Welcome to International Network for Natural Sciences | INNSpub

Paper Details

Research Paper | October 1, 2013

| Download

Assessment of genetic variability of 36 Populations of Sainfoin (Onobrychis sativa) based on RAPD markers

Mohamad Rasouli, Ali Ashraf Jafari, Seyed Reza Tabaei-Aghdaei, Parvin Salehi Shanjani, Farokh Darvish

Key Words:

Int. J. Biosci.3(10), 15-26, October 2013

DOI: http://dx.doi.org/10.12692/ijb/3.10.15-26


IJB 2013 [Generate Certificate]


Random amplified polymorphic DNA (RAPD) markers have been used to characterize the genetic diversity of 36 Iranian populations of sainfoin (Onobrychis sativa Scop.). Five out of 20 tested RAPD primers produced 79 polymorphic bands and the average band produced for each primer was 15.8 polymorphic bands. The highest and lowest percentage of polymorphic loci was obtained for the population Divandara (80%) and the population Aligodarz3 (49%), respectively, with average 66%. Dendrograms were prepared using cluster analysis based on Nei’s distance coefficients. Clustering pattern, made on the basis of RAPD data, grouped the accessions differently and gave no clear indication of origin/source. Further examination of the different components of genetic variation by analysis of molecular variance indicated that larger proportions of variability existed within populations (78%). The results also showed that comprehensive germplasm collection in major geographic regions and exploitation of the existing variation are required to widen the genetic base and sample the full extent of the available variation in breeding strategies for sainfoin.


Copyright © 2013
By Authors and International Network for
Natural Sciences (INNSPUB)
This article is published under the terms of the Creative
Commons Attribution Liscense 4.0

Assessment of genetic variability of 36 Populations of Sainfoin (Onobrychis sativa) based on RAPD markers

Badoux S. 1965. Etude des caracteres morphologiques, physiologiques et agronomiques de populations d’esparcette (Onobrychis spp.). Recherche Agronomique Suisse 4, 111–190.

Ahangarian S, Kazempour Osaloo SH, Maassoumi AA. 2007. Molecular phylogeny of the tribe Hedysareae with special reference to Onobrychis (Fabaceae) as inferred from nrDNA ITS sequences. Iranian Journal of Botany 13, 64–4. (In Persian)

Bardakci F. 2001. Random amplified polymorphic DNA (RAPD) markers. Turkish journal of biology 25, 185-196.

Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism, Am. J. Hum. Genet 32, 314–331.

Brummer EC. 1999. Capturing heterosis in forage crop cultivar development. Crop science 39, 943-954. http://dx.doi.org/10.2135/cropsci1999.0011183X003 900040001x

Cruzan MB. 1998. Genetic markers in plant evolutionary ecology. Ecology 79, 400-412. http://dx.doi.org/10.1890/-0012-9658(1998)(0400: GMIPEE) 2.0.CO:2

Delgado I, Salvia J, Buil I, Andre´SC. 2008. The agronomic variability of a collection of sainfoin accessions. Span J Agric Res 6, 401-407.

Emre I, Turgut-balik D, Sahin A, Kursat M. 2007. Total electrophoretic band patterns of some Onobrychis species growing in Turkey. American-Eurasian Journal of Agricultural & Environmental Science 2, 123-126.

Sa´nchez-Ye´lamo MD. 2006. Rapid characterisation of some species of the genus Onobrychis Miller (Leguminosae: Papilionoideae) by isozyme methods. Seed Science and Technology 34, 297–306.

Arslan E, Ertugru LK. 2010.Genetic relationships of the genera Onobrychis, Hedysarum, and Sartoria using seed storage proteins Turk J Biol 34, 67-73. doi:10.3906/biy-0812-24

Carbonero CH. 2011. Sainfoin (Onobrychis vicifolia), A Forage Legume with Great Potential for Sustainable Agriculture, an Insight on ITS Morphological, Agronomical, Cytological and Genetic Characterization. A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 228, 74-86.

Elena T. 2006. Cytological aspects of the Onobrychis genus. Bulletin USAMV 62, 154–58.

Excoffier L, Laval G, Schneider S. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary bioinformatics online 1, 47-50.

Excoffier L, Smouse PE, Quattro GM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479-491.

Gherardi M, Mangin B, Goffinet B, Bonnet D, Huguet T. 1998. A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers. Theoretical and applied genetics 96, 406-412.

Gustine DL, Voigt PW, Brummer EC, Papadopoulos YA. 2002. Genetic variation of RAPD markers for North American white clover collections and cultivars. Crop Science 42, 343–347. http://dx.doi.org/10.2135/cropsci2002.0343

Gupta VS, Ramakrishna W, Rawat SR, Ranjekar PK. 1994. (CAC) 5 detects DNA fingerprints and sequences homologous to gene transcripts in rice. Biochem. Genet 32, 8. http://dx.doi.org/10.1007/BF00557234

Hamrick JL, Godt MJW. 1996. Effects of life history traits on genetic diversity in plant species. Philosophical Transaction of the Royal Society of London B Series: Biological Science 351, 1292-1298. http://dx.doi.org/10.1098/rstb.1996.0112

Hamrick JL, Godt MJW. 1989. Allozyme diversity in plant species, In: Plant population genetics, breeding and genetic resources (eds. Brown, AHD, Clegg MT, Kahler AL, Weir B.S.), 43-63. Sinauer Associates, Sunderland, MA.

Huff DR. 1997. RAPD characterization of heterogeneous perennial ryegrass cultivars. Crop Science 37, 557-564. http://dx.doi.org/10.2135/cropsci1997.0011183X003700020041x

Huff DR, Peakall R, Smouse PE. 1993. RAPD variation within and among natural populations of outcrossing buffalo grass (Buchloe dactyloides Nutt. Engelm). Theoretical and applied genetics 86, 927-934.

Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, Van deWiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, alcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A. 1997. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories. Molecular breeding 3, 381-390.

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 biology 3, 9.

Kidwell KK, Austin DF, Osborn TC. 1994. RFLP evaluation of nine Medicago accessions representing the original germplasm sources of North American alfalfa cultivars. Crop science 34, 230-236. http://dx.doi.org/10.2135/cropsci1994.0011183X003 400010042x

Lu Y, Sun Y, Foo Y, McNabb WC, Olan. 2000. Phenolic glycosides of forage legume Onobrychis viciifolia, Phytochemistry 55, 67-75. http://dx.doi.org/10.1016/S00319422%2800%29001 43-6

Maureira IJ, Ortega F, Campos H, Osborn TC. 2004. Population structure and combining ability of diverse Medicago sativa germplasms. Theor Appl Genet 109, 775-782 http://dx.doi.org/10.1007/s00122-004-1677-x

McClelland M, Welsh J, 1994. DNA fingerprinting by arbitrarily primed PCR. PCR methods and applications 4, 59-65.

Mengoni A, Gori A, Bazzicalupa M. 2000. Use of RAPD and microsatellite (SSR) variation to assess genetic relationships among populations of tetraploid alfalfa, Medicago sativa. Plant breeding 119, 311-317. http://dx.doi.org/10.1046/Fj.1439 0523.2000.00501.x

Morgante M, Olivieri AM. 1993. PCR-amplified microsatellites as markers in plant genetics. PCR-amplified microsatellites as markers in plant genetics. The plant journal 3, 175-182. http://dx.doi.org/10.1046/j.1365-313X.1993.t01-9-00999.x

Nei M. 1972. Genetic distance between populations. American naturalist 106, 283-292. http://dx.doi.org/10.1086/282771

Nei M. 1973. Analysis of gene diversity in subdivided populations Proc. Natl. Acad. Sci (USA) 70, 3321-3323. http://dx.doi.org/10.1073/pnas.70.12.3321

Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583-590.

Nosrati H, Hosseinpour Feizi MA, Seyed Tarrah S, Razban Haghighi A. 2011. A study of the relationship between eco-geographical factors and genetic similarity in different populations of Onobrychis viciifolia using RAPDs. Journal of Plant Biology No. 7, spring. (In Persian).

Vos P, Hogers R,  Bleeker M,  Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman  J, Kuiper  M.   995.  AFLP:  A  new technique for DNA fingerprinting, Nucleic Acids Research 23, 4407-4414. http://dx.doi.org/10.1093/nar/23.21.4407

Polhill RM. 1981. Hedysareae DC. In: Advances in legume systematic I, eds. Polhill, RM, Raven, populations of alfalfa (Medicago sativa) using RAPD molecular markers. Theoretical and applied genetics 96, 406-412.

Provan J, Thomas, WTB, Forster BP, Powell W. 1999. Copia-SSR: A simple marker technique which can be used on total genomic DNA. Genome 42, 363-366. http://dx.doi.org/10.1139/gen-42-2-363

Pupilli F, Labombarda P, Scotti C, Arcioni S. 2000. RFLP analysis allows for the identification of alfalfa ecotypes plant breeding 119, 271-276. http://dx.doi.org/10.1046/j.1439-0523.2000.00478.x

Rechinger KH. 1984.Onobrychis. In: Flora Iranica, ed. Rechinger KH, No. 157, 387–464.

Riday H, Brummer EC. 2004. Dissection of heterosis in alfalfa hybrids. In: Hopkins A, Wang Z-Y, Mian R, Sledge M, Barker RE, eds. Molecular breeding of forage and turf. Kluwer Academic Publishers, Dordrecht, the Netherlands, 315-324. http://dx.doi.org/10.1007/1-4020-2591-2_27

Riday H, Brummer EC, Campbell TE, Luth D, Cazcarro PM. 2003. Comparisons of genetic and morphological distance with heterosis between Medicago sativa subsp. sativa and subsp. falcata. Euphytica 131, 37-45.

Rohlf FJ. 1972. An empirical comparison of three ordination techniques in numerical taxonomy. Systematic zoology 21, 271-280. http://dx.doi.org/10.1093/sysbio/21.3.271

Rumball W, Claydon RB. 2005. Germplasm release  ‘G35’  Sainfoin  (Onobrychis  vicifolia).  Jour. Agri. Res. 48, 127-128.

Lerma S, Cantrellrg A, Conway JM, Ray IM. 2003. AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates. Genome 46, 51-58.

Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW. 1984. Ribosomal spacer length polymorphism in barley: mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA, 83, 1757–1761. http://dx.doi.org/10.1073/pnas81.24.8014

Skroch P, Nienhuis J. 1995.  Impact of  scoring error and reproducibility RAPD data on RAPD based estimates of genetic distance. Theoretical and applied genetics 91, 1086-1091. http://dx.doi.org/10.1007/BF00223923

Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic zoology 35, 627-632. http://dx.doi.org/10.2307/2413122

Sneath, PHA, Sokal, RR. 1973. Numerical taxonomy. Freeman, San Francisco 573 P.

Soltis PS, Soltis DE, Doyle JJ. 1992. Molecular systematics of plants. Chapman and Hall, New York.

Tautz D. 1989. Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic acids research 17, 6463-6471.

Tavoletti S, Bingham ET, Yandell BS, Veronesi F, Osborn TC. 1996. Half tetrad analysis in alfalfa using multiple the United States of America 93, 10918-10922.

Tuna M, Khadka DK, Shrestham K, Arumuganathm K, Golan-goldhirsh A. 2004. Characterization of natural orchardgrass (Dactylis glomerata L.) populations of the Thrace Region of Turkey based  on ploidy and  DNA polymorphisms. Euphytica 135, 39–46. http://dx.doi.org/10.1023/B:EUPH.0000009537.08697.4e

Vandemark GJ, Hughes TJ, Larsen RC. 2005. Genetic similarities between alfalfa cultivars based on sequence related amplified polymorphism (SRAP) DNA markers. Plant & Animal Genomes XIII Conference (January 15–19), San Diego, CA.

Welsh J, McClelland M. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic acids research 18, 7213-7218. http://dx.doi.org/10.1093/nar/18.24.7213

Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic acids research 18, 6531-6535. http://dx.doi.org/10.1093/nar/18.22.6531

Yildiz B, Ciplak B, Aktoklu E. 1999. Fruit morphology of sections of the genus Onobrychis Miller (Fabaceae) and its phylogenetic implications.-Israel Journal of Plant Sciences 47, 269–282.

Yu K, Pauls KP. 1994. Optimization of DNA extraction and PCR procedures for RAPD analysis in plants. In: Griffin HG, Griffin AM, eds. PCR technology: Current innovations. CRC Press, Boca Raton: 193-200.

Zabeau M, Vos P. 1993. Selective restriction fragment amplification A general method for DNA Finger printing. European Patent Application 92402629.7 (Publ. No. 0534858A1)


Style Switcher

Select Layout
Chose Color
Chose Pattren
Chose Background