Single-Nucleus Transcriptome Analysis Provides New Insights Into B Chromosome Elimination in Sorghum.

B chromosomes are supernumerary entities found in many plant species, with some exhibiting tissue-specific elimination. In Sorghum purpureosericeum, extensive B chromosome elimination occurs during embryogenesis affecting most of the embryonic organs, leaving the B chromosome maintained mainly in limited regions of meristems. The dynamics of the process and rarity of the transcripts associated with elimination make capturing it challenging. To address this, we performed single-nucleus RNA sequencing (snRNA-seq) on embryos undergoing B chromosome elimination. This approach enabled detection of more B-linked transcripts compared to previous methods. Notably, we identified nuclei with B-specific transcripts, which predominantly clustered in a single cluster in both replicates of B-positive embryos. Further analysis of these clusters revealed three subpopulations with divergent transcriptional profiles. One subpopulation showed gene expression patterns suggesting active elimination of the B chromosome, while the other subpopulations are expected to exhibit regular segregation of the B chromosome and/or preparation for the elimination process. Our analysis provides resolution so far missing in current studies and highlights a clear benefit of the single-cell approaches for studying specific behaviour of the B chromosomes.