Rare Alleles Delay Flowering Time in Maize.

Rare alleles can have positive, negative or neutral effect on the fitness of an individual in a population. In maize (Zea mays ssp. mays), rare alleles can contribute in inbreeding depression or heterosis through complementation, and may play a role in complex quantitative traits such as yield, adaptation and kernel composition. It is important to understand the role of rare alleles in maize genetic architecture in order to aid in the selection and development of future elite breeding lines. 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. It is the goal of modern plant breeders to increase the frequency of beneficial alleles and decrease the frequency of deleterious alleles in the germplasm of maize. But, 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 have bulk-pollen random-mated the Teo-Syn population five and nine times, prior to self-pollination to create 1045 selfed (S₁) families.  In 2014 and 2015, the combined S1 progenies were evaluated for various domestication and agronomic traits in field trials grown in two replications in Columbia, Missouri. The original S₀ parents were genotyped via RAD-GBS, identifying about 59K SNPs, which were used to conduct genome wide association analysis (GWAS) employing the mixed linear model (MLM) method (Q+K) to control for population structure of flowering time (Days to Anthesis and Days to Silking). We identified four significant QTLs for flowering time in Teo-Syn population and the results are quite similar to the QTL profiles compared to the Teosinte near isogenic line (Teo NIL). The highest QTL for both DTA and DTS was located on chromosome 10 and is likely to contain the photoperiod gene, ZmCCT; similarly, second highest QTL on chromosome 8, a candidate gene include vgt1; followed by rest of the two significant QTLs on chromosome 4 and 3. Our result also suggests that rare alleles from teosinte delay flowering time in Maize, and we intend to explore further to test if these rare alleles are involved in epistatic interactions in the Teo-Syn population.