK, Terzaghi M, Brundu G, Cicatell A, Laouar M, Guarino F, Castiglione S (2022) Genetic diversity and differentiation of eleven Medicago species from Campania region revealed by nuclear and chloroplast microsatellites markers. Genes 13:97. https://doi.org/10.3390/genes13010097

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

Earl DA, VonHoldt BM (2012) Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361. https://doi.org/10.1007/s12686-011-9548-7

Emami-Tabatabaei SS, Small E, Assadi M, Dehshiri MM, Mehregan I (2021) Genetic variation among Iranian Medicago polymorpha L. populations based on SSR markers. Genet Resour Crop Evol 68(4):1411–1424. https://doi.org/10.1007/s10722-020-01071-7

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. https://doi.org/10.1111/j.1365-294x.2005.02553.x

Freeland JR (2020) Molecular ecology, 3rd edn. Wiley, Oxford, p 384

Friedman J (2020) The evolution of annual and perennial plant life histories: ecological correlates and genetic mechanisms. Ann Rev Ecol Evol Syst 51:461–481. https://doi.org/10.1146/annurev-ecolsys-110218-024638

Germain-Aubrey CC, Nelson C, Soltis DE, Soltis PS, Gitzendanner MA (2016) Are microsatellite fragment lengths useful for population-level studies? the case of Polygala lewtonii (Polygalaceae). Appl Plant Sci 4(2):1500115. https://doi.org/10.3732/apps.1500115

Godwin ID, Aitken EAB, Smith LW (1997) Application of inter simple sequence repeat (ISSR) markers to plant genetics. Electrophoresis 18:1524–1528. https://doi.org/10.1002/elps.1150180906

Haddoudi L, Hdira S, Cheikh NB, Mahjoub A, Abdelly C, Ludidi N, Badri M (2021) Assessment of genetic diversity in Tunisian populations of Medicago polymorpha based on SSR markers. Chil J Agric Res 81(1):53–61. https://doi.org/10.4067/s0718-58392021000100053

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

Hannachi AS, Boussaid M, Marrakchi M (1998) Genetic variability organization and gene flow in natural populations of Medicago polymorpha L. prospected in Tunisia. Genet Sel Evol 30:S121. https://doi.org/10.1186/1297-9686-30-S1-S121

Heyn CC (1963) The annual species of Medicago. Magnes Press, The Hebrew University, Jerusalem, p 154

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(14):1801–1806. https://doi.org/10.1093/bioinformatics/btm233

Jiang H, Waseem M, Wang Y, Basharat S, Zhang X, Li Y, Liu P (2023) Development of simple sequence repeat markers for sugarcane from data mining of expressed sequence tags. Front Plant Sci 14:1199210. https://doi.org/10.3389/fpls.2023.1199210

Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R, Remm M (2018) Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics 34(11):1937–1938. https://doi.org/10.1093/bioinformatics/bty036

Lepais O, Aissi A, Véla E, Beghami Y (2022) Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations. Heredity 129(3):169–182. https://doi.org/10.1038/s41437-022-00550-0

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. https://doi.org/10.1590/S1415-47572007000300015

Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27(21):2957–2963. https://doi.org/10.1093/bioinformatics/btr507

Marques AC, Ferraro-Peyret C, Michaud F, Song L, Smith E, Fabre G, Willig A, Wong MML, Xing X, Chong C, Brayer M, Fenouil T, Hervieu V, Bancel B, Devouassoux M, Balme B, Meyronet D, Menu P, Lopez J, Xu Z (2022) Improved NGS-based detection of microsatellite instability using tumor-only data. Front Oncol 12:969238. https://doi.org/10.3389/fonc.2022.969238

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

Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3(1):175–182

Olivieri I, Gouyon PH, Prosperi JM (1991) Life cycles of some Mediterranean invasive plants. In: Groves RH, Castri FDI (eds) Biogeography of Mediterranean invasions. Cambridge University Press, Cambridge, pp 145–157

Parsa A (1948) Medicago in Flora de l'Iran. - Publication du Ministere de r Education, Museum l'Histoire Naturelle de Tehran, Tehran. 171–181

Peakall R, Smouse PE (2006) GENAIEx 6: genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

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. https://doi.org/10.1111/j.1471-8286.2005.01155.x

Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959. https://doi.org/10.1093/genetics/155.2.945

Prosperi JM, Angevian M, Bonnin I, Chaulet E, Genier G, Jenczewski E, Olivieri I, Ronfort J (1996) Genetic diversity, preservation and use of genetic resources of Mediterranean legumes: alfa and medics (part of workshop: the genus Medicago in the Mediterranean region: current and prospects in research: 1995 October, Hammamet, Tunisie). Cah Options Mediterr 18:71–89

Reed DH, Frankham R (2003) Correlation between fitness and genetic diversity. Conserv Biol 17:230–237

Ronfort J, Bataillon T, Santoni S, Delalande M, David JL, Prosperi JM (2006) Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biol 13:6–28. https://doi.org/10.1186/1471-2229-6-28

Šarhanová P, Pfanzelt S, Brandt R, Himmelbach A, Blattner FR (2018) SSR-seq: genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring. Ecol Evol 8(22):10817–10833. https://doi.org/10.1002/ece3.4533

Small E (1988) Pollen-ovule patterns in tribe Trifolieae (Leguminosae). Plant Syst Evol 160(3–4):195–205. https://doi.org/10.1007/BF00936047

Small E (2011) Alfalfa and relatives: evolution and classification of Medicago. NRC Research Press, Ottawa

Soltis PS, Soltis DE, Savolainen V, Crane PR, Barraclough TG (2002) Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proc Natl Acad Sci USA 99:4430–4435. https://doi.org/10.1073/pnas.032087199

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

Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am J Bot 99(2):193–208. https://doi.org/10.3732/ajb.1100394

Zareei R, Small E, Assadi M, Mehregan I (2022) Genetic structure of Medicago sinskiae using microsatellite data reveals its fast expansion throughout western and southwestern Iran. Collect Bot 41:e2002. https://doi.org/10.3989/collectbot.2022.v41.002

Zhu Y, Sheaffer CC, Barnes DK (1996) Forage yield and quality of six annual Medicago species in the north-central USA. Agron J 88(6):955–960. https://doi.org/10.2134/agronj1996.00021962003600060019x

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

Zoghalami A, Hassen H, Seklani H, Robertson L, Ak S (1996) Distribution des luzernes annuelles en Tunisie centrale en fonction des facteurs edaphiques et climatiques. Fourrages (france) 145:5–16