Institute of Crop Science, Chinese Academy of Agricultural Sciences, National Key Facilities for Crop Genetic Resources and Improvement, Beijing, China.
J Integr Plant Biol. 2011 Aug;53(8):641-52. doi: 10.1111/j.1744-7909.2011.01051.x. Epub 2011 Jul 19.
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.
单核苷酸多态性（SNP）是一种常见的遗传变异形式，普遍存在于玉米基因组中。本研究利用 Illumina GoldenGate assay 对 1536 个 SNP 标记进行基因分型，通过关联分析鉴定了玉米自交系耐旱性的功能遗传变异。在 80 个系中，对具有良好调用质量的测定中的 1006 个多态性 SNP（占总数的 65.5%）进行了遗传多样性、群体结构和亲缘关系的估计。分析表明，最好的固定亚群数量是六个，这与它们的原始来源和仅使用简单序列重复标记的结果一致。在胁迫和充分供水条件下进行的成对连锁不平衡（LD）和关联作图表明，每个染色体的物理距离内，LD 在 100-500kb 范围内迅速下降，29 个 SNP 与一个或多个环境中的至少两个表型性状相关，这些性状与耐旱或耐旱相关基因有关。这些耐旱 SNP 可以转化为功能标记，然后通过标记辅助选择用于玉米改良。
