A Bayesian hybrid inference method is developed which infers hybrids and backcrosses across two generations using sampled genomes from two populations. The method improves on that of Chakraborty and Rannala (2023) by accounting for uncertainty of population haplotype frequencies and correctly marginalizing over haplotypes while still modeling linkage and recombination across the genome. In analyses of simulated data the new method produced posterior probabilities nearly identical to the method of Chakraborty and Rannala (2023) when sample sizes were large. For small sample sizes, posterior probabilities produced by the new method tended to be lower as expected since it accounts for additional uncertainties of population haplotype frequencies. Statistical performance of the new method as measured by the ROC (Receiver Operation Characteristic) curve, appears equivalent to that of Chakraborty and Rannala (2023). The new method is applied to three recently published datasets for populations of kiwifruit (genus Actinidia), plateau fence lizard (Sceloporus tristichus) and puma (Puma concolor).

For fifteen years, bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), has severely impacted kiwifruit cultivation. To some extent, all cultivated varieties are susceptible, resulting in production losses and plant mortality, although different degrees of resilience to the disease are known. Current prevention relies on careful prophylaxis and cultivating less susceptible varieties, as no resistant varieties have been licensed yet. However, some genotypes within the genus Actinidia show resistance. Recent studies have focused on identifying genes associated with resistance or susceptibility to Psa. In this study, a high-resolution interspecific linkage map (A. chinensis var. chinensis × A. arguta) was constructed using SNP markers obtained through ddRAD sequencing. Controlled cane inoculations of the interspecific population were followed by lesion length and infection assessments over six weeks. QTL mapping identified a major QTL on Chr28 and two minor QTLs on Chr4 and Chr17 linked to resistance in A. arguta. A susceptibility-associated QTL was also detected on Chr9 in A. chinensis var. chinensis. RNA-seq analysis of infected sub-cortical tissues from parental genotypes revealed differentially expressed genes, highlighting candidate genes potentially involved in resistance and susceptibility mechanisms. These findings enhance our understanding of genetic resistance and provide valuable targets for breeding Psa-resistant kiwifruit cultivars.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07369-x.

KPGD: A kiwifruit pangenome database for comprehensive mining of genetic diversity in the genus Actinidia.

In this study, we report a high-quality chromosome-level genome assembly of Actinidia chinensis var. chinensis 'Guimi No. 2'. This cultivar, discovered in Guizhou karst ecosystems, exhibits resistance to Pseudomonas syringae pv. actinidiae (Psa). Using a combination of MGI short-read sequencing, PacBio HiFi long-read sequencing, and Hi-C technology, we generated a genome assembly of 608.43 Mb with a contig N50 of 20.70 Mb, and 99.70% of the assembly was successfully anchored onto 29 pseudochromosomes. The quality value (QV) and the LTR Assembly Index (LAI) of the assembled genome were 72.23 and 10.10. The BUSCO analysis indicated that the genome assembly and gene model prediction were 98.40% and 96.56% complete, respectively. A total of 251.15 Mb of repetitive sequences and 45,986 protein-coding genes were annotated. This genome assembly provides critical insights into A. chinensis's genomic architecture and serves as a foundational resource for elucidating disease resistance mechanisms against Psa, while enabling comparative phylogenomic studies across the Actinidia genus.

Members belonging to the genus Actinidia are perennial dioecious fruit trees. Variation in male and female floral organs during growth is crucial in sex determination. Previous studies have been limited to individual kiwifruit species ( Actinidia chinensis and Actinidia deliciosa ), and although two sex determination genes have been identified, their differential expression has not been linked to differences in pistil development. In the present study, we investigated male and female flower development in two kiwifruit species, namely, A. chinensis and Actinidia eriantha . Kiwifruit flower development was divided into seven stages. The first four stages are common to both male and female flower development in kiwifruits, and the primary stage of male and female flower development in kiwifruits begins at stage 5, which is largely reflected by the absence of development of ovule primordia in male kiwifruit, whereas differences in flower development between the two kiwifruit species are primarily in the timing of the initiation of the squaring stage, time required for the later stages of flower development (stage 6), and size of flower buds. Quantitative results demonstrated that SyGl was persistently and highly expressed after stage 4 in male kiwifruit flowers, possibly causing abnormal development of the pistil and ovary malformation in male kiwifruit flowers. In contrast, FrBy was up-regulated in male flowers of A. chinensis and A. eriantha during late developmental stages (stage 5 or stage 6), coinciding with pollen maturation. We propose that this peaked expression is linked to the programmed degradation of the anther chorionic layer, facilitating timely dehiscence and pollen maturation. Altogether, the findings of this study link the stages of kiwifruit flower development in the two species with their phenological periods and flower bud morphology, thus providing a reference for future comparison of flower development stages and gene expression during development in kiwifruits.

ABSTRACT Actinidia arguta (Siebold & Zucc.) Planch. ex Miq. is one of the major species of the genus Actinidia and has distinct characteristics such as small size and smooth-fruited. The fruits of A. arguta are rich in essential nutrients and bioactive compounds. Due to their tolerance to low temperatures, they can be cultivated in Asia and several varieties have been developed for better efficacy. Investigation of the fruits of A. arguta through extensive chromatographic techniques yielded 22 flavonoid derivatives including one new compound. The new compound, argutiflavone (13), had a flavanone structure with a glucose and an acetylated rhamnose according to the 1D and 2D NMR and MS data. The isolated compounds showed antioxidant and α-glucosidase inhibitory activity although the efficacy differed depending on the structures. Among the isolated compounds, flavolignans (20–22) exerted the strongest efficacy among isolated compounds. Four cultivars of A. arguta fruits contained high amounts of flavonoids. Taken together, the fruits of A. arguta , which contains a high content of flavonoids, will be beneficial to health based on their actions.

Actinidia polysaccharides: A potential bioactive substance - extraction, structure, and bioactivity studies.

Actinidia suberifolia C.Y. Wu (Actinidiaceae), an endemic species of Yunnan province in China, exhibits substantial therapeutic importance in daily life. Given its narrow distribution and small population size, complete genome sequence is needed to reveal its phylogenetic position in Actinidia. In this study, we assembled and annotated the complete chloroplast genome of A. suberifolia and conducted the phylogenetic analysis among the genus Actinidia. The results showed that A. suberifolia had a typical quadripartite structure, exhibiting a total length of 156,716 bp and consisting of two inverted repeats (IRs) of 23,805 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 88,437 bp and 20,669 bp. A maximum-likelihood (ML) phylogenetic tree including A. suberifolia and 21 related species indicated that it was close to Actinidia latifolia. The study will offer valuable genetic resources and improve the phylogenetic resolution of Actinidia.

The chloroplast genome, as an important evolutionary marker, can provide a new breakthrough direction for the population evolution of plant species. Actinidia deliciosa represents one of the most economically significant and widely cultivated fruit species in the genus Actinidia. In this study, we sequenced and analyzed the complete chloroplast genomes of seven cultivars of Actinidia. deliciosa to detect the structural variation and population evolutionary characteristics. The total genome size ranged from 156,404 bp (A. deliciosa cv. Hayward) to 156,495 bp (A. deliciosa cv. Yate). A total of 321 simple sequence repeats (SSRs) and 1335 repetitive sequences were identified. Large-scale repeat sequences may facilitate indels and substitutions, molecular variations in A. deliciosa varieties' chloroplast genomes. Additionally, four polymorphic chloroplast DNA loci (atpF-atpH, atpH-atpI, atpB, and accD) were detected, which could potentially provide useful molecular genetic markers for further population genetics studies within A. deliciosa varieties. Site-specific selection analysis revealed that six genes (atpA, rps3, rps7, rpl22, rbcL, and ycf2) underwent protein sequence evolution. These genes may have played key roles in the adaptation of A. deliciosa to various environments. The population evolutionary analysis suggested that A. deliciosa cultivars were clustered into an individual evolutionary branch with moderate-to-high support values. These results provided a foundational genomic resource that will be a major contribution to future studies of population genetics, adaptive evolution, and genetic improvement in Actinidia.

In today's health-conscious era, fruits are essential for a balanced diet, with the kiwi fruit standing out for its exceptional nutrient density and health benefits and commonly known as 'Green kiwi,' this fruit is belongs to the family Actinidiaceae and the genus Actinidia, species deliciosa. The kiwi is rich in a diverse array of nutrients including vitamins, minerals, and phytochemicals such as triterpenoids, saponins, amino acids, carotenoids, phenolic compounds (flavonoids, polyphenols, anthraquinones, and coumarins), carbohydrates, and sugars. These constituents contribute to its significant pharmacological effects, including antioxidant, anti-diabetic, anti-inflammatory, anti-platelet, and anti-tumor activities. Notably, its high vitamin C content suggests potential therapeutic benefits for severe conditions like cancer and heart disease. This review offers an overview of the botanical aspects, chemical components, and recent biological and pharmacological findings related to kiwi fruit.

Actinidia species are fruit trees with various functions, such as providing edible fruit, serving as ornamental plants, and having medicinal benefits. However, the taxonomy of Actinidia species is controversial due to widespread hybridization, the history of divergence and polyploid speciation among Actinidia species also remains unclear. In this study, we conducted comparative analyses of the chloroplast genomes and ploidy among multiple Actinidia species. The genes clpP, infA, ndhD, ndhK, and rpl20 were absent from these chloroplast genomes. The ycf2 and rpl20 genes in the Actinidia species were under positive selection. Several regions (rps16–trnQ-UUG, trnS-GCU–trnR-UCU, ndhC–trnV-UAC, rbcL–accD, rps12–psbB, trnN-GUU–ndhF, ycf1–trnN-GUU, and trnH-GUG–psbA) and genes (ycf1, ycf2, accD, rpl20) exhibited high variability, which could potentially serve as molecular markers in species delineation and other phylogenetic studies. Through divergence time estimation, the Actinidia genus originated 23 million years ago (Ma), and experienced a tetraploidization event in ~ 20 Ma. Subsequently, Actinidia has undergone extensive diploidization. Our findings will provide valuable information in species identification, breeding programs, and conservation efforts for Actinidia species.

Kiwifruit (Actinidia deliciosa) belongs to the family Actinidiaceae, and the genus Actinidia is a highly nutritious fruit abundant with essential vitamins, minerals, polyphenols, flavonoids, and the unique enzyme actinidin, which aids digestion. These components contribute to kiwifruit’s role as a functional food with significant therapeutic potential. Kiwifruit supports various physiological functions, including immune enhancement, cardiovascular health, and digestive regulation. Its rich fiber content promotes gut microbiota growth, improving digestion and reducing constipation. The presence of polyphenols, carotenoids (lutein, zeaxanthin), and flavonoids strengthens antioxidant defenses, reduces inflammation, and helps prevent chronic diseases such as cardiovascular disorders, neurodegenerative conditions, and metabolic syndrome. The low fiber content makes it beneficial for blood sugar regulation, aiding in diabetes management. The actinidin enzyme present in kiwifruit makes it particularly beneficial for individuals with digestive disorders by enhancing protein digestion and nutrient absorption. Additionally, its prebiotic properties foster the growth of beneficial gut bacteria, contributing to better digestive and immune health. Kiwifruit is rich in antioxidants and also supports skin health by promoting collagen synthesis, reducing oxidative stress, and maintaining hydration. Emerging research highlights its potential neuroprotective effects, suggesting a role in reducing cognitive decline and oxidative stress in the brain. Its cardioprotective properties help regulate blood pressure, and improve vascular function. With applications in functional foods, nutraceuticals, and pharmaceuticals, kiwifruit continues to gain attention for its preventive healthcare potential. Incorporating kiwifruit into the diet provides a natural approach to enhancing overall well-being, making it a valuable component in promoting longevity and reducing the risk of chronic diseases. This review seeks to provide a comprehensive knowledge of kiwifruit's nutritional profile, bioactive properties, therapeutic potential, and commercial importance, offering scientifically backed recommendations for individuals.

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of the most successfully domesticated fruits in the twentieth century. Despite the rich wild resources and diverse phenotypes within this genus, insights into the genomic changes are still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections of Actinidia, leading to the assembly and annotation of 14 haplotype genomes with sizes spanning from 602.0 to 699.6Mb. By compiling these haplotype genomes, we constructed a super pan-genome for the genus. We identified numerous structural variations (SVs, including variations in gene copy number) and highly diverged regions in these genomes. Notably, significant SV variability was observed within the intronic regions of the MED25 and TTG1 genes across different materials, suggesting their potential roles in influencing fruit size and trichome formation. Intriguingly, our findings indicated a high genetic divergence between two haplotype genomes, with one individual, tentatively named Actinidia × leiocacarpae, from sect. Leiocacarpae. This likely hybrid with a heterozygous genome exhibited notable genetic adaptations related to resistance against bacterial canker, particularly through the upregulation of the RPM1 gene, which contains a specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, we also discussed the interlineage hybridizations and taxonomic treatments of the genus Actinidia. Overall, the comprehensive pan-genome constructed here, along with our findings, lays a foundation for examining genetic compositions and markers, particularly those related to SVs, to facilitate hybrid breeding aimed at developing desired phenotypes in kiwifruits.

Inter-specific hybridisation between natural populations within the genus Actinidia is a common phenomenon and has been used in breeding programmes. Hybridisation between species increases the diversity of breeding populations, incorporating new desirable traits into potential cultivars. We explored genomic prediction in Actinidia breeding, focusing on the closely related species Actinidia arguta and Actinidia melanandra. We investigated the potential of genomic selection by analysing four quantitative traits across intra-specific A. arguta crosses and inter-specific crosses between A. arguta and A. melanandra. The continuous distributions of the studied traits in both intra-specific and inter-specific crosses indicated a polygenic background. A linear mixed model approach was used, incorporating the factor of year of season and a marker-based relationship matrix instead of pedigree as a random effect. After evaluation, the best model was applied to assess variance components and heritability for each quantitative trait. Expanding beyond intra-specific crosses, predictive ability was calculated to investigate inter-specific cross effect. Considering predictive ability, this study explored the impacts of sample size and population structure. A reduction in sample size correlated with decreased predictive ability, while the influence of population structure was particularly pronounced in inter-specific crosses. Finally, the prediction accuracy of genomic estimated breeding values, for parental genotypes, revealed an inter-species effect on prediction confidence. Considering the imbalance in genotype numbers between intra- and inter-specific cross populations, this research highlights the difficulty of genomic prediction in hybrid populations. Understanding prediction accuracy in inter-species crossing designs provides valuable insights for optimising genomic selection.

In breeding programmes, accurate estimation of breeding values is crucial for selecting superior genotypes. Traditional methods rely on phenotypic observations and pedigree information to estimate variance components and heritability. However, pedigree errors can significantly affect the accuracy of these estimates, especially in long-lived perennial vines. This study evaluates the effect of pedigree errors on breeding value predictions in kiwiberry breeding and explores the benefits of using genomic selection. We applied Best Linear Unbiased Prediction (BLUP) to estimate breeding values for each genotype for a given trait. Four scenarios with varying degrees of alteration in pedigree-based relationship matrices were used to represent inaccurate relationships between genotypes. Pedigree-based breeding values were compared with genomic estimated breeding values for one vine-related and four fruit-related quantitative traits. The results showed that as the degree of altered population structure increased, the prediction accuracy of pedigree-based breeding values decreased. In contrast, genomic selection, which uses marker inheritance, maintained realised relationships between genotypes, making it a more robust method for predicting genetic merit. In kiwiberries, as in all species of the genus Actinidia, only female vines bear fruit. The genotypic merit of fruit-related traits in male genotypes can only be estimated indirectly. Marker-based predictions outperformed pedigree-based predictions, especially for genotypes without phenotypic observations, such as male siblings. This study reviewed the induced population structures and introduced genomic selection into the kiwiberry breeding programme. We demonstrated that genomic selection provides more accurate breeding values by capturing true genetic relationships and reducing the effects of misidentified relationships between individuals.

Actinidia kolomikta (Maxim) Maxim. is a winter-hardy species of the genus Actinidia Lindl., whose fruits are valued for their high content of vitamin C and other bioactive compounds. The use of biotechnological propagation methods significantly accelerates the production of quality planting materials for this crop. This study revealed the regeneration features of promising A. kolomikta cultivars. The main morphometric parameters of explants were determined in regard to the effect of different iron chelates (FeEDTA and FeEDDHA) and cytokinins (6-benzylaminopurine, meta-Topolin, and 2-izopentyladenine) in the Quoirin and Lepoivre medium. FeEDTA-supplemented media were optimal for explant culture. Meta-Topolin was found to promote the formation of adventitious microshoots at the base of explants and bud activation, which increased the multiplication rate by 1.5 and 1.7 times compared to the media with 6-benzylaminopurine and 2-izopentyladenine. The morpho-anatomical studies revealed the structural organization of assimilation tissues and the stomatal apparatus of A. kolomikta under different culture conditions (field, in vitro, and ex vitro). The stomata in vitro were round and had a larger area, lower thickness, and a lower layer number of mesophyll compared to field conditions. The transfer from in vitro to ex vitro caused gradual normalization of the leaf structure: a decrease in the stomatal number and area, changes in shape (from round to elliptical), and an increase in the mesophyll thickness.

BackgroundKiwifruit, belonging to the genus Actinidia, represents a unique fruit crop characterized by its modern cultivars being genetically diverse and exhibiting remarkable variations in morphological traits and adaptability to harsh environments. However, the genetic mechanisms underlying such morphological diversity remain largely elusive.ResultsWe report the high-quality genomes of five Actinidia species, including Actinidia longicarpa, A. macrosperma, A. polygama, A. reticulata, and A. rufa. Through comparative genomics analyses, we identified three whole genome duplication events shared by the Actinidia genus and uncovered rapidly evolving gene families implicated in the development of characteristic kiwifruit traits, including vitamin C (VC) content and fruit hairiness. A range of structural variations were identified, potentially contributing to the phenotypic diversity in kiwifruit. Notably, phylogenomic analyses revealed 76 cis-regulatory elements within the Actinidia genus, predominantly associated with stress responses, metabolic processes, and development. Among these, five motifs did not exhibit similarity to known plant motifs, suggesting the presence of possible novel cis-regulatory elements in kiwifruit. Construction of a pan-genome encompassing the nine Actinidia species facilitated the identification of gene DTZ79_23g14810 specific to species exhibiting extraordinarily high VC content. Expression of DTZ79_23g14810 is significantly correlated with the dynamics of VC concentration, and its overexpression in the transgenic roots of kiwifruit plants resulted in increased VC content.ConclusionsCollectively, the genomes and pan-genome of diverse Actinidia species not only enhance our understanding of fruit development but also provide a valuable genomic resource for facilitating the genome-based breeding of kiwifruit.

The kiwifruit, Actinidia genus, has emerged as a nutritionally rich and economically significant crop with a history rooted in China. This review paper examines the global journey of the kiwifruit, its genetic diversity, and the role of advanced breeding techniques in its cultivation and improvement. The expansion of kiwifruit cultivation from China to New Zealand, Italy, Chile and beyond, driven by the development of new cultivars and improved agricultural practices, is discussed, highlighting the fruit's high content of vitamins C, E, and K. The genetic resources within the Actinidia genus are reviewed, with emphasis on the potential of this diversity in breeding programs. The review provides extensive coverage to the application of modern omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, which have revolutionized the understanding of the biology of kiwifruit and facilitated targeted breeding efforts. It examines both conventional breeding methods and modern approaches, like marker-assisted selection, genomic selection, mutation breeding, and the potential of CRISPR-Cas9 technology for precise trait enhancement. Special attention is paid to interspecific hybridization and cisgenesis as strategies for incorporating beneficial traits and developing superior kiwifruit varieties. This comprehensive synthesis not only sheds light on the current state of kiwifruit research and breeding, but also outlines the future directions and challenges in the field, underscoring the importance of integrating traditional and omics-based approaches to meet the demands of a changing global climate and market preferences.

The mitochondrial genome (mitogenome) of Actinidia macrosperma, a traditional medicinal plant within the Actinidia genus, remains relatively understudied. This study aimed to sequence the mitogenome of A. macrosperma, determining its assembly, informational content, and developmental expression. The results revealed that the mitogenome of A. macrosperma is circular, spanning 752,501 bp with a GC content of 46.16%. It comprises 63 unique genes, including 39 protein-coding genes (PCGs), 23 tRNA genes, and three rRNA genes. Moreover, the mitogenome was found to contain 63 SSRs, predominantly mono-nucleotides, as well as 25 tandem repeats and 650 pairs of dispersed repeats, each with lengths equal to or greater than 60, mainly comprising forward repeats and palindromic repeats. Moreover, 53 homologous fragments were identified between the mitogenome and chloroplast genome (cp-genome), with the longest segment measuring 4296 bp. This study represents the initial report on the mitogenome of the A. macrosperma, providing crucial genetic materials for phylogenetic research within the Actinidia genus and promoting the exploitation of species genetic resources.

Global health and treatment approaches aim to combine complementary and alternative medicine with evidence-based medicine to better comprehend the human body’s metabolic processes. The kiwi fruit frequently referred to as the "Chinese gooseberry" belongs to the Actinidiaceae family and is classified as Actinidia genus andspecies deliciosa. Kiwi fruit has seen a significant increase in demand recently because of its high vitamin C content.Kiwi fruit is also a great source of antioxidants, carotenoids, iron, and dietary fiber. These could help regulate blood sugar, reduce blood pressure, promote wound healing, and enhance intestinal health. Antioxidants such as vitamin C, choline, lutein, and zeaxanthin help the body eliminate free radicals and may shield the body from a number of illnesses and inflammations. Contributing significantly to the flavonoid and phenolic contents in kiwi fruit, it is a primary source of phytochemicals such as caffeic acid, gallic acid, syringic acid, salicylic acid, ferulic acid, and protocatechuic acid. Numerous pharmacological qualities, such as anti-diabetic, anti- tumor, anti-inflammatory, anti-ulcer, antioxidant activity, hypoglycemia, hypolipidemic, and many more, have been linked to kiwi fruit and its constituents. In addition to these, kiwi fruit is traditionally used to treat microbiological infections, rheumatoid arthritis, hepatitis, edema, and renal issues. The fiber in kiwi fruit promotes the fruit's ability to retain water, which helps to shorten transit times and preserves the person's gastrointestinal health. Studies are also being conducted on the homeostatic balance, weight maintenance, and insulin and glucose balance in relation to kiwi fruit consumption. Keywords: Actinidia deliciosa, Chinese gooseberry, Hypoglycemia, Kiwi, Cancer