The genome of a low-seeded mandarin, Premier, displays major structural changes due to gamma irradiation

The mandarin (Citrus reticulata) variety Premier (11C017) is a gamma-irradiated mutant hybrid derived from a cross between Murcott and Ellendale. The variety Premier exhibits favorable traits, including good fruit size and productivity similar to its progenitor variety (01C011), along with a reduced seed count compared to the progenitor. Here, we developed haplotype-resolved genomes for both Premier and its parental line Ellendale using PacBio HiFi and Hi-C sequencing, followed by a combination of de novo and reference-guided assembly approaches. The size of the assemblies ranged from 320 to 337 Mb, with N50s more than 31 Mb, and more than 98% BUSCO for the assembly and annotation. Comparative analysis revealed multiple structural rearrangements including inversions, translocations, and duplications in the Premier haplotypes relative to the parental genomes. Notably, we identified heterozygous reciprocal translocations (between Chr2 and Chr4 in haplotype 1, and Chr5 and Chr7 in haplotype 2) and a large heterozygous inversion (∼22 Mb on Chr2 of haplotype 1) as prominent rearrangements unique to Premier. These complex structural variants may disrupt normal meiotic pairing and gamete formation, potentially contributing to the observed reduction in seed number. These findings suggest that structural rearrangements may play a significant role in the reduction of the seed content of gamma-irradiated plants.