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

TL;DR

The mandarin variety Premier has fewer seeds due to unique DNA rearrangements caused by gamma irradiation, which may help breed better fruit varieties.

Contribution

The study identifies specific structural genomic changes in a gamma-irradiated mandarin variety linked to reduced seed count.

Findings

Premier's genome shows structural rearrangements like inversions and translocations not found in its parents.

These changes may disrupt meiotic pairing and gamete formation, leading to fewer seeds.

The findings suggest structural variants can be used to develop low-seed mandarin varieties.

Abstract

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.

Mandarin oranges are an important fruit crop, and seedless or low‐seed varieties are highly desirable for consumers. The variety Premier is a new type of mandarin developed from its parents Murcott and Ellendale and shows good fruit size and productivity but has fewer seeds. We analyzed the complete genetic makeup of Premier and its parents Ellendale and Murcott to understand why Premier has fewer seeds. Our study found that Premier's genome has unique structural changes, including rearrangements and inversions of large DNA segments, that are not present in its parents. These changes could interfere with normal cell division during reproduction, leading to fewer seeds in Premier fruits. These findings suggest that specific changes in the DNA structure may help create low‐seed or seedless fruit varieties, which could be useful for breeding better mandarins in the future.

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