Study of polymorphism of maize using dna and protein markers
DOI:
https://doi.org/10.5219/874Keywords:
RAPD, SSR, SDS-PAGE, SCoT, old maize, dendrogramAbstract
In the present investigation 40 genotypes of maize from Czechoslovakia, Hungary, Poland, Union of Soviet Socialist Republics, Slovakia and Yugoslavia were analysed using 20 start codon targeted (SCoT) markers, 10 simple sequence repeat (SSR) markers, 13 random amplified polymorphic (RAPD) markers and using SDS-PAGE markers. Twenty SCoT primers produced 114 DNA fragments with an average of 5.7 bands per primer. Out of the total of 114 amplified fragments, 86 (76.43 %) were polymorphic, with an average of 4.30 polymorphic bands per primer. Ten SSR primers revealed a total of 65 alleles ranging from 4 (UMC1060) to 8 (UMC2002 and UMC1155) alleles per locus with a mean value of 6.50 alleles per locus. 20 SCoT primers produced total 114 fragments across 40 maize genotypes, of which 86 (76.43 %) were polymorphic with an average of 4.30 polymorphic fragments per primer and number of amplified fragments ranged from 2 (SCoT 45) to 8 (SCoT 28 and SCoT 63). The number of total scorable protein bands was twentythree as a result of SDS-PAGE technique but those that were not cosistent in reproducibility and showed occasional variation in sharpness and density were not considered. Based on these bands forty accessions of maize were screened. Out of twentythree polypeptide bands, 6 (31%) were commonly present in all accessions and considered as monomorphic, while 17 (65%) showed variations and considered as polymorphic. The dendrogram of 40 old maize genotypes based on SSR, SCoT, RAPD and SDS-PAGE markers using UGMA algorithm was constructed.
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Abd El-Azeem, R. M., Hashem, M. H. and Abd-El-Haleem, S. H. M. 2015. Detection of genetic variability in Zea mays inbred lines using SSRs and SRAP markers. Egypt. J. Genet. Cytol., vol. 44, p. 291-307.
Al-Badeiry, N. A. H., Merza, T. K. and Al-Saadi, A. H. 2013. Assessment of genetic diversity and relationships among maize (Zea mays L.) varieties in Iraq using random amplified polymorphic DNA (RAPD) markers. J. Life Sci., vol. 7, no. 12, p. 1260-1271.
Al-Badeiry, N. A. H., Al-Saadi, A. H., Merza, T. K. 2014. Analysis of Genetic Diversity in Maize (Zea mays L.) Varieties Using Simple Sequence Repeat (SSR) Markers. Journal of Babylon University, vol. 22, no. 6, p. 1768-1774.
AL-Huqail, A. A., Abdelhaliem, E. 2015. Evaluation of Genetic Variations in maize Seedlings Exposed to Electric Field Based on Protein and DNA Markers. BioMed Research International, vol. 2015, p. 1-15. https://doi.org/10.1155/2015/874906
Al-Qurainy, F., Khan, S., Nadeem, M. and Tarroum, M. 2015. SCoT marker for the assessment of genetic diversity in Saudi Arabian date palm cultivars. Pakistan Journal of Botany, vol. 47, no. 2, p. 637-643.
Balážová, Ž., Vivodík, M., Gálová, Z. 2016. Evaluation of molecular diversity of central European maize cultivars. Emirates Journal of Food and Agriculture, vol. 28, no. 2, p. 93-98. https://doi.org/10.9755/ejfa.2015-05-204
Bošeľová, D. and Žiarovská, J. 2016. Direct PCR as the platform of Hedera helix, L. genotypying without the extraction of DNA. Journal of Central European Agriculture, vol. 17, no. 4, p. 941-949. https://doi.org/10.5513/jcea01/17.4.1795
Bruel, D. C., Carpentieri-Pípolo, V., Ruas, C. F., Gerage, A. C. and de Souza, S. G. H. 2007. Assessment of genetic diversity in maize inbred lines using RAPD markers. Crop Breed. Appl. Biotechnol., vol. 7, p. 173-178. https://doi.org/10.12702/1984-7033.v07n02a09
Collard, B. C. Y. and Mackill, D. J. 2009. Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Plant Molecular Biology Reporter, vol. 27, p. 86-93. https://doi.org/10.1007/s11105-008-0060-5
De Vasconcelos, M. J. V., Antunes, M. S., Barbosa, S. M. and De Carvalho, C. H. S. 2008. RAPD analysis of callus regenerated and seed grown plants of maize (Zea mays L.). Rev. Bras. Milho e Sorgo, vol. 7, no. 2, p. 93-104. https://doi.org/10.18512/1980-6477/rbms.v7n2p93-104
Dubreuil, P. and Charcosset, A. 1998. Genetic diversity within and among maize populations: a comparison between isozyme and nuclear RFLP loci. Theor Appl Genet., vol. 96, p. 577-587. https://doi.org/10.1007/s001220050776
Dymek, K., Dejmek, P., Panarese, V., Vincente, A. A., Wadsö, L., Finnie, C., Galindo, F. G. 2012. Effect of pulsed electric field on the germination of barley seeds. LWT-Food Science and Technology, vol. 47, no. 1, p. 161-166. https://doi.org/10.1016/j.lwt.2011.12.019
Efendi, R., Sunarti, S., Musa, Y., Farid, B. M., Danial Rahim, M. and Azrai, M. 2015. Selection of Homozygosity and Genetic Diversity of Maize Inbred using Simple Sequence Repeats (SSRs) Marker. Int. J. Curr. Res. Biosci. Plant Biol., vol. 2, no. 3, p. 19-28.
Elçi, E. and Hançer, T. 2015. Genetic analysis of Maize (Zea mays L.) hybrids using microsatellite markers. Tarim Bilimleri Dergisi - Journal of Agricultural Sciences, vol. 21, p. 192-198.
Fang-Yong, Ch. and Ji-Honga, L. 2014. Germplasm genetic diversity of Myrica rubra in Zhejiang Province studied using inter-primer binding site and start codon-targetedpolymorphism markers. Scientia Horticulturae, vol. 170, p. 169-175. https://doi.org/10.1016/j.scienta.2014.03.010
Freitas, I. R. A., Gananca, F., Santos, T. M., Carvalho, M. A. A., Motto, M., Vieira, M. C. 2005. Evaluation of maize germplasm based on zein polymorphism from the archipelago of Madeira. Maydica, vol. 50, p. 105-112.
Gajeraa, B. B., Kumara, N., Singha, A. S., Punvara, B. S., Ravikirana, R., Subhasha, N. and Jadejab, G. C. 2010. Assessment of genetic diversity in castor (Ricinus communis L.) using RAPD and ISSR markers. Ind. Crops Prod., vol. 32, p. 491-498. https://doi.org/10.1016/j.indcrop.2010.06.021
Gajera, H. P., Bambharolia, R. P., Domadiya, R. K., Patel, S. V., Golakiya, B. A. 2014. Molecular characterization and genetic variability studies associated with fruit quality of indigenous mango (Mangifera indica L.) cultivars. Plant Systematics and Evolution, vol. 300, no. 5, p. 1011-1020. https://doi.org/10.1007/s00606-013-0939-y
Galvão, K. S., Ramos, H. C., Santos, P. H., Entringer, G. C., Vettorazzi, J. C., Pereira, M. G. 2015. Functional molecular markers (EST-SSR) in the full-sib reciprocal recurrent selection program of maize (Zea mays L.). Genet Mol Res., vol. 14, no. 3, p. 7344-7355. https://doi.org/10.4238/2015.july.3.10
Gay, J. P. 1984. Fabuleux mais-Histoire et avenir d'une plante. AGPM, Pau; 295 p.
Hamoud, M. A., El-Shanshory, A. R., Al-Sodany, Y. M., El-Karim, M. S. G. 2005. Genetic diversity among Ipomoea carnea jacq. Populations from different habitats types in Nile-Delta region of Egypt. The Egyptian Journal of Experimental Biology, vol. 1, p. 1-9.
Hanafy, M. S., Mohamed, H. A. and Abd El-Hady, E. A. 2006. Effect of low frequency electric field on growth characteristics and protein molecular structure of wheat plant. Romanian Journal of Biophysics, vol. 16, no. 4, p. 253-271.
Huang, L., Huang, X., Yan, H., Yin, G., Zhang, X., Tian, Y., Zhang, Y., Jiang, X., Yan, Y., Ma, X., Peng, Y., Zhou, J., Nie, G. 2014. Constructing DNA fingerprinting of Hemarthria cultivars using EST-SSR and SCoT markers. Genetic Resources and Crop Evolution, vol. 61, no. 6, p. 1047-1055. https://doi.org/10.1007/s10722-014-0107-4
Idris, A. E., Hamza, N. B., Yagoub, S. O., Ibrahim, A. I. A. and El-Amin, H. K. A. 2012. Maize (Zea mays L.) genotypes diversity study by utilization of Inter-Simple Sequence Repeat (ISSR) markers. Australian Journal of Basic and Applied Sciences, vol. 6, no. 10, p. 42-47.
Ignjatovic-Micic, D., Ristic, D., Babic, V., Andjelkovic, V. and Vancetovic, J. 2015. A simple SSR analysis for genetic diversity estimation of maize landraces. Genetika, vol. 47, no. 1, p. 53-62. https://doi.org/10.2298/GENSR1501053I
Iqbal, J., Shinwari, Z. K., Rabbani, M. A., Khan, S. A. 2014. Genetic variability assessment of maize (Zea mays L.) germplasm based on total seed storage proteins banding pattern using SDS-PAGE. European academic research, vol. 2, no. 2, p. 2144-2160.
Iqbal, J., Shinwari, Z. K. and Rabbani, M. A. 2014. Investigation of total seed storage proteins of Pakistani and Japanese maize (Zea mays L.) through SDS-PAGE markers. Pakistan Journal of Botany, vol. 46, no. 3, p. 817-822.
Jiang, L. F., Qi, X., Zhang, X. Q., Huang, L. K., Ma, X. and Xie, W. G. 2014. Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers. Genetics and Molecular Research, vol. 13, no. 2, p. 4406-4418. https://doi.org/10.4238/2014.June.11.4
Kallamadi, P. R., Ganga Rao Nadigatlab, V. P. R., Mulpurib, S. 2015. Molecular diversity in castor (Ricinus communis L.). Industrial Crops and Products, vol. 66, p. 271-281. https://doi.org/10.1016/j.indcrop.2014.12.061
Kanagarasu, S., Nallathambi, G., Ganesan, K. N., Kannan, S., Shobhana, V. G. and Senthi, N. 2013. Determination of genetic polymorphism among indigenous and exotic maize inbreds using microsatellite markers. African Journal of Biotechnology, vol. 12, no. 39, p. 5723-5728.
Kanti, M., Anjani, K., Usha Kiran, B. and Vivekananda, K. 2015. Agro-morphological and molecular diversity in Castor (Ricinus communis L.) germplasm collected from Andaman and Nicobar Islands, India. Czech J. Genet. Plant Breed., vol. 51, no. 3, p. 96-109. https://doi.org/10.17221/205/2014-CJGPB
Khan, A. H., Khan, N., Minhas, N. M., Ghafoor, A., Rabbani, M. A. 2014. Diversity in seed storage proteins in maize genetic resources: I. variation in alcohol soluble zein protein fraction. International Journal of Agricurtural and Biological Engineering, vol. 16, p. 1015-1018.
Lawton, J. W. 2006. Isolation of zein using 100% ethanol. Cereal Chemistry, vol. 83, no. 5, p. 565-568. https://doi.org/10.1094/CC-83-0565
Mahjbi, A., Baraket, G., Oueslati, A., Salhi-Hannachi, A. 2015. Start Codon Targeted (SCoT) markers provide new insights into the genetic diversity analysis and characterization of Tunisian Citrus species. Biochemical Systematics and Ecology, vol. 61, p. 390-398. https://doi.org/10.1016/j.bse.2015.07.017
Masojc´, P., Mysków, B. and Milczarski, P. 2001. Extending a RFLP-based genetic map of rye using random amplified polymorphic DNA (RAPD) and isozyme markers. Theor. Appl. Genet., vol. 102, no. 8, p. 1273-1279. https://doi.org/10.1007/s001220000512
Molin, D., Coelho, C. J., Máximo, D. S., Ferreira, F. S., Gardingo, J. R. and Matiello, R. R. 2013. Genetic diversity in the germplasm of tropical maize landraces determined using molecular markers. Genetics and Molecular Research, vol. 12, no. 1, p. 99-114. https://doi.org/10.4238/2013.January.22.8
Mrutu, B. A., Feyissa, T. and Ndunguru, J. 2014. Assessment of genetic diversity of maize inbred lines and hybrids in Southern Highlands of Tanzania by using Random amplified Polymorphic DNA (RAPD) markers. Am. J. Res. Commun., vol. 2, no. 4, p. 84-99.
Mukharib, D. S., Patil, V, C., Biradar, D. P., Salimath, P. M. and Chimmad, V. P. 2010. Assessment of molecular diversity in selected maize inbreds. Karnataka J. Agric. Sci., vol. 23, no. 3, p. 409-412.
Osipova, E. S., Koveza, O. V., Troitskij, A. V., Dolgikh, Y. I., Shamina, Z. B. and Gostimskij, S. A. 2003. Analysis of specific RAPD and ISSR fragments in maize (Zea mays L.) somaclones and development of SCAR markers on their basis. Russ. J. Genet., vol. 39, no. 12, p. 1412-1419. https://doi.org/10.1023/B:RUGE.0000009156.74246.bc
Osman, G., Munshi, A., Altf, F. and Mutawie, H. 2013. Genetic variation and relationships of Zea mays and Sorghum species using RAPD-PCR and SDS-PAGE of seed proteins. African Journal of Biotechnology, vol. 12, no. 27, p. 4269-4276. https://doi.org/10.5897/ajb12.2644
Paetkau, D., Calvert, W., Stirling, I., Strobeck, C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol. Ecol., vol. 4, p. 347-354. https://doi.org/10.1111/j.1365-294X.1995.tb00227.x PMid:7663752
Prasanna, B., Vasal, S., Kashun, B. and Singh, N. N. 2001. Quality protein maize. Current Science, vol. 81, no. 10, p. 1308-1319.
Ranjan, S., Poosapati, A., Vardhan, H. et al., 2013. Seed storage protein profile of few leguminous grains grown in india using SDSPAGE. International Journal of Advanced Biotechnology and Research, vol. 4, no. 4, p. 505-510.
Ražná, K., Bežo, M., Hlavačková, L., Žiarovská, J., Miko, M., Gažo, J., Habán, M. 2016. MicroRNA (miRNA) in food resources and medicinal plant. Potravinarstvo, vol. 10, no. 1, p. 188-194. https://doi.org/10.5219/583
Roy, N. S. and Kim, N. S. 2016. Genetic diversity analysis of maize lines using AFLP and TE-based molecular marker systems. Genes Genom., vol. 38, p. 1005-1012. https://doi.org/10.1007/s13258-016-0461-z
Sa, K. J., Park, J. Y., Park, K. C. et al., 2012. Analysis of genetic mapping in a waxy/dent maize RIL population using SSR and SNP markers. Genes Genom., vol. 34, p. 157-164. https://doi.org/10.1007/s13258-011-0208-9
Saker, M., Nagchtigall, M., Kuehne, T. A. 2005. Comparative assessment of DNA fingerprinting by RAPD, SSR and AFLP in genetic analysis of some barley genotypes. Egypt J Genet Cytol., vol. 34, p. 81-97.
Salami, H. A., Sika, K. C., Padonou, W., Aly, D., Yallou, C., Adjanohoun, A., Kotchoni, S. and Baba-Moussa, L. 2016.Genetic Diversity of Maize Accessions (Zea mays L.) Cultivated from Benin Using Microsatellites Markers. American Journal of Molecular Biology, vol. 6, p. 12-24. https://doi.org/10.4236/ajmb.2016.61002
Satya, P., Karana, M., Jana, S., Mitraa, S., Sharma, A., Karmakar, P. G., Rayb, D. P. 2015. Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producingspecies. Meta Gene, vol. 3, p. 62-70. https://doi.org/10.1016/j.mgene.2015.01.003
Sawant, S. V., Singh, P. K., Gupta, S. K., Madnala, R., Tuli, R. 1999. Conserved nucleotide sequences in highly expressed genes in plants. Journal of Genetics, vol. 78, no. 2, p. 123-131. https://doi.org/10.1007/BF02924562
Shahlaei, A., Torabi, S., Khosroshahli, M. 2014. Efficiacy of SCoT and ISSR marekers in assesment of tomato (Lycopersicum esculentum Mill.) genetic diversity. International Journal of Biosciences, vol. 5, no. 2, p. 14-22. https://doi.org/10.12692/ijb/5.2.14-22
Shiri, M. R., Choukan, R. and Aliyev, R. T. 2014. Study of genetic diversity among maize hybrids using SSR markers and morphological traits under two different irrigation conditions. Crop Breeding Journal, vol. 4, no. 1, p. 65-72.
Simões, K. S., Silva, S. A., Machado, E. L. and Brasileiro, H. S. 2017. Development of TRAP primers for Ricinus communis L. Genetics and Molecular Research, vol. 16, no. 2, p. 100-113. https://doi.org/10.4238/gmr16029647
Sun, D. F., Ren, W. B., Sun, Gl., Peng, J. H. 2011. Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley. Euphytica, vol. 178, p. 31-43. https://doi.org/10.1007/s10681-010-0260-6
Vasal, S. K. 1999. Quality protein maize story. Proceedings of workshop on improving human nutrition through agriculture: the role of international agricultural research. IRRI, Los Banos, Philippines, p. 1-16.
Vivodík, M., Gálová, Z., Balážová, Ž., Petrovičová, L. 2016. Start codon targeted (SCoT) polymorphism reveals genetic diversity in European old maize (Zea mays L.) genotypes. Potravinarstvo, vol. 10, no. 1, p. 563-569. https://doi.org/10.5219/660
Vivodík, M., Gálová, Z., Balážová, Ž., Petrovičová, L., Kuťka Hlozáková, T. 2016. Genetic variation and relationships of old maize genotypes (Zea mays L.) detected using SDS-PAGE. Potravinarstvo, vol. 10, no. 1, p. 532-536. https://doi.org/10.5219/661
Vyhnánek,T., Trojan, V., Štiasna, K., Presinszká, M., Hřivna, L., Mrkvicová, E., Havel, L. 2015. Testing of DNA isolation for the identification of Hemp. Potravinarstvo, vol. 9, no. 1, p. 393-397. https://doi.org/10.5219/509
Weber, J. L. 1990. Informativeveness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, p. 524-530. https://doi.org/10.1016/0888-7543(90)90195-Z
Weir, B. S. 1990. Genetic data analysis. Methods for discrete population genetic data, 1990 p. ISBN 0-87893-872-9
Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A. and Tingey, S. V. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res., vol. 18, p. 6531-6535. https://doi.org/10.1093/nar/18.22.6531 PMid:1979162
Wrigley, C. W. 1992. Identification of cereal varieties by gel electrophoresis of the grain proteins. Heidelberg: Springer - Verlag, p. 17-41. https://doi.org/10.1007/978-3-662-01639-8_2
Zhang, J., Xie, W., Wang, Y. and Zhao, X. 2015. Potential of Start Codon Targeted (SCoT) Markers to Estimate Genetic Diversity and Relationships among Chinese Elymus sibiricus Accessions. Molecules, vol. 20, no. 4, p. 5987-6001. https://doi.org/10.3390/molecules20045987
Žiarovská, J., Senková, S., Bežo, M., Ražná, K., Masnica, M., Labajová, M. 2013. ISSR markers as a tool to distinguish Idt and SSS populations of Zea mays L. Journal of Central European Agriculture, vol. 14, no. 2, p. 489-499. https://doi.org/10.5513/JCEA01/14.2.1227
Žiarovská, J., Grygorieva, O., Zeleňáková, L., Bežo, M., Brindza, J. 2015. Identification of sweet chesnut pollen in bee pollen pellet using molecular analysis. Potravinarstvo, vol. 9, no. 1, p. 352-358. https://doi.org/10.5219/497
Žiarovská, J., Kyseľ, M., Cimermanová, R., Knoteková, L. 2017. Effect of DNA extraction method in the Rosa Canina L. identification under different processing temperature. Potravinarstvo Slovak Journal of Food Sciences, vol. 11, no. 1, p. 190-196. https://dx.doi.org/10.5219/717
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