Association mapping of drought tolerance genes

Association analysis through linkage disequilibrium is a useful new tool for the dissection of complex traits and identification of superior alleles at genes identified. Presented here are the results in the search for DNA polymorphisms associated with drought tolerance, a highly quantitative trait in maize, using the candidate gene approach. The drought association mapping test characterized 350 drought affected and well watered maize genotypes in 5 locations over 2 years. Drought tolerance and metabolic component traits from different tissues were measured and associated with 1536 Single Nucleotide Polymorphism (SNP) markers from drought candidate genes. Fifteen SNPs were associated with field phenotypes, including grain yield under water stress, when analyzed singly, but only two were still associated with drought related traits when the experiment wide error rate was corrected to an acceptable level. One hundred and one SNPs were associated with the metabolic products, including genes for ABA and carbohydrate metabolism, transcription and signaling factors, and chromatin remodeling, when analyzed singly, but only 11 were still associated with the corrected error rate. The candidate gene approach for association analysis of quantitative traits appears to have the greatest chance of success when the trait can be broken down into component traits that are well characterized at the biochemical level, with known pathways that can be used to drive the choice of gene candidates. Lessons learned in this study will be used in a new association study to seek genes giving resistance to aflatoxin accumulation in maize, another highly quantitative trait, starting from candidate pathways.