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

• Published in: Journal of integrative plant biology 2011-08, Vol.53 (8), p.641-652
• Main Authors: Hao, Zhuanfang, Li, Xinhai, Xie, Chuanxiao, Weng, Jianfeng, Li, Mingshun, Zhang, Degui, Liang, Xiaoling, Liu, Lingling, Liu, Sisi, Zhang, Shihuang
• Format: Article
• Language: English
• Subjects: Adaptation, Physiological - genetics; Alleles; association analysis; Chromosome Mapping; chromosomes; Chromosomes, Plant - genetics; corn; drought tolerance; Droughts; functional variation; Gene Frequency - genetics; genes; Genetic Markers; genetic variation; Genetics, Population; Genome-Wide Association Study; genotype; inbred lines; Inbreeding; linkage disequilibrium; Linkage Disequilibrium - genetics; maize (Zea mays L.); marker-assisted selection; Phenotype; Polymorphism, Single Nucleotide - genetics; Population Dynamics; population structure; Quantitative Trait, Heritable; single nucleotide polymorphism; SNPs; Zea mays - genetics; 单核苷酸多态性; 抗旱性; 标记基因型; 玉米自交系; 简单重复序列; 识别功能; 遗传变异
• ISSN: 1672-9072; 1744-7909
• DOI: 10.1111/j.1744-7909.2011.01051.x

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.