CRISPR-mediated centromere fission generates neo-chromosomes with distorted meiotic inheritance in Arabidopsis

Centromeres are essential for chromosome segregation and are epigenetically defined by CENH3/CENP-A nucleosomes. Centromere position along chromosomes varies within and between species, ranging from telocentric to metacentric architectures. Yet, how centromere position influences chromosome inheritance and karyotype evolution remains poorly understood. To reposition the centromere, we used CRISPR-Cas9 to break the centromeric satellite array of Arabidopsis thaliana chromosome 3. Fission chromosomes rapidly acquired telomeres, converting a metacentric into two stable telocentric neo-chromosomes. Neo-centromere formation involved genetic restructuring and de novo satellite higher-order repeat formation, together with epigenetic remodeling of CENH3 and DNA methylation. Crossing the six-chromosome fission line to five-chromosome wild type produced a meiosis-specific trivalent that mis-segregated and generated aneuploidy. Trivalent recombination doubled through two obligate crossovers, which were shifted towards the telomeres. Inheritance was strongly distorted in favor of the wild type centromere, as telocentrics segregated into inviable monosomic gametes. The reciprocal trisomic gametes were associated with centromere-proximal recombination, demonstrating that crossover position governs trivalent segregation. Distortion further increased when CENH3 was over-expressed, implicating centromere strength in the outcomes of trivalent meiosis. Our results reveal rapid centromere remodeling following karyotype change, and how trivalent centromere architecture distorts inheritance, with implications for hybrid incompatibility and synthetic chromosome design.