Genome-Wide Association Study (GWAS) Reveals an SNP Associated with Downy Mildew Resistance in Maize


  • Nay Nay Oo Doctor of Philosophy Program in Agricultural Sciences, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen campus, Nakhon Pathom 73140, Thailand.
  • Vinitchan Ruanjaichon National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
  • Kularb Laosatit Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.
  • Theerayut Toojinda
  • Jintana Unartngam Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kam-phaeng Saen campus, Nakhon Pathom 73140, Thailand.


Preonosclerospora spp, maize, quantitative trait loci (QTL), single nucleotide polymorphism (SNP)


Downy Mildew, caused by the fungus Peronosclerospora spp. is one of the most destructive diseases of maize and can cause severe damage in crops around the world, especially in tropical Asia. Host resistance is an effective mean of control DM and is reported to be controlled by many genes. Therefore, the identification of markers linked to the target quantitative trait loci (QTL) was required in a marker-assisted breeding program. In this study, Genome-Wide association study (GWAS) analysis using 262 maize inbred lines and 434,871 single nucleotide polymorphism (SNP) markers was performed to identify genomic regions and candidate genes associated with resistance to the DM. The result showed that one significant QTL was identified on chromosome 1 associated with the trait DM resistance, containing one candidate gene, Zm00001d029516, according to its function in plant protection mechanism. This QTL/SNP locus should be validated and will be useful for marker-assisted selection and for a better understanding of DM disease resistance in maize


Agrama, H., M. Moussa, M. Naser, M. Tarek and A. Ibrahim. 1999. Mapping of QTL for downy mildew resistance in maize. Theoretical Applied Genetics 99(3): 519-523.

Ashan, M. D., M. Miftahudin, R. Reflinur, M. B. Pabendo, S. B. Santoso and A. Salim. 2020. QTL Mapping linked to downy mildew resistance genes in maize (Zea mays). Biodiversity Journal 21(8):3735-3743.

Bradbury, P. J., Z. Zhang, D. E. Kroon, T. M. Casstevens, Y. Ramdoss and E. S. Buckler. 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19): 2633-2635. doi:10.1093/bioinformatics/btm308.

Brito, D. P., D. Jeffers, D. G. de León, M. Khairallah, M. C. Cruz, G. V. Cardelas, S. A. Rivero and G. Srinivasan. 2001. Cartografía de QTL de la resistencia a la pudrición de la mazorca (Fusarium moniliforme) en maíz de Valles Altos, México. Agrociencia 35(2): 181-196.

Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto, E. S. Buckler and S. E. Mitchell. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLOS one 6(5): e19379.

Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology 14(8): 2611-2620.

George, M., B. Prasanna, R. Rathore, T. Setty, F. Kasim, M. Azrai, S. Vasal, O. Balla, D. Hautea and A. Canama. 2003. Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theoretical Applied Genetics 107(3): 544-551.

Guo, H., C. Xiao, Q. Liu, R. Li, Z. Yan, X. Yao and H. Hu. 2021. Two galacturonosyl transferases function in plant growth, stomatal development, and dynamics. Plant Physiology 187(4): 2820-2836.

Jadhav, K., N. Senthil, P. Tamilarasi, K. Ganesan, V. Paranidharan, M. Raveendran and J. Ramalingam. 2019. QTL mapping for sorghum downy mildew disease resistance in maize (Zea mays L.) in recombinant inbred line population of UMI79 X UMI936 (w). Current Plant Biology 20: 100124.

Jampatong, C., S. Jampatong, C. Jompuk, T. Sreewongchai, P. Grudloyma, C. Balla and N. Prodmatee. 2013. Mapping of QTL affecting resistance against sorghum downy mildew (Peronosclerospora sorghi) in maize (Zea mays L). Maydica 58(2): 119-126.

Janruang, P. 2020. Morphology, Pathogenicity and Phylogeny of Corn Downy Mildew Fungi in Thailand. PhD Thesis, Kasetsart University, Thailand: 260 p.

Janruang, P. and J. Unartngam. 2018. Morphological and molecular based identification of corn downy mildew distributed in Thailand. International Journal of Agricultural Technology 14(6): 845-860.

Jeffers, D., H. Cordova, S. Vasal, G. Srinivasan, D. Beck and M. Barandiaran. 2000. Status in breeding for resistance to maize diseases at CIMMYT. Paper presented at the Proc. 7th Asian Regional Maize Workshop. PCARRD, Los Baos, Philippines.

Kim, H. C., K. H. Kim, K. Song, J. Y. Kim and B. M. Lee. 2020. Identification and validation of candidate genes conferring resistance to downy mildew in maize (Zea mays L.). Genes 11(2): 191.

Knapp, S. J. 1998. Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Science 38(5): 1164-1174.

Knapp, S., W. Stroup and W. Ross. 1985. Exact confidence intervals for heritability on a progeny mean basis 1. Crop Science 25(1): 192-194.

Lipka, A. E., F. Tian, Q. Wang, J. Peiffer, M. Li, P. J. Bradbury, M. A. Gore, E. S. Buckler and Z. Zhang. 2012. GAPIT: genome association and prediction integrated tool. Bioinformatics 28(18): 2397-2399.

Liu, X., M. Huang, B. Fan, E. S. Buckler and Z. Zhang. 2016. Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies. PLOS Genetics 12(2): e1005767. doi:10.1371/journal.pgen.1005767

Lohithaswa, H., K. Jyothi, K. S. Kumar and S. Hittalmani. 2015. Identification and introgression of QTLs implicated in resistance to sorghum downy mildew (Peronosclerospora sorghi (Weston and Uppal) CG Shaw) in maize through marker-assisted selection. Journal of Genetics 94(4): 741-748.

Ma, X., F. Feng, Y. Zhang, I. E. Elesawi, K. Xu, T. Li, H. Mei, H. Liu, N. Gao and C. Chen. 2019. A novel rice grain size gene OsSNB was identified by genome-wide association study in natural population. PLOS Genetics 15(5): e1008191.

Mohan, M., S. Nair, A. Bhagwat, T. Krishna, M. Yano, C. Bhatia and T. Sasaki. 1997. Genome mapping, molecular markers and marker-assisted selection in crop plants. Molecular Breeding 3(2): 87-103.

Nair, S. K., B. M. Prasanna, A. Garg, R. Rathore, T. Setty and N. Singh. 2005. Identification and validation of QTLs conferring resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in maize. Theoretical Applied Genetics 110(8): 1384-1392.

Nallathambi, P., K. M. Sundaram and S. Arumugachamy. 2010. Inheritance of resistance to sorghum downy mildew (Peronosclerospera sorghi) in maize (Zea mays L.). International Journal of Agriculture, Environment Biotechnology 3(3): 285-293.

Niu, S., Q. Song, H. Koiwa, D. Qiao, D. Zhao, Z. Chen, X. Liu and X. Wen. 2019. Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing. BMC Plant Biology 19(1): 328. doi:10.1186/s12870-019-1917-5

Phumichai, C., J. Chunwongse, S. Jampatong, P. Grudloyma, T. Pulam, W. Doungchan, A. Wongkaew and N. Kongsiri. 2012. Detection and integration of gene mapping of downy mildew resistance in maize inbred lines though linkage and association. Euphytica 187(3): 369-379.

Portwood, J. L., M. R. Woodhouse, E. K. Cannon, J. M. Gardiner, L. C. Harper, M. L. Schaeffer, J. R. Walsh, T. Z. Sen, K. T. Cho and D. A. Schott. 2019. MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic acids research 47(D1): D1146-D1154.

R Core Team. 2018. R: A language and environment for statistical computing. In: R foundation for statistical computing Vienna, Austria.

Rashid, Z., P. K. Singh, H. Vemuri, P. H. Zaidi, B. M. Prasanna and S. K. Nair. 2018. Genome-wide association study in Asia-adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance. Scientific Reports 8(1): 1-12.

Rey, J.I, J. Cerono, and J. Lúquez. (2009). Identification of quantitative trait loci for resistant to maize ear rot caused by Fusarium moniliforme Sheldon and common rust caused by Puccinia sorghi in Argentinian maize germplasm. Revista de la Facultad de Agronomía, La Plata, 108(1):1-8.

Rossi, E. S., M. C. Kuki, R. J. Pinto, C. A. Scapim, M. V. Faria and N. De Leon. 2020. Genomic-wide association study for white spot resistance in a tropical maize germplasm. Euphytica 216(1): 1-15.

Sabry, A., D. Jeffers, S. Vasal, R. Frederiksen and C. Magill. 2006. A region of maize chromosome 2 affects response to downy mildew pathogens. Theoretical Applied Genetics 113(2): 321-330.

Unartngam, J. 2019. Inoculation techniques of plant pathogens to evaluate plant resistance (in Thai). The Thai phytopathological Society: 104-114.

Ward, J., M. Laing and A. Cairns. 1997. Management practices to reduce gray leaf spot of maize. Crop Science 37(4): 1257-1262.

Xin, Z. and J. Chen. 2012. A high throughput DNA extraction method with high yield and quality. Plant Methods 8(1): 26. doi:10.1186/1746-4811-8-26

Yen, T. T. O., B. Prasanna, T. Setty and R. Rathore. 2004. Genetic variability for resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in the tropical/sub-tropical Asian maize germplasm. Euphytica 138(1): 23-31.






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