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Hybrids occasionally exhibit genetic interactions resulting in reduced fitness in comparison to their parents. Studies of Arabidopsis thaliana have highlighted the role of immune conflicts, but less is known about the role of other factors in hybrid incompatibility in plants. Here, we present a new hybrid incompatibility phenomenon in this species. We have characterized a new case of F hybrid incompatibility from a cross between the A. thaliana accessions Krotzenburg-0 (Kro-0) and BG-5, by conducting transcript, metabolite and hormone analyses, and identified the causal loci through genetic mapping. The F hybrids showed arrested growth of the main stem, altered shoot architecture, and altered concentrations of hormones in comparison to parents. The F phenotype could be rescued in a developmental-stage-dependent manner by shifting to a higher growth temperature. These F phenotypes were linked to two loci, one on chromosome 2 and one on chromosome 3. The F generation segregated plants with more severe phenotypes which were linked to the same loci as those in the F . This study provides novel insights into how previously unknown mechanisms controlling shoot branching and stem growth can result in hybrid incompatibility.

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