Evaluation of diversity and population structure of durum wheat (Triticum durum L.) using Dof markers

Document Type : Original Article

Authors

1 Department of Plant Production and Genetics, Faculty of Agricultural Sciences and Engineering, Campus of Agriculture and Natural Resources, Razi University, Kermanshah, Iran

2 Dryland Agricultural Research Institute, Sararood Branch, Agricultural Research, Education and Extension Organization (AREEO), Kermanshah, Iran

3 Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran.

Abstract

Introduction: Assessment of the genetic diversity of crops is vital to plant breeding and heritage conservation programs. Genetic diversity in plant species is important for selecting the right parents for hybridization and producing suitable offspring. The genetic diversity of durum wheat compared to other crops has decreased significantly during the time, initially due to the domestication of the plant and gradually due to the use of uniform and modified germplasm, which has shown this to be a threat.
Materials and methods: Genetic diversity and population structure of a set of durum wheat germplasm, including 36 durum wheat landraces and five new cultivars, were evaluated using 15 Dof markers.
Results: The total number of amplified bands was 117, of which 79 were polymorphic with an average polymorphism of 62.32%. The mean polymorphism information content, marker index, and resolving power in the population were 0.34, 1.61 and 1.9, respectively. According to the indices calculated in this study, Dof16, Dof20, Dof31 and Dof35 markers are more suitable for studying the genetic diversity of durum wheat. Population structure analysis divided germplasm into three subgroups (K=3). The molecular analysis of variance based on three subgroups obtained from STRUCTURE for Dof markers showed that the variance within and between subgroups was 85% and 15% of the total variance, respectively. Principal coordinate analysis partly corresponded to the result of population structure and divided the germplasm into three groups.
Conclusion: The results of the present study showed a high level of polymorphism and diversity in Dof markers, indicating the efficiency of these markers in differentiating durum wheat genotypes in this study. Due to the very high conservation of Dof sequences, this specific marker is significant in plants, so this marker can be used to study genetic diversity in different plant species.

Keywords

References

Alipour, H., Bihamta, M. R., Mohammadi, V., Peyghambari, S. A., Bai, G., & Zhang, G. 2017. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Frontiers in Plant Science, 8, 1293. https://doi.org/10.3389/fpls.2017.01293
Altıntaş, S., Toklu, F., Kafkas, S., Kilian, B., Brandolini, A., & Özkan, H. 2008. Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers. Plant Breeding, 127 (1), 9-14.  https://doi.org/10.1111/j.1439-0523.2007.01424.x
Anderson, J. A., Churchill, G. A., & Auntrique, J. E. 1993. Optimizing parental for genetic linkage maps. Genome, 36 (1), 181-186. https://doi.org/10.1139/g93-024
Baloch, F. S., Alsaleh, A., Shahid, M. Q., Ciftci, V., Saenz de Maria, L., Aasim, M., Nadeem, M. A., Aktas, H., Ozkan, H., & Hatipoglu, R. 2017. A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from central fertile crescent. PLoS One, 12 (1), e0167821. https://doi.org/10.1371/journal.pone.0167821
Carvalho, A., Lima-Brito, J., Maçãs, B., & Guedes-Pinto, H. 2009. Genetic diversity and variation among botanical varieties of old Portuguese wheat cultivars revealed by ISSR assays. Biochemical Genetics, 47 (3-4), 276-294. https://doi.org/10.1007/s10528-009-9227-5
Ditta, A., Zhou, Z., & Cai, X. 2018. Assessment of genetic diversity, population structure, and evolutionary of uncharacterized genes in a novel germplasm collection of diploid and allotetraploid Gossypium accessions using EST and genomic SSR markers. International Journal of Molecular Sciences, 19 (8), 2401. https://doi.org/10.3390/ijms19082401
Dubcovsky, J., & Dvorak, J. 2007. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science, 316 (5833), 1862-1866. https://doi.org/10.1126/science.1143986
Evanno, G., Regnaut, S., & Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14 (8), 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
Gupta, S., Malviya, N., Kushwaha, H., Nasim, J., Bisht, N. C., Singh, V. K., & Yadav, D. 2015. Insights into structural and functional diversity of Dof (DNA binding with one finger) transcription factor. Planta, 241 (3), 549-562. https://doi.org/10.1007/s00425-014-2239-3
Hayden, M., Tabone, T., Nguyen, T., Coventry, S., Keiper, F., Fox, R., Chalmers, K., Mather, D., & Eglinton, J. 2009. An informative set of SNP markers for molecular characterisation of Australian barley germplasm. Crop and Pasture Science, 61 (1), 70-83. https://doi.org/10.1071/CP09140
Hu, X., Ren, J., Ren, X., Huang, S., Sabiel, S. A., Luo, M., Nevo, E., Fu, C., Peng, J., & Sun, D. 2015. Association of agronomic traits with SNP markers in durum wheat (Triticum turgidum L. durum (Desf.)). PLoS One, 10, e0130854. https://doi.org/10.1371/journal.pone.0130854
Karp, A., Kresovich, S., Bhat, K. V., Ayad, W. G., & Hodgkin, T. 1997. Molecular tools in plant genetic resources conservation: a guide to the technologies. IPGRI. Rome.
Kang, H. G., & Singh, K. 2000. Characterization of salicylic acid-responsive Arabidopsis Dof domain proteins: overexpression of OBP3 leads to growth defects. The Plant Journal, 21 (4), 329-339. https://doi.org/10.1046/j.1365-313x.2000.00678.x
Kono, H., Imanishi, M., Negi, S., Tatsutani, K., Sakaeda, Y., Hashimoto, A., Nakayama, C., Futaki, S., & Sugiura, Y. 2012. Rational design of DNA sequence-specific zinc fingers. FEBS Letters, 586 (6), 918-923. https://doi.org/10.1016/j.febslet.2012.02.025
Kumar, M., Mishra, G. P., Singh, R., Kumar, J., Naik, P. K., & Singh, S. B. 2009. Correspondence of ISSR and RAPD markers for comparative analysis of genetic diversity among different apricot genotypes from cold arid deserts of trans-Himalayas. Physiology and Molecular Biology of Plants, 15 (3), 225-236. https://doi.org/10.1007/s12298-009-0026-6
Kummerfeld, S. K., & Teichmann, S. A. 2006. DBD: a transcription factor prediction database. Nucleic Acids Research, 34, 74-81. https://doi.org/10.1093/nar/gkj131
Mahjoob, B., Najafi-Zarini, H., & Hashemi, S. H. R. 2014. Assesment of genetic relationships among 36 Brassica genotypes using ISSR molecular markers. Journal of Crop Breeding, 6 (14), 96-106. [In Persian]. http://jcb.sanru.ac.ir/article-1-322-en.html
Melchinger, A. 1993. Use of RFLP markers for analysis of genetic relationships among breeding materials and prediction of hybrid performance. International Crop Science I . CSSA, Madison, WI, USA Chap. 81, 621-628. https://doi.org/10.2135/1993.internationalcropscience.c98
Moreno-Risueno, M. A., Martinez, M., Vicente-Carbajosa, J., & Carbonero, P. 2007. The family of Dof transcription factors: from green unicellular algae to vascular plants. Molecular Genetics and Genomics, 277 (4), 379-390. https://doi.org/10.1007/s00438-006-0186-9
Mousapour Gorgi, A., Pocazi, P., Polgar, Z., & Taller, J. 2011. Efficiency of arbitrarily amplified dominant markers (SCoT, ISSR and RAPD) for diagnostic fingerprinting in tetrapoid potato. American Journal of Potato Research, 88, 226-237. https://doi.org/10.1007/s12230-011-9187-2
Powell, W. W., Koput, K. W., & Smith-Doerr, L. 1996. Interorganizational collaboration and the locus of innovation: Networks of learning in biotechnology. Administrative Science Quarterly, 41 (1), 116-145. https://doi.org/10.2307/2393988
Pritchard, J. K., Stephens, M., Rosenberg, N. A., & Donnelly, P. 2000. Association mapping in structured populations. The American Journal of Human Genetics, 67 (1), 170-181. https://doi.org/10.1086/302959
Riechmann, J. L., & Ratcliffe, O. J. 2000. A genomic perspective on plant transcription factors. Current Opinion in Plant Biology, 3 (5), 423-434. https://doi.org/10.1016/s1369-5266(00)00107-2
Rouhian, S., Ahmadi, D. N., & Sorkheh, K. 2017. Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (Hordeum vulgare L.) germplasm. Genes & Genomics, 39, 567-579. https://doi.org/10.1007/s13258-016-0510-7
Spataro, G., Tiranti, B., Arcaleni, P., Bellucci, E., Attene, G., Papa, R., Zeuli, P. S., & Negri, V. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics, 122 (7), 1281-1291. https://doi.org/10.1007/s00122-011-1530-y
Takatsuji, H. 1998. Zinc-finger transcription factors in plants. Cellular and Molecular Life Sciences, 54, 582-596. https://doi.org/10.1007/s000180050186
Xynias, I. N., Mylonas, I., Korpetis, E. G., Ninou, E., Tsaballa, A., Avdikos, I. D., & Mavromatis, A. G. 2020. Durum wheat breeding in the Mediterranean region: Current status and future prospects. Agronomy, 10 (3), 432. https://doi.org/10.3390/agronomy10030432
Yanagisawa, S. 2002. The Dof family of plant transcription factors. Trends in Plant Science, 7 (12), 555-560. https://doi.org/10.1016/s1360-1385(02)02362-2
Yanagisawa, S., & Izui, K. 1993. Molecular cloning of two DNA binding Proteins of maize that are structurally different but interact with the same sequence motif. Journal of Biochemical Chemistry, 268 (21), 6028-6036.
Yanagisawa, S., & Schmidt, R. J. 1999. Diversity and similarity among recognition sequences of Dof transcription factors. The Plant Journal, 17 (2), 209-214. https://doi.org/10.1046/j.1365-313X.1999.00363.x

Files

Share

How to cite

Statistics