title: Identification of functional genetic variations underlying drought tolerance in maize using SNP markers.
abstract: 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.
authors.affiliation: Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facilities for Crop Genetic Resources and Improvement, Beijing, China.
authors.forename: Zhuanfang
authors.initials: Z
authors.lastname: Hao
authors.forename: Xinhai
authors.initials: X
authors.lastname: Li
authors.forename: Chuanxiao
authors.initials: C
authors.lastname: Xie
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Weng
authors.forename: Mingshun
authors.initials: M
authors.lastname: Li
authors.forename: Degui
authors.initials: D
authors.lastname: Zhang
authors.forename: Xiaoling
authors.initials: X
authors.lastname: Liang
authors.forename: Lingling
authors.initials: L
authors.lastname: Liu
authors.forename: Sisi
authors.initials: S
authors.lastname: Liu
authors.forename: Shihuang
authors.initials: S
authors.lastname: Zhang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D055864:Droughts; D005787:Gene Frequency / Q000235:genetics; D005819:Genetic Markers; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D007178:Inbreeding; D015810:Linkage Disequilibrium / Q000235:genetics; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011157:Population Dynamics; D019655:Quantitative Trait, Heritable; D003313:Zea mays / Q000235:genetics*
chemical_list: D005819:Genetic Markers