Three-dimensional image analysis reveals uneven centromere distribution in root cell nuclei of Arabidopsis haploids

Centromere distribution within the nucleus fundamentally influences chromatin architecture by constraining interactions among chromosomes. We performed whole-mount fluorescence in situ hybridization analyses of the root cortical cell files of Arabidopsis thaliana haploids and diploids using a centromere-specific DNA probe to determine the spatial profiles of nuclear volume and the number of centromere signals. In all root regions, the nuclear volume in haploids was smaller than that in diploids; in the mature zone, it was nearly half that in diploids, but in the proliferation zone, it increased rapidly. The number of centromere signals throughout the root region was relatively unchanged in haploids (approximately 5) and diploids (approximately 8). We also examined the three-dimensional distribution of centromeres within the nuclei of root cortical cells in both haploids and diploids. The distance between the centromere centroid and the nuclear centroid was greater in haploids than in diploids, indicating that centromere distribution was more uneven in haploids than in diploids. The uneven centromere distribution in haploids may affect chromatin compartmentalization, potentially leading to alterations in chromosomal organization and higher-order chromatin structures.