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Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions

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Abstract

Drought can cause severe reduction in maize production, and strongly threatens crop yields. To dissect this complex trait and identify superior alleles, 350 tropical and subtropical maize inbred lines were genotyped using a 1536-SNP array developed from drought-related genes and an array of 56,110 random SNPs. The inbred lines were crossed with a common tester, CML312, and the testcrosses were phenotyped for nine traits under well-watered and water-stressed conditions in seven environments. Using genome-wide association mapping with correction for population structure, 42 associated SNPs (P ≤ 2.25 × 10−6 0.1/N) were identified, located in 33 genes for 126 trait × environment × treatment combinations. Of these genes, three were co-localized to drought-related QTL regions. Gene GRMZM2G125777 was strongly associated with ear relative position, hundred kernel weight and timing of male and female flowering, and encodes NAC domain-containing protein 2, a transcription factor expressed in different tissues. These results provide some good information for understanding the genetic basis for drought tolerance and further studies on identified candidate genes should illuminate mechanisms of drought tolerance and provide tools for designing drought-tolerant maize cultivars tailored to different environmental scenarios.

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Acknowledgments

This research was supported by the Generation Challenge Program and the National Hi-Tech Research and Development Program of China (2012AA10A307) and the National Natural Science Foundation of China (31101156).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Yadong Xue, Xuehai Zhang, Xiaobo Zhang, Yonglian Zheng & Jianbing Yan

  2. USDA-ARS Corn Host Plant Research Resistance Unit, Mississippi State University, Box 9555, Starkville, MS, 39762, USA

    Marilyn L. Warburton

  3. Generation Challenge Program, Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico

    Mark Sawkins & Jean-Marcel Ribaut

  4. Department of Crop and Soil Sciences, Cornell University, Ithaca, NY, 14853, USA

    Tim Setter

  5. International Maize and Wheat Improvement Center, Apdo. Postal 6-641, 06600, Mexico, D.F., Mexico

    Yunbi Xu

  6. Nakhon Sawan Field Crops Research Center (NSFCRC), Takfa, Nakhon Sawan, 60190, Thailand

    Pichet Grudloyma

  7. Kenya Agricultural Research Institute (KARI), RRC Mtwapa, P.O. Box 16, Mtwapa, Kenya

    James Gethi

  8. Maize Research Institute, Sichuan Agricultural University, Ya’an, China

    Wanchen Li

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  1. Yadong Xue
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  2. Marilyn L. Warburton
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  3. Mark Sawkins
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  4. Xuehai Zhang
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  9. Jean-Marcel Ribaut
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  10. Wanchen Li
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  11. Xiaobo Zhang
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  13. Jianbing Yan
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Correspondence to Jianbing Yan.

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Communicated by T. Lubberstedt.

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Xue, Y., Warburton, M.L., Sawkins, M. et al. Genome-wide association analysis for nine agronomic traits in maize under well-watered and water-stressed conditions. Theor Appl Genet 126, 2587–2596 (2013). https://doi.org/10.1007/s00122-013-2158-x

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