Super pan-genome maps the hidden genetic architecture behind kiwifruit diversity

A research team uncovered the most comprehensive genomic landscape to date for the kiwifruit genus Actinidia, constructing a super pan-genome based on 14 haplotype-resolved genomes. The study identifies extensive structural variations—including gene copy-number changes, insertions, deletions, and translocations—that shape key fruit traits such as size, epidermal trichomes, and disease resistance. Notably, unique genomic signatures were discovered in a highly resistant wild individual, including expanded RPM1 gene clusters and a resistance-associated translocation. These findings not only deepen the biological understanding of Actinidia diversity but also provide high-value genetic resources for accelerating breeding strategies focused on fruit quality and canker resistance.

Kiwifruit species exhibit exceptional morphological and genetic diversity, yet domestication has occurred only within the last century, and most commercial cultivars originate from a narrow genetic base. Compounding this vulnerability, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) poses a major threat to global kiwifruit production, with highly susceptible cultivars such as ‘Hongyang’ suffering severe economic losses. Although certain wild germplasm shows strong resistance, the genomic basis of this resistance—and the broader genetic architecture underlying fruit traits—remains poorly resolved. Due to these challenges, deeper genomic analyses are urgently needed to identify key structural variations and gene functions that drive phenotypic diversity across the genus.

Researchers from Sichuan University and collaborating institutions published (DOI: 10.1093/hr/uhaf067) a new genomic study on March 3, 2025, in Horticulture Research, presenting a super pan-genome for the entire Actinidia genus. The team generated high-quality, haplotype-resolved genomes for seven representative taxa and integrated them into a unified pan-genomic framework. Their analyses uncovered structural variations responsible for differences in fruit morphology, epidermal traits, and canker resistance. The work also highlighted unique genomic adaptations in a highly Psa-resistant wild individual tentatively named Actinidia × leiocacarpae.

The researchers assembled 14 haplotype genomes with sizes ranging from 602–699 Mb and identified more than 45,000 gene families, forming a super pan-genome comprising core, softcore, dispensable, and private gene sets. Remarkably, dispensable genes accounted for nearly half of all gene families, reflecting extensive genomic diversity across Actinidia. Structural variation (SV) analysis revealed tens of thousands of insertions, deletions, inversions, duplications, and translocations. These SVs often occurred in or near genes linked to key phenotypes. For fruit-related traits, the team found significant SVs in the intronic regions of MED25, a gene associated with fruit size regulation, and in TTG1, which influences trichome formation—features that vary widely among kiwifruit species.

The most striking discovery came from A. × leiocacarpae, a wild highly resistant individual. This material displayed unusually high heterozygosity and expanded RPM1 disease-resistance gene clusters, including a unique ∼3 kb translocation affecting the final exon–intron structure of a key RPM1 copy. RNA-seq analyses showed this gene was strongly induced after Psa infection, while susceptible cultivars exhibited weaker responses. The study also uncovered allele-specific expression patterns shaped by SVs, demonstrating how haplotype-level diversity contributes to defense activation and fruit development.

The authors emphasize that structural variations, rather than single-nucleotide changes alone, form the primary genetic drivers of phenotypic complexity in kiwifruit. They note that SVs within regulatory regions can reshape gene expression, alter immune responses, and modify fruit traits, offering powerful levers for breeders. The team highlights that the wild genotype A. × leiocacarpae exemplifies how hybrid lineage origins and haplotype divergence can create natural reservoirs of disease resistance—resources that remain underutilized in breeding programs.

The construction of a genus-wide super pan-genome provides an unprecedented genomic blueprint for accelerating kiwifruit improvement. SV-based markers identified in genes related to fruit size, epidermal traits, and disease resistance can now guide precision breeding and genomic selection. Importantly, the unique resistance mechanisms uncovered in A. × leiocacarpae offer immediate opportunities for developing cultivars resilient to Psa outbreaks. The findings also establish a model framework for studying hybrid lineages, allele-specific regulation, and structural evolution in perennial fruit crops—supporting long-term efforts to enhance yield stability, environmental adaptability, and germplasm conservation.

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References

DOI

10.1093/hr/uhaf067

Original Source URL

https://doi.org/10.1093/hr/uhaf067

Funding information

This study was supported by the Second Tibetan Plateau Scientific Expedition and Research program (No. 2019QZKK0502), Natural Science Innovative Foundation Research Group of Sichuan Province, Research and Demonstration of Key Technology Innovations for Cangxi’s Characteristic Agricultural Industry (No. 25NSFTD0107).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.