Hostname: page-component-cd9895bd7-gbm5v Total loading time: 0 Render date: 2024-12-27T21:59:23.046Z Has data issue: false hasContentIssue false
  • English
  • Français

Sequence-related amplified polymorphism and inter-simple sequence repeat marker-based genetic diversity and nuclear DNA content variation in common vetch (Vicia sativa L.)

Published online by Cambridge University Press:  15 July 2015

Abdullah Cil  and
Iskender Tiryaki
Abdullah Cil
Affiliation:
East Mediterranean Agriculture Research Institute, Yuregir, Adana, Turkey
Iskender Tiryaki*
Affiliation:
Department of Agricultural Biotechnology, Faculty of Agriculture, Canakkale Onsekiz Mart University, Canakkale17100, Turkey
*
*Corresponding author. E-mail: itiryaki@comu.edu.tr
Get access Rights & Permissions [Opens in a new window]

Abstract

Genetic diversity of 30 common vetch (Vicia sativa L.) lines and cultivars obtained from various resources or collected from natural flora of Turkey was evaluated by using 55 sequence-related amplified polymorphism (SRAP) and five inter-simple sequence repeat (ISSR) primer sets, and their nuclear DNA contents were determined by flow cytometer. A total of 188 polymorphic loci were detected, with an average of 3.62 loci per primer. The percentage of polymorphic loci was 82.1%. The polymorphism information content values ranged from 0.12 to 0.96, with an average of 0.63. The genetic distance coefficients were in the range of 0.112–0.627. Cluster analysis revealed that the 27 lines and three cultivars could be divided into two main groups. No polyploidy was detected within any vetch lines tested while significant (P< 0.0001) nuclear DNA content differences were determined. The present study revealed that fast and accurate fingerprinting analysis could be done using SRAP and ISSR markers, which indicated existing significant variation among common vetch lines and cultivars.

Keywords

DNA contentgenetic relationshipgenome sizeinter-simple sequence repeatpolymorphism information contentsequence-related amplified polymorphismVicia sativa
Type
Research Article
Information
Plant Genetic Resources , Volume 14 , Issue 3 , September 2016 , pp. 183 - 191
Copyright
Copyright © NIAB 2015 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amarowicz, R, Troszynska, A and Pegg, RB (2008) Antioxidative and radical scavenging effects of phenolics from Vicia sativum . Fitoterapia 79: 121–122.Google Scholar
Arumuganathan, K and Earle, ED (1991) Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter 9: 208–218.Google Scholar
Avcioğlu, R (2000) Türkiye hayvancılığında kaba yem üretim stratejileri. Uluslararası Hayvan Besleme Kongresi 1: 448–455.Google Scholar
Başbağ, M, Hoşgören, H and Aydin, A (2013) Vicia taxan the flora of Turkey. Anadolu Journal of Agricultural Sciences 28: 59–66.Google Scholar
Bennett, MD, Price, HJ and Johnston, JS (2008) Anthocyanin inhibits propidium iodide DNA fluorescence in Euphorbia pulcherrima: implications for genome size variation and flow cytometry. Annals of Botany 101: 777–790.CrossRefGoogle ScholarPubMed
Bennetzen, JL, Ma, J and Devos, KM (2005) Mechanisms of recent genome size variation in flowering plants. Annals of Botany 95: 127–132.Google Scholar
Botstein, D, White, R, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics 32: 314–331.Google Scholar
Chen, S, Zhou, J, Chen, Q, Chang, Y, Du, J and Meng, H (2013) Analysis of the genetic diversity of garlic (Allium sativum L.) germplasm by SRAP. Biochemical Systematics and Ecology 50: 139–146.Google Scholar
Chung, J, Kim, T, Suresh, S, Lee, S and Cho, G (2013) Development of 65 novel polymorphic cDNA-SSR markers in common vetch (Vicia sativa subsp. sativa) using next generation sequencing. Molecules 18: 8376–8392.Google Scholar
Davis, PH (1970) Flora of Turkey and the East Aegean Islands. Edinburgh, UK: Edinburgh University.Google Scholar
Dolezel, J, Bartos, J, Voglmayr, H, and Greilhuber, J (2003) Nuclear DNA content and genome size of trout and human. Cytometry A 51: 127–128; author reply: 129.Google Scholar
Dolezel, J and Bartos, J (2005) Plant DNA flow cytometry and estimation of nuclear genome size. Annals of Botany 95: 99–110.Google Scholar
Frediani, M, Caputo, P, Venora, G, Ravalli, C, Ambrosio, M and Cremonini, R (2005) Nuclear DNA contents, rDNAs, and karyotype evolution in Vicia subgenus Vicia: II Section Peregrinae. Protoplasma 226: 181–190.Google Scholar
Fufa, H, Baenziger, PS, Beecher, BS, Dweikat, I, Graybosch, RA and Eskridge, KM (2005) Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars. Euphytica 145: 133–146.Google Scholar
Graham, MJ, Nivkell, CD and Rayburn, AL (1994) Relationship between genome size and maturity group in soybean. Theoretical and Applied Genetics 88: 429–432.Google Scholar
Gregory, TR (2003) Is small indel bias a determinant of genome size? Trends in Genetics 19: 485–488.Google Scholar
Greilhuber, J (1998) Intraspecific variation in genome size: a critical reassessment. Annals of Botany 82: 27–35.Google Scholar
Harlan, JR (1971) Agricultural origins: centers and noncenters. Science 174: 468–474.Google Scholar
Huang, C, Liu, G, Bai, C and Wang, W (2013) Genetic relationships of Cynodon arcuatus from different regions of China revealed by ISSR and SRAP markers. Scientia Horticulturae 162: 172–180.Google Scholar
Hussein, AA, Siddig, MA, Abdalla, AWH, Dweikat, I and Baenziger, S (2014) SSR and SRAP markers-based genetic diversity in sorghum (Sorghum bicolor (L.) Moench) accessions of Sudan. International Journal of Plant Breeding and Genetics 8: 89–99.Google Scholar
Kalendar, R, Tanskanen, J, Immonen, S, Nevo, E and Schulman, AH (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proceedings of the National Academy of Sciences of the USA 97: 6603–6607.Google Scholar
Kumar, P, Gupta, VK, Misra, AK, Modi, DR and Pandey, BK (2009) Potential of molecular markers in plant biotechnology. Plant Omics 2: 141–162.Google Scholar
Li, G and 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 . Theoretical and Applied Genetics 103: 455–461.Google Scholar
Li, G, McVetty, PBE and Quiros, CF (2013) SRAP molecular marker technology in plant science. In: Andersen, SB (ed) Plant Breeding from Laboratories to Fields. Copenhagen: InTech. Doi: 5772/54511.Google Scholar
Maxted, N (1995) An ecogeographical study of Vicia subgenus Vicia . Systematic and Ecogeographic Studies on Crop Genepools 8 . Rome, Italy: International Plant Genetic Resources Institute.Google Scholar
Michaelson, MJ, Price, HJ, Johnston, JS and Ellison, JR (1991) Variation of nuclear DNA content in Helianthus annuus (Asteraceae). American Journal of Botany 78: 1238–1243.Google Scholar
Murray, BG (2005) When does intraspecific C-value variation become taxonomically significant? Annals of Botany 95: 119–125.Google Scholar
Nei, M (1972) Genetic distance between populations. American Naturalist 106: 283–292.Google Scholar
Noirot, M, Barre, P, Duperray, C, Hamon, S and Kochko, A (2005) Investigation on the causes of stoichiometric error in genome size estimation using heat experiments: consequences on data interpretation. Annals of Botany 95: 111–118.Google Scholar
Ohri, D, Bhargava, A and Chatterjee, A (2004) Nuclear DNA amounts in 112 species of tropical hardwoods – new estimates. Plant Biology 6: 555–561.Google Scholar
Pastor-Cavada, E, Juan, R, Pastor, JE, Alaiz, M, Giron-Calle, J and Vioque, J (2008) Antioxidative activity in the seeds of 28 Vicia species from southern Spain. Journal of Food Biochemistry 35: 1373–1380.Google Scholar
Petrov, D (1997) Slow but steady: reduction of genome size through biased mutation. The Plant Cell 9: 1900–1901.Google Scholar
Potokina, E, Duncan, AV, Eggi, EE and Tomooka, N (2000) Population diversity of the Vicia sativa agg. (Fabaceae) in the flora of the former USSR deduced from RAPD and seed protein analyses. Genetic Resources and Crop Evolution 47: 171–183.Google Scholar
Potokina, E, Blattner, R, Alexandrova, T and Bachmann, K (2002) AFLP diversity in the common vetch (Vicia sativa L.) on the world scale. Theoretical and Applied Genetics 105: 58–67.Google Scholar
Price, HJ (1976) Evolution of DNA content in higher plants. Botanical Reviews 42: 27–52.Google Scholar
Price, HJ, Hodnett, G and Johnston, JS (2000) Sunflower (Helianthus annuus) leaves contain compounds that reduce nuclear propidium iodide fluorescence. Annals of Botany 86: 929–934.CrossRefGoogle Scholar
Raina, SN (1990) Genome organization and evolution in the genus Vicia . In: Kawano, S (ed) Biological Approaches and Evolutionary Trends in Plants. London: Academic Press, pp. 183–201.Google Scholar
Rayburn, AL, Auger, JA, Benzinger, ES and Hepburn, AG (1989) Detection of intraspecific DNA content variation in Zea mays L. by flow cytometry. Journal of Experimental Botany 40: 1179–1183.Google Scholar
Rayburn, AL, Biradar, DP, Bullock, DG, Nelson, RL, Gourmet, C and Wetzel, JB (1997) Nuclear DNA content diversity in Chinese soybean introductions. Annals of Botany 80: 321–325.Google Scholar
Robarts, DWH and Wolfe, AD (2014) Sequence-related amplified polymorphism (SRAP) markers: a potential resource for studies in plant molecular biology. Applications in Plant Sciences 2: 1–13.Google Scholar
Sabanci, CO (1999) Plant genetic resources programme in Turkey with special reference to forage legumes. In: Bennett, SJ and Cocks, PS (eds) Genetic Resources of Mediterranean Pasture and Forage Legumes. The Netherlands: Kluwer Academic, pp. 150–162.Google Scholar
SAS, I (1997) SAS/STAT Software: Changes and Enhancements through Release 6.12. Cary, NC: SAS Inst.Google Scholar
Smarda, P and Bures, P (2010) Understanding intraspecific variation in genome size in plants. Preslia 82: 41–61.Google Scholar
Sun, G, William, M, Liu, J, Kasha, K and Pauls, K (2001) Microsatellite and RAPD polymorphisms in Ontario corn hybrids are related to the commercial sources and maturity ratings. Molecular Breeding 7: 13–24.Google Scholar
Swift, HH (1950) The constancy of deoxyribose nucleic acid in plant nuclei. Proceedings of the National Academy of Sciences of the USA 36: 643–654.Google Scholar
Tamura, K, Dudley, J, Nei, M and Kumar, S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596–1599.Google Scholar
Tar'an, B, Zhang, C, Warkenting, T, Tullu, A and Vandenberg, A (2005) Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters. Genome 48: 257–272.Google Scholar
Thomas, CAJ (1971) The genetic organization of chromosomes. Annual Review of Genetics 5: 237–256.Google Scholar
Tinker, N, Fortin, M and Mather, D (1993) Random amplified polymorphic DNA and pedigree relationships in spring barley. Theoretical and Applied Genetics 85: 976–984.Google Scholar
Tiryaki, I and Tuna, M (2012) Determination of intraspecific nuclear DNA content variation in common vetch (Vicia sativa L.) lines and cultivars based on two distinct internal reference standards. Turkish Journal of Agriculture and Forestry 36: 645–653.Google Scholar
Walker, DJ, Monino, I and Correal, E (2006) Genome size in Bituminaria bituminosa (L.) C.H. Stirton (Fabaceae) populations: separation of “true” differences from environmental effects on DNA determination. Environmental and Experimental Botany 55: 258–265.Google Scholar
Yeh, FC, Yang, RC, Boyle, TBJ, Ye, Z and Mao, JK (1997) Popgene, the user friendly shareware for population genetic analysis. University of Alberta, Canada. Molecular Biology and Biotechnology Centre.Google Scholar
Zaefizadeh, M and Goliev, R (2009) Diversity and relationships among durum wheat landraces (Subconvars) by SRAP and phenotypic marker polymorphism. Research Journal of Biological Science 4: 960–966.Google Scholar
Zeitkiewicz, E, Rafalski, A and Labuda, D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20: 176–183.Google Scholar
Supplementary material: File

Cil and Tiryaki supplementary material

Figure S1

Download Cil and Tiryaki supplementary material(File)
File 42.6 KB
Supplementary material: File

Cil and Tiryaki supplementary material

Table S1

Download Cil and Tiryaki supplementary material(File)
File 22.3 KB
Supplementary material: File

Cil and Tiryaki supplementary material

Table S2

Download Cil and Tiryaki supplementary material(File)
File 19.4 KB
Supplementary material: File

Cil and Tiryaki supplementary material

Cil and Tiryaki supplementary material 1

Download Cil and Tiryaki supplementary material(File)
File 15 KB