Genic and Non-genic Contributions to Quantitative Trait Variation in Maize as Detected via GWAS

The genomic distribution of trait-associated SNPs (TASs) discovered in genome-wide association studies (GWAS) can provide insights into the genetic architecture of complex traits and contribute to the design of future studies. Here we report on a set of GWAS in maize that identified TASs underlying five quantitative traits (leaf length, leaf width, upper leaf angle, days to anthesis, and days to silking) measured across a large panel of samples and examined the characteristics of the discovered TASs. A set of mostly (~87%) genic SNPs was generated via an analysis of RNA-seq reads. This SNP set was complemented with a set of maize HapMap SNPs that contains approximately equal proportions of genic and non-genic SNPs. TASs were identified with a genome scan while controlling for polygenic background effects. TASs were enriched in non-genic regions, particularly within a 5kb window upstream of genes, but depleted in nonsynonymous sites. Across maize quantitative traits, TASs collectively explained 44~59% of the total phenotypic variation, and on average, 79% of these explained variation were further attributed to TASs located in genes or within 5kb upstream of genes (which comprises only 13% of the genome). TASs tagged 80 candidate genes under analysis including ligueless2 (upper leaf angle; two genic TASs); rough sheath1 (leaf width; one upstream non-genic TAS); and zea agamous5 (days to silking; one genic and one non-genic TASs). The diverse functions of TAS-implicated candidate genes indicate that complex genetic networks shape these traits.