Epistasis Analysis of Rare Alleles from Teosinte in Maize Genetic Architecture

Since maize domestication, inbreeding and selection over the last century have removed many strong deleterious alleles, but there are still rare alleles with smaller effects segregating in maize germplasm. The wild ancestor of maize, teosinte (Zea mays ssp. parviglumis), has not been inbred and, therefore, has more deleterious alleles than maize with larger effects that are masked by heterozygosity. The study of rare alleles and their involvement in complex agronomic traits has been limited in the current available germplasm of maize due to low statistical power. A new genetic resource, the Teosinte Synthetic (Teo-Syn), was developed by our lab by randomly mating backcrossed (BC₁) progeny of 11 parviglumis accessions in the B73 background, yielding an expected genetic ratio of ~25% teosinte and ~75% B73. We conducted a genome wide association study (GWAS) for the maize flowering time traits: Days to Anthesis (DTA), Days to Silking (DTS) and Anthesis-Silk interval (ASI). We identified several significant QTLs for the flowering time in Teo-Syn population and the results are quite similar to the QTL profiles compared to the Teosinte near isogenic lines. Similarly, epistasis analysis revealed strong bi-locus interactions for DTA and DTS, explaining 46% and 56% of the phenotypic variation, respectively. Our preliminary results suggest that the flowering time in maize has a complex genetic architecture, and rare alleles putatively from teosinte are involved in epistatic interactions that significantly contribute to phenotypic variation in maize.