Fine-Mapping Small Effect Flowering Time QTLs in Maize: Genetic Architecture Is Complex.

Flowering time in maize is a complex trait important for adaptation of plants to their local environment. In the nested association mapping (NAM) population, more than 40 flowering time quantitative trait loci (QTL), each associated with small, additive effects, were previously identified. Our study is a targeted approach to fine-map two linked small effect flowering time QTL on chromosome 3. A recombinant chromosome near isogenic line (RC-NIL) population was developed using the temperate inbred B73 and a near isogenic line, NIL0028 which carried a 43 cM introgression on chromosome 3 from a tropical inbred line Tzi8 in B73 background. Initial NAM analysis identified two QTL in this chromosome region, each conferring a change of about half a day in flowering time. Homozygous recombinant lines were selected from more than 3000 F₂s by genotyping across the QTL regions. High-density marker coverage across QTL regions was achieved using genotyping-by-sequencing of selected RC-NILs. These lines were phenotyped in 30 replications across 12 environments. Although significant interaction among the genotypes and environments was detected, the magnitude of the interaction variation was several folds smaller than the genetic variation. We validated the effects of QTL originally mapped in NAM and identified a third QTL between them. The three QTL combined explain about 35 % of the phenotypic variation in flowering time. No significant epistatic interactions among the QTL pairs were observed. One flowering time QTL was fine-mapped to a 3.8 megabase region containing 57 candidate genes. Putative roles of two of the candidate genes in flowering time regulation in maize were explored as their known orthologues are directly involved in the flowering time pathways in other plant species. This study highlights the challenges involved in dissection of small effect QTL in maize. Furthermore our results emphasize the highly polygenic nature of an adaptive trait in an outcrossing species such as maize.