Genetic Variance for Root Length in Arabidopsis thaliana

1 Efforts to identify loci underlying complex traits generally assume that most genetic variance is 2 additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the 3 narrow-sense heritability for this trait was statistically zero. This low additive genetic variance 4 likely explains why no associations to root length could be found using standard additive-model5 based genome-wide association (GWA) approaches. However, the broad-sense heritability for 6 root length was significantly larger, and we therefore also performed an epistatic GWA analysis 7 to map loci contributing to the epistatic genetic variance. This analysis revealed four interacting 8 pairs involving seven chromosomal loci that passed a standard multiple-testing corrected 9 significance threshold. Explorations of the genotype-phenotype maps for these pairs revealed 10 that the detected epistasis cancelled out the additive genetic variance, explaining why these loci 11 were not detected in the additive GWA analysis. Small population sizes, such as in our 12 experiment, increase the risk of identifying false epistatic interactions due to testing for 13 associations with very large numbers of multi-marker genotypes in few phenotyped individuals. 14 Therefore, we estimated the false-positive risk using a new statistical approach that suggested 15 half of the associated pairs to be true positive associations. Our experimental evaluation of 16 candidate genes within the seven associated loci suggests that this estimate is conservative; we 17 identified functional candidate genes that affected root development in four loci that were part of 18 three of the pairs. In summary, statistical epistatic analyses were found to be indispensable for 19 confirming known, and identifying several new, functional candidate genes for root length using 20 a population of wild-collected A. thaliana accessions. We also illustrated how epistatic 21 cancellation of the additive genetic variance resulted in an insignificant narrow-sense, but 22 significant broad-sense heritability that could be dissected into the contributions of several 23 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/008789 doi: bioRxiv preprint first posted online Sep. 4, 2014;