Start codon targeted (scot) polymorphism reveals genetic diversity in european old maize (Zea mays L.) Genotypes

Authors

  • Martin Vivodí­k Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Zdenka Gálová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Želmí­ra Balážová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra
  • Lenka Petrovičová Slovak University of Agriculture, Faculty of Biotechnology and Food Sciences, Department of Biochemistry and Biotechnology, Tr. A. Hlinku 2, 949 76 Nitra

DOI:

https://doi.org/10.5219/660

Keywords:

Dendrogram, Maize, Molecular markers, SCoT analysis

Abstract

Maize (Zea mays L.) is one of the world's most important crop plants following wheat and rice, which provides staple food to large number of human population in the world. It is cultivated in a wider range of environments than wheat and rice because of its greater adaptability. Molecular characterization is frequently used by maize breeders as an alternative method for selecting more promising genotypes and reducing the cost and time needed to develop hybrid combinations. 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. These 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 polymorphic information content (PIC) value ranged from 0.374 (ScoT 45) to 0.846 (SCoT 28) with an average of 0.739. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared. The hierarchical cluster analysis showed that the maize genotypes were divided into two main clusters. Unique maize genotype (cluster 1), Zuta Brzica, originating from Yugoslavia separated from others. Cluster 2 was divided into two main clusters (2a and 2b). Subcluster 2a contained one Yugoslavian genotype Juhoslavanska and subcluster 2b was divided in two subclusters 2ba and 2bb. The present study shows effectiveness of employing SCoT markers in analysis of maize, and would be useful for further studies in population genetics, conservation genetics and genotypes improvement.

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References

Ahmad, S., Khan, S., Ghaffar, M., Ahmad, F. 2011. Genetic diversity analysis for yield and other parameters in maize (Zea mays L.) genotypes. Asian Journal Agriculture Science, vol. 3, no. 5, p. 385-388.

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.

Arya, L., Narayanan, R. K., Verma, M., Singh, A. K., Gupta, V. 2014. Genetic diversity and population structure analyses of Morinda tomentosa Heyne, with neutral and gene based markers. Genetic Resources and Crop Evolution, vol. 61, no. 8, p. 1469-1479. https://doi.org/10.1007/s10722-014-0168-4

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.

Balážová, Ž., Petrovičová, L., Gálová, Z., Vivodík, M. 2016. Molecular characterization of rye cultivars. Potravinarstvo, vol. 10, no. 1, p. 54-58. https://doi.org/10.5219/522

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

Fang-Yonga, 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

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

Gao, Y. H., Zhu, Y. Q., Tong, Z. K., Xu, Z. Y., Jiang, X. F., Huang, CH. H. 2014. Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker. Biochemical Systematics and Ecology, vol. 57, p. 221-226. https://doi.org/10.1016/j.bse.2014.08.002

Gálová, Z., Vivodík, M., Balážová, Ž., Kuťka Hlozáková, T. 2015. Identification and differentiation of Ricinus communis L. using SSR markers. Potravinarstvo, vol. 9, no. 1, p. 556-561. https://doi.org/10.5219/516

Goncalves, L. S., Rodrigues, R., do Amaral Junior, A. T., Karasawa, M., Sudre, C. P. 2009. Heirloom tomato gene bank: Assessing genetic divergence based on morphological, agronomic and molecular data using a Ward-modified location model. Genetics and Molecular Research, vol. 8, no. 1, p. 364-374. https://doi.org/10.4238/vol8-1gmr549 PMid:19440972

Gorji, A. M., Poczai, P., Polgar, Z., Taller, J. 2011. Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetraploid potato. American Journal of Potato Research, vol. 88, no. 3, p. 226-237. https://doi.org/10.1007/s12230-011-9187-2

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.

Iqbal, J., Shinwari, Z. K., Rabbani, M. A. and Khan, S. A. 2015. Genetic divergence in maize (Zea mays L.) germplasm using quantitative and qualitative traits. Pakistan Journal of Botany, vol. 47, no. SI, p. 227-238.

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

Joshi, C. P., Zhou, H., Huang, X., Chiang, V. L. 1997. Context sequences of translation initiation codon in plants. Plant Molecular Biology, vol. 35, no. 6, p. 993-1001. https://doi.org/10.1023/A:1005816823636 PMid:9426620

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

Kuťka-Hlozáková, T., Gálová, Z., Gregová, E., Vivodík, M., Balážová, Ž., Miháliková, D. 2016. RAPD analysis of the genetic polymorphism in European wheat genotypes. Potravinarstvo, vol. 10, no. 1, p. 1-6. https://doi.org/10.5219/520

Luo, C., He, X. H., Chen, H., Hu, Y., Ou, S. J. 2012. Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genetic Resources and Crop Evolution, vol. 59, no. 7, p. 1505-1515. https://doi.org/10.1007/s10722-011-9779-1

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

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 PMid:23359029

Rajesh, M. K., Sabana, A. A., Rachana, K. E., Rahman, S., Jerard, B. A., Karun, A. 2015. Genetic relationship and diversity among coconut (Cocos nucifera L.) accessions revealed through SCoT analysis. Biotechnology, vol. 5, no. 6, p. 999-1006. https://doi.org/10.1007/s13205-015-0304-7

Que, Y., Pan, Y., Lu, Y., Yang, C., Yang, Y., Huang, N. and Xu, L. 2014. Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism. Biomed Research International, vol. 2014, p. 1-10. https://doi.org/10.1155/2014/468375

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 producing species. 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

Shehata, A. I., Al-Ghethar, H. A., Al-Homaidan, A. A. 2009. Application of simple sequence repeat (SSR) markers for molecular diversity and heterozygosity analysis in maize inbred lines. Saudi Journal of Biological Sciences, vol. 16, no. 2, p. 57-62. https://doi.org/10.1016/j.sjbs.2009.10.001 PMid:23961043

Štefúnová, V., Bežo, M., Žiarovská, J., Ražná, K. 2015. Detection of the genetic variability of Amaranthus by RAPD and ISSR markers. Pakistan Journal of Botany, vol. 47, no. 4, p. 1293-1301.

Terra, T. F., Wiethölter, P., Almeida, C. C., Silva, S. D. A. et al. 2011. Genetic variability in maize and teosinte populations estimated by microsatellites markers. Ciência Rural., vol. 41, no. 2, p. 205-211. https://doi.org/10.1590/S0103-84782011005000005

Weber, J. L. 1990. Informativeveness of human (dC-dA)n x (dG-dT)n polymorphism. Genomics, vol. 7, no. 4, p. 524-530. https://doi.org/10.1016/0888-7543(90)90195-Z

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., Ražná, K. and Labajová, M. 2013. Using of inter microsatellite polymorphism to evaluate gamma-irradiated Amaranth mutants. Emirates Journal of Food and Agriculture, vol. 25, no. 9, p. 673-681. https://doi.org/10.9755/ejfa.v25i9.15879

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

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Published

2016-11-17

How to Cite

Vivodí­k, M. ., Gálová, Z. ., Balážová, Želmí­ra ., & Petrovičová, L. . (2016). Start codon targeted (scot) polymorphism reveals genetic diversity in european old maize (Zea mays L.) Genotypes. Potravinarstvo Slovak Journal of Food Sciences, 10(1), 563–569. https://doi.org/10.5219/660

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