Identification of Inter simple sequence repeat regions associated with agro-morphological traits in maize genome

Document Type : Research Paper


1 M.Sc. in Agricultural Biotechnology, Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Urmia University, Urmia, Iran

2 Professor, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran

3 Assistant Professor, Department of Plant Genetics and Production, Faculty of Agriculture, University of Maragheh, Maragheh, Iran

4 Associate Professor, Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Razi, Kermanshah, Iran

5 Assistant Professor, Seed and Plant Certification and Registration Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

6 Associate Professor, Department of Plant Breeding and Biotechnology, Urmia University, Urmia, Iran


Maize (Zea mays L.) as a model plant is important from agricultural, feed and industrial point view. Most of economically important traits and morphological traits are controlled by several genes and also influenced by environment effects and hence possessed complicated genetic control. This research was aimed to study the genetic control and identification of genomic regions controlling agro-morphological traits in maize germplasm using association analysis approach. Maize inbred lines were evaluated based on morphological and 16 ISSR primers. Results of morphological and genetically evaluations trials revealed existence of genetic variability in the studied germplasm which is mandatory item for successful association analysis study. Analysis of population structure using 81 ISSR loci divided the population into 2 sub-populations. Among studied lines, lines 1387/193/chase (Mashhad population) and 66*1388 (Mashhad population) showed maximum genetic admixture. Association analysis using MLM model represented 25 ISSR loci which possessed significant relation with studied traits. Positive markers identified in this research, could effectively applied in marker assisted selection programs to achieve suitable parental lines and also improvement of trait of interest. Also, this is resulted that inter simple sequence regions have acceptable ability and performance in association mapping of maize.


Amirtaimoori, S. and Chizari, A.H. 2008. Investigation of sustainable self-sufficiency in maize production in Iran: Total factor productivity approach. Pajouhesh and Sazandegi 79: 169-177. (In Persian with English Abstract).##Barakat, M.N., El-Shafei, A.A. and Al-Doss, A.A. 2009.Identification of molecular markers linked to northern corn leaf blight resistance in yellow population of maize. Genes, Genomes and Genomics 3: 89-95.##Breseghello, F. and Sorrells, M.E. 2006. Association analysis as a strategy for improvement of quantitative traits in plants. Crop Science 46: 1323-1330.##Buckler, E.S., Holland, J.B., Bradbury, P.J., Acharya, C.B., Brown, P.J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J.C., Goodman, M.M., Harjes, C., Guill, K., Kroon, D.E., Larsson, S., Lepak, N.K., Li, H., Mitchell, S.E., Pressoir, G., Peiffer, J.A., Rosas, M.O., Rocheford, T.R., Romay, M.C., Romero, S., Salvo, S., Sanchez Villeda, H., da Silva, H.S., Sun, Q., Tian, F., Upadyayula, N., Ware, D., Yates, H., Yu, J., Zhang, Z., Kresovich, S. and McMullen, M.D. 2009. The genetic architecture of maize flowering time. Science 325: 714-718.##Cai, H., Chu, Q., Gu, R., Yuan, L., Liu, J., Zhang, X., Chen, F., Mi, G. and Zhang, F. 2012. Identification of QTLs for plant height, ear height and grain yield in maize (Zea mays L.) in response to nitrogen and phosphorus supply. Plant Breeding 131: 502-510.##Cardwell, V. B. 1982. Fifty years of Minnesota corn production: Sources of yield increase. Agronomy Journal 74: 984-990.##Chen, J., Ding, J., Li, H., Li, Z., Sun, X., Li, J., Wang, R., Dai, X., Dong, H., Song, W., Chen, W., Xia, Z. and Wu, J. 2012. Detection and verification of quantitative trait loci for resistance to Fusarium ear rot in maize. Molecular Breeding 30: 1649-1656.##Chen, Y., Chen, J. and Wu, J. 2014. Fine mapping of gene Rab1 for red glume collar in maize. Acta Agriculturae Boreali-Sinica 29: 7-12.##Chen, J., Zhang, L., Liu, S., Li, Z., Huang, R., Li, Y., Cheng, H., Li, X., Zhou, B., Wu, S., Chen, W., Wu, J. and Ding, J. 2016. The genetic basis of natural variation in kernel size and related traits using a four-way cross population in maize. PLoS ONE 11: e0153428.##Ding, J., Li, H., Wang, Y., Zhao, R., Zhang, X., Chen, J., Xia, Z. and Wu, J. 2012. Fine mapping of Rscmv2, a major gene for resistance to sugarcane mosaic virus in maize. Molecular Breeding 30: 1593-1600.##Ding, J., Ali, F., Gengshen, C., Li, H., Mahuku, G., Yang, N., Narro, L., Magorokosho, C., Makumbi, D. and Yan, J. 2015a. Genome-wide association mapping reveals novel sources of resistance to northern corn leaf blight in maize. BMC Plant Biology 15: 206: 1-11.##Ding, J., Zhang, L., Chen, J., Li, X., Li, Y., Cheng, H., Huang, R., Zhou, B., Li, Z., Wang, J. and Wu, J. 2015b. Genomic dissection of leaf angle in maize (Zea mays L.) using a four-way cross mapping population. PLoS ONE 10: e0141619.##Domenyuk, V.P., Verbitskaya, T.G., Belousov, A.A. and Sivolap,I. M. 2002. Marker analysis of quantitative traits in maize by ISSR–PCR. Russian Journal of Genetics 38(10): 1161-1168.##Ersoz, E.S., Yu, J. and Buckler, E.S. 2009. Applications of linkage disequilibrium and association mapping in maize. In Kriz,A.L. and Larkins,B.A. (Eds.). Molecular genetic approaches to maize improvement. Springer-Verlag, New York, NY.pp: 173-195.##Evanno, G., Regnaut, S. and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology14: 2611- 2620.##Fraley, R.T. 2009. Molecular genetic approaches to maize improvement–an introduction. In: Kriz, A. L. and Larkins, B. A. (Eds.). Molecular genetic approaches to maize improvement. Springer, Berlin Heidelberg.pp: 3-6.##Gupta, P.K., Rustgi, S. and Kulwal, P.L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology 57: 461-485.##Holland, J.B. 2007. Genetic architecture of complex traits in plants. Current Opinion in Plant Biology 10: 156-161.##Idris, A.E., Hamza, N.B., Yagoub, S.O., Ibrahim, A.I.A. and El-Ami, 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 6: 42-47.##Jun, T.H., Van, K., Kim, M.Y., Lee, S. H. and Walker, D.R. 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162: 179-191.##Karimi, H. 2007. Forage crops breeding and cultivation. Tehran University Press, Tehran, Iran. 428 p. (In Persian).##Krakowsky, M.D., Lee, M., Garay, L., Woodman-Clikeman, W., Long, M.J., Sharopova, N., Frame, B. and Wang, K. 2006. Quantitative trait loci for callus initiation and totipotency in maize (Zea mays L.). Theoretical and Applied Genetics 113: 821-830.##Le Clerc, V., Bazante, F., Baril, C., Guiard, J. and Zhang, D. 2005. Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers. Theoretical and Applied Genetics 110: 294-302.##Li, X., Zhou, Z., Ding, J., Wu, Y., Zhou, B., Wang, R., Ma, J., Wang, S., Zhang, X., Xia, Z., Chen, J. and Wu, J. 2016. Combined linkage and association mapping reveals QTL and candidate genes for plant and ear height in maize. Frontiers in Plant Science7: 833.##Ministry of Jihad-e-Agriculture. 2015. Agricultural statistics, Vol. 1: Crop plants. General Directorate of Statistics and Information, Ministry of Jihad-e-Agriculture, Tehran, Iran. (In Persian).##Mohammadi, S.A. and Prasanna, B.M. 2003. Analysis of genetic diversity in crop plants- salient statistical tools and considerations. Crop Science 43: 1235-1248.##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 Research12: 99-114.##Moose, S.P. and Mumm, R.H. 2008. Molecular plant breeding as the foundation for 21stcentury crop improvement. Plant Physiology 147: 969-977.##Muhammad, R.W., Qayyum, A., Ahmad, M.Q., Hamza, A., Yousaf, M., Ahmad, B., Younas, M., Malik, W., Liaqat, S. and Noor, E. 2017. Characterization of maize genotypes for genetic diversity on the basis of inter simple sequence repeats. Genetics and Molecular Research 16(1): gmr16019438.doi: 10.4238/gmr16019438.##Murray, M.G. and Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 4321-4325.##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. Russian Journal of Genetics 39(12): 1412-1419.##Pritchard, J.K., Stephens, M., Rosenberg, N.A. and Donnelly, P. 2000. Association mapping in structured populations. American Journal of Human Genetics67: 170-181.##Sergio T.S., Cláudio Lopes De Souza, J.R., Antonio Augusto Franco, G., Adelmo Rezende, S., Alexandre Franco, G., Claudete Aparecida, M., Luciana Lasry, B. and Anete Pereira, D.S. 2003. Molecular mapping in tropical maize (Zea mays L.) using microsatellite markers. 2: Quantitative trait loci (QTL) for grain yield, plant heigth, ear height and grain moisture. Hereditas 139: 107-115.##Mikic, S., Kondic-Spika, A., Brbaklic, L., Stanisavljevic, D., Trkulja, D., Tomicic, M., Nastasic, A., Kobiljski, B., Prodanovic, S. and Momirovic, G.S.2016. Multiple marker-traits associations for maize agronomic traits. Chilean Journal of Cultural Research 76: 300-306.##Sibov, S. T., de Souza, C. L., Garcia, A. A. F., Silva, A. R., Garcia, A. F., Mangolin, C. A., Lasry Benchimol, L. and Pereira de Souza, A. 2003. Molecular mapping in tropical maize (Zea mays L.) using microsatellite markers. 2: Quantitative trait loci (QTL) for grain yield, plant height, ear height and grain moisture. Hereditas 139 (2): 107-115.##Spataro, G., Tiranti, B., Arcaleni, P., Bellucci, E., Attene, G., Papa, R. and Negri, V. 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122: 1281-1291.##Tajbakhsh, M. 1996. Maize: Agronomy, breeding, pests and diseases. Ahrar Press, Tabriz, Iran.136 p. (In Persian).##Tracy, W.F., Whitt, S.R. and Buckler, E.S. 2006. Recurrent mutation and genome evolution: Example of sugary1 and the origin of sweet maize. Crop Science 46: 1-7.##Tuberosa, R., Gill, B. S. and Quarrie, S. A. 2002. Cereal genomics: Ushering in a brave new world. Plant Molecular Biology 48: 445-449.##Walbot, V. 2009. 10 reasons to be tantalized by the B73 maize genome. PLoS Genet 5:e1000723.##Xu, D.L., Cai, Y.L., Lv, X.G., Dai, G.Q., Wang, G.Q., Wang, J.G., Sun, H.Y. and Tan, H.N. 2009. QTL mapping for plant-tape traits in maize. Journal of Maize Science 17: 27-31.##Yan, J., Warburton, M. and Crouch, J. 2011. Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Science 51: 433-449.##Zhu, C., Gore, M., Buckler, E.S. and Yu, J. 2008. Status and prospects of association mapping in plants. The Plant Genome 1: 5-20.##Zhang, Z.M., Zhao, M.J., Ding, H.P., Rong, T.Z. and Pan T. 2006. Quantitative trait loci analysis of plant height and ear height in maize (Zea mays L.). Russian Journal of Genetics 42: 306-310.##Zhang, Q., Zhang, L., Evers, J., van der Werf, W., Zhang, W. and Duan, L. 2014. Maize yield and quality in response to plant density and application of a novel plant growth regulator. Field Crops Research 164: 82-89.##Zwonitzer, J. C. J., Coles, N. D. N., Krakowsky, M. D., Arellano, C., Holland, J. B., McMullen, M. D., Pratt, R.C. and Balint-Kurti, P.J. 2010. Mapping resistance quantitative trait loci for three foliar diseases in a maize recombinant inbred line population: Eevidence for multiple disease resistance? Phytopathology 100: 72-79.