J Integr Plant Biol. ›› 2011, Vol. 53 ›› Issue (8): 641-652.DOI: 10.1111/j.1744-7909.2011.01051.x

• Plant-environmental Interactions • Previous Articles     Next Articles

Identification of Functional Genetic Variations Underlying Drought Tolerance in Maize Using SNP Markers

Zhuanfang Hao1, Xinhai Li1, Chuanxiao Xie1, Jianfeng Weng1, Mingshun Li1, Degui Zhang1, Xiaoling Liang2, Lingling Liu1, Sisi Liu1 and Shihuang Zhang1*   

  1. 1Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facilities for Crop Genetic Resources and Improvement, Beijing 100081, China
    2Institute of Food Crops Science, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China
  • Received:2010-11-30 Accepted:2011-04-27 Published:2011-05-12
  • About author:*Corresponding author. Tel: +86 10 8210 8566; Fax: +86 10 8210 8747; E-mail: cshzhang2000@yahoo.com.cn


Single nucleotide polymorphism (SNP) is a common form of genetic variation and popularly exists in maize genome. An Illumina GoldenGate assay with 1 536 SNP markers was used to genotype maize inbred lines and identified the functional genetic variations underlying drought tolerance by association analysis. Across 80 lines, 1 006 polymorphic SNPs (65.5% of the total) in the assay with good call quality were used to estimate the pattern of genetic diversity, population structure, and familial relatedness. The analysis showed the best number of fixed subgroups was six, which was consistent with their original sources and results using only simple sequence repeat markers. Pairwise linkage disequilibrium (LD) and association mapping with phenotypic traits investigated under water-stressed and well-watered regimes showed rapid LD decline within 100–500 kb along the physical distance of each chromosome, and that 29 SNPs were associated with at least two phenotypic traits in one or more environments, which were related to drought-tolerant or drought-responsive genes. These drought-tolerant SNPs could be converted into functional markers and then used for maize improvement by marker-assisted selection.

Hao Z, Li X, Xie C, Weng J, Li M, Zhang D, Liang X, Liu L, Liu S, Zhang S (2011) Identification of functional genetic variations underlying drought tolerance in maize using SNP markers. J. Integr. Plant Biol. 53(8), 641–652.

Key words: association analysis, drought tolerance, functional variation, maize (Zea mays L.), single nucleotide polymorphism

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