Harnessing Triploid Loquat to Unlock Aneuploid Diversity for Advanced Breeding

Triploid plants are widely valued in horticulture for desirable traits such as seedlessness, yield improvement, and stress resilience. However, most triploids exhibit low fertility, and the chromosomal behavior of their progeny remains poorly understood. Aneuploid offspring can carry novel phenotypes, but their unpredictable formation and viability have limited breeding applications. Loquat, a perennial fruit tree with a narrow genetic base, presents both challenges and opportunities for introducing variation. Understanding how triploid loquat transmits chromosomes and how these chromosomal differences translate into phenotype is essential for developing more efficient improvement strategies. Based on these challenges, this study aimed to systematically investigate chromosome inheritance and phenotypic responses in triploid-derived hybrid populations.

Researchers from the College of Horticulture and Landscape Architecture at Southwest University reported new findings on triploid loquat reproduction. The study, published (DOI: 10.1093/hr/uhaf023) on May 1, 2025, in Horticulture Research, analyzed hybrid populations produced by crossing a fertile triploid loquat line (Q24) with diploid cultivars. The work characterized chromosome-level karyotype variation, segregation distortion patterns, and phenotypic effects, revealing how triploid reproduction generates diverse aneuploid germplasm and identifying genes linked to enhanced aneuploid viability.

Using an improved SSR-qPCR molecular karyotype approach, the team examined 178 progenies from three cross combinations. The overwhelming majority (93.82%) of offspring displayed chromosome numbers between 34 and 46, forming a rich spectrum of aneuploids rather than stable euploids. A total of 160 distinct karyotypes were identified among 166 aneuploid plants, demonstrating high chromosomal variation frequency. Notably, some chromosomes were transmitted preferentially: chromosome 5 exhibited the highest disomic transmission rate, while chromosome 12 showed the lowest. Functional annotation suggested that stress-related genes on chromosome 5 may confer increased tolerance to genomic imbalance, whereas gene-dosage sensitivity on chromosome 12 reduced its transmission.

Whole-genome resequencing further revealed segregation distortion in offspring, especially in loci associated with stress response and cell cycle regulation. Among these, the EjRUN1 gene stood out. Overexpression of EjRUN1 homologs in triploid Arabidopsis thaliana significantly increased seed viability, confirming its role in aneuploid tolerance. Phenotypically, aneuploids displayed both reduced average growth compared to euploids and meaningful trait diversification, with chromosome dosage influencing plant height, stem thickness, and leaf morphology.

"Our work demonstrates that triploid loquat is not merely a reproductive endpoint, but a powerful biological engine for generating genetic diversity," the authors noted. "By identifying how specific chromosomes and alleles contribute to aneuploid viability and phenotypic expression, we provide a clearer roadmap for breeders. This research shows that aneuploidy, often viewed as detrimental, can be strategically harnessed to create valuable new germplasm resources more rapidly than traditional breeding allows."

This study offers a practical framework for accelerating loquat breeding by deliberately utilizing aneuploid populations generated from fertile triploids. The ability to link chromosome dosage with trait outcomes enables more targeted selection, while genes like EjRUN1 present future opportunities for enhancing aneuploid robustness through molecular breeding or gene editing. Beyond loquat, these findings have broader implications for fruit tree breeding, where long generation cycles have historically slowed cultivar innovation. The approach demonstrated here may be applied to other perennial crops to expand genetic diversity and develop varieties with improved resilience, productivity, and market qualities.