Genetic Mapping of Genotype-by-Ploidy Effects in Arabidopsis thaliana

Plants can express different phenotypic responses following polyploidization, but ploidy-dependent phenotypic variation has so far not been assigned to specific genetic factors. To map such effects, segregating populations at different ploidy levels are required. The availability of an efficient haploid inducer line in Arabidopsis thaliana allows for the rapid development of large populations of segregating haploid offspring. Because Arabidopsis haploids can be self-fertilised to give rise to homozygous doubled haploids, the same genotypes can be phenotyped at both the haploid and diploid ploidy level. Here, we compared the phenotypes of recombinant haploid and diploid offspring derived from a cross between two late flowering accessions to map genotype x ploidy (G x P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels. This implies that mapping power will increase when phenotypic measurements of monoploids are included in QTL analyses. A multi-trait analysis further revealed pleiotropic effects for a number of the ploidy-specific QTLs as well as opposite effects at different ploidy levels for general QTLs. Taken together, we provide evidence of genetic variation between different Arabidopsis accessions being causal for dissimilarities in phenotypic responses to altered ploidy levels, revealing a G x P effect. Additionally, by investigating a population derived from late flowering accessions, we revealed a major vernalisation-specific QTL for variation in flowering time, countering the historical bias of research in early flowering accessions.

Automated summary

Plants can exhibit different phenotypic responses after polyploidization, and the genetic factors responsible for ploidy-dependent phenotypic variation have not yet been identified. In this study, a population of segregating haploid and diploid offspring derived from Arabidopsis thaliana with different ploidy levels was compared to map the genotype x ploidy (G x P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels, indicating that including phenotypic measurements of haploids in QTL analyses can increase mapping power. The study also revealed pleiotropic effects and opposite effects at different ploidy levels for some QTLs. Overall, the research provides evidence that genetic variation between different Arabidopsis accessions is responsible for differences in phenotypic responses to altered ploidy levels, demonstrating a G x P effect.