Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits

Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity

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 699.6 Mb. 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.

A translocation between chromosome 6 and 8 influences lncRNA_MYB114 and PpRPP13 expression and underpins red leaf trait and powdery mildew resistance in peach

Red leaf peach has important ornamental value owing to its characteristic leaf coloration. However, this species is highly susceptible to powdery mildew, and the mechanisms of red leaf formation, resistance to powdery mildew, and their relationship remain unclear. We performed population genetic analyses of red leaf peach, revealing that the translocation of chromosomes 6 and 8 is genetically linked to both the red leaf trait and powdery mildew resistance. Bulk segregant analysis-sequencing, genome resequencing, and expression analysis indicated that the PpMYB114 and the resistance gene PpRPP13 are responsible for the red leaf phenotype and powdery mildew resistance, respectively. The chromosomal translocation causes a promoter fragment of PpRPP13 on chromosome 8 to integrate into the antisense chain of PpMYB114 on chromosome 6, thereby enhancing the expression of PpMYB114 and inhibiting the expression of PpRPP13. Further, lncRNA-seq identified a new antisense lncRNA, lncRNA_MYB114, which is generated by the translocation and can activate PpMYB114 expression to synthesize anthocyanin. Moreover, the overexpression of PpRPP13 resulted in enhanced resistance to powdery mildew. In summary, these results revealed the molecular mechanism of a chromosomal translocation altering the expression of PpMYB114 and PpRPP13 to form the red leaf phenotype that is linked to powdery mildew susceptibility.

Pan-genome analysis reveals the evolution and diversity of Malus

Malus Mill., a genus of temperate perennial trees with great agricultural and ecological value, has diversified through hybridization, polyploidy and environmental adaptation. Limited genomic resources for wild Malus species have hindered the understanding of their evolutionary history and genetic diversity. We sequenced and assembled 30 high-quality Malus genomes, representing 20 diploids and 10 polyploids across major evolutionary lineages and geographical regions. Phylogenomic analyses revealed ancient gene duplications and conversions, while six newly defined genome types, including an ancestral type shared by polyploid species, facilitated the detection of strong signals for extensive introgressions. The graph-based pan-genome captured shared and species-specific structural variations, facilitating the development of a molecular marker for apple scab resistance. Our pipeline for analyzing selective sweep identified a mutation in MdMYB5 having reduced cold and disease resistance during domestication. This study advances Malus genomics, uncovering genetic diversity and evolutionary insights while enhancing breeding for desirable traits.

An intronic SNP in the Carotenoid Cleavage Dioxygenase 1 (CsCCD1) controls yellow flesh formation in cucumber fruit (Cucumis sativus L.)

Vitamin A is a crucial yet scarce vitamin essential for maintaining normal metabolism and bodily functions in humans and can only be obtained from food. Carotenoids represent a diverse group of functional pigments that act as precursors for vitamins, hormones, aroma volatiles and antioxidants. As a vital vegetable in the world, elevated carotenoid levels in cucumber fruit produce yellow flesh, enhancing both visual appeal and nutritional value. However, the genetic mechanisms and regulatory networks governing yellow flesh in cucumbers remain inadequately characterized. In this study, we employed map-based cloning to identify a Carotenoid Cleavage Dioxygenase 1 (CsCCD1) as a key genetic factor influencing yellow flesh in cucumbers. A causal single nucleotide polymorphism (SNP) in the eighth intron of CsCCD1 led to aberrant splicing, resulting in a truncated transcript. The truncated protein has significantly decreased enzyme activity and increased carotenoid accumulation in the fruit. CRISPR/Cas9-generated CsCCD1 knockout mutants exhibited yellow flesh and significantly higher carotenoid content compared to wild-type cucumbers. Metabolic profiling indicated a marked accumulation of β-cryptoxanthin in the flesh of these knockout mutants. The intronic SNP was shown to perfectly segregate with yellow flesh in 159 diverse cucumber germplasms, particularly within the semi-wild ecotype Xishuangbanna, known for its substantial carotenoid accumulation. Furthermore, transient overexpression of CsCCD1 in yellow-fleshed Xishuangbanna cucumbers restored a white flesh phenotype, underscoring the critical role of CsCCD1 in determining flesh colour in both cultivated and semi-wild cucumbers. These findings lay a theoretical foundation for breeding high-nutrient yellow-fleshed cucumber varieties.

Meta genetic analysis of melon sweetness

KEY MESSAGE

Through meta-genetic analysis of Cucumis melo sweetness, we expand the description of the complex genetic architecture of this trait. Integration of extensive new results with published QTL data provides an outline towards construction of a melon sweetness pan-QTLome. An ultimate objective in crop genetics is describing the complete repertoire of genes and alleles that shape the phenotypic variation of a quantitative trait within a species. Flesh sweetness is a primary determinant of fruit quality and consumer acceptance of melons. Cucumis melo is a diverse species that, among other traits, displays extensive variation in total soluble solids (TSS) content in fruit flesh, ranging from 20 Brix in non-sweet to 180 Brix in sweet accessions. We present here meta-genetic analysis of TSS and sugar variation in melon, using six different populations and fruit measurements collected from more than 30,000 open-field and greenhouse-grown plants, integrated with 15 published melon sweetness-related quantitative trait loci (QTL) studies. Starting with characterization of sugar composition variation across 180 diverse accessions that represent 3 subspecies and 12 of their cultivar-groups, we mapped TSS and sugar QTLs, and confirmed that sucrose accumulation is the key variable explaining TSS variation. All modes-of-inheritance for TSS were displayed by multi-season analysis of a broad half-diallel population derived from 20 diverse founders, with significant prevalence of the additive component. Through parallel genetic mapping in four advanced bi-parental populations, we identified common as well as unique TSS QTLs in 12 chromosomal regions. We demonstrate the cumulative less-than-additive nature of favorable TSS QTL alleles and the potential of a QTL-stacking approach. Using our broad dataset, we were additionally able to show that TSS variation displays weak genetic correlations with melon fruit size and ripening behavior, supporting effective breeding for sweetness per se. Our integrated analysis, combined with additional layers of published QTL data, broadens the perspective on the complex genetic landscape of melon sweetness and proposes a scheme towards future construction of a crop community-driven melon sweetness pan-QTLome.

A pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium

The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids; thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (∼370 Mb) and the B genome being the largest (∼700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which ∼65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.

Genome-Wide Identification and Expression Analysis of TCP Transcription Factors Responding to Multiple Stresses in Arachis hypogaea L

The TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING-CELL-FACTOR (TCP) gene family, a plant-specific transcription factor family, plays pivotal roles in various processes such as plant growth and development regulation, hormone crosstalk, and stress responses. However, a comprehensive genome-wide identification and characterization of the TCP gene family in peanut has yet to be fully elucidated. In this study, we conducted a genome-wide search and identified 51 TCP genes (designated as AhTCPs) in peanut, unevenly distributed across 17 chromosomes. These AhTCPs were phylogenetically classified into three subclasses: PCF, CIN, and CYC/TB1. Gene structure analysis of the AhTCPs revealed that most AhTCPs within the same subclade exhibited conserved motifs and domains, as well as similar gene structures. Cis-acting element analysis demonstrated that the AhTCP genes harbored numerous cis-acting elements associated with stress response, plant growth and development, plant hormone response, and light response. Intraspecific collinearity analysis unveiled significant collinear relationships among 32 pairs of these genes. Further collinear evolutionary analysis found that peanuts share 30 pairs, 24 pairs, 33 pairs, and 100 pairs of homologous genes with A. duranensis, A. ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Moreover, we conducted a thorough analysis of the transcriptome expression profiles in peanuts across various tissues, under different hormone treatment conditions, in response to low- and high-calcium treatments, and under low-temperature and drought stress scenarios. The qRT-PCR results were in accordance with the transcriptome expression data. Collectively, these studies have established a solid theoretical foundation for further exploring the biological functions of the TCP gene family in peanuts, providing valuable insights into the regulatory mechanisms of plant growth, development, and stress responses.

Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia

Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide. The genomic data of several kiwifruit species have been released, providing an unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter- and intra-species genetic diversity and facilitate utilization for kiwifruit breeding. Here, we generated a kiwifruit super pan-genome using 15 high-quality assemblies of eight Actinidia species. For gene-based pan-genome, a total of 61,465 gene families were identified, and the softcore and dispensable genes were enriched in biological processes like response to endogenous stimulus, response to hormone and cell wall organization or biogenesis. Then, structural variations (SVs) against A. chinensis 'Donghong' were identified and then used to construct a graph-based genome. Further population-scale SVs based on resequencing data from 112 individuals of 20 species revealed extensive SVs which probably contributed to the phenotypic diversity among the Actinidia species. SV hotspot regions were found contributed to environmental adaptation. Furthermore, we systematically identified resistance gene analogs (RGAs) in the 15 assemblies and generated a pan-RGA dataset to reveal the diversity of genes potentially involved in disease resistance in Actinidia. The pan-genomic data obtained here is useful for evolutionary and functional genomic studies in Actinidia, and facilitates breeding design.

Allelic variation in an expansin, MdEXP-A1, contributes to flesh firmness at harvest in apples

Flesh firmness is a core quality trait in apple breeding because of its correlation with ripening and storage. Quantitative trait loci (QTLs) were analyzed through bulked segregant analysis sequence (BSA-seq) and comparative transcriptome analysis (RNA-seq) to explore the genetic basis of firmness formation. In this study, phenotypic data were collected at harvest from 251 F1 hybrids derived from 'Ruiyang' and 'Scilate', the phenotype values of flesh firmness at harvest were extensively segregated for two consecutive years. A total of 11 candidate intervals were identified on chromosomes 03, 05, 06, 07, 13, and 16 via BSA-seq analysis. We characterized a major QTL on chromosome 16 and selected a candidate gene encoding expansin MdEXP-A1 by combining RNA-seq analysis. Furthermore, the genotype of Del-1166 (homozygous deletion) in the MdEXP-A1 promoter was closely associated with the super-hard phenotype of F1 hybrids, which could be used as a functional marker for marker-assisted selection (MAS) in apple. Functional identification revealed that MdEXP-A1 positively expedited fruit softening in both apple fruits and tomatoes that overexpressed MdEXP-A1. Moreover, the promoter sequence of TE-1166 was experimentally validated containing two binding motifs of MdNAC1, and the absence of the MdEXP-A1 promoter fragment reduced its transcription activity. MdNAC1 also promotes the expression of MdEXP-A1, indicating its potential modulatory role in quality breeding. These findings provide novel insight into the genetic control of flesh firmness by MdEXP-A1.

Pan-genome analyses of 11 Fraxinus species provide insights into salt adaptation in ash trees

Ash trees (Fraxinus) exhibit rich genetic diversity and wide adaptation to various ecological environments, and several species are highly salt tolerant. Dissecting the genomic basis of salt adaptation in Fraxinus is vital for its resistance breeding. Here, we present 11 high-quality chromosome-level genome assemblies for Fraxinus species, which reveal two unequal subgenome compositions and two recent whole-genome triplication events in their evolutionary history. A Fraxinus pan-genome was constructed on the basis of structural variations and revealed that presence-absence variations (PAVs) of transmembrane transport genes have likely contributed to salt adaptation in Fraxinus. Through whole-genome resequencing of an F1 population from an interspecies cross of F. velutina 'Lula 3' (salt tolerant) with F. pennsylvanica 'Lula 5' (salt sensitive), we mapped salt-tolerance PAV-based quantitative trait loci (QTLs) and pinpointed two PAV-QTLs and candidate genes associated with Fraxinus salt tolerance. Mechanistically, FvbHLH85 enhances salt tolerance by mediating reactive oxygen species and Na+/K+ homeostasis, whereas FvSWEET5 enhances salt tolerance by mediating osmotic homeostasis. Collectively, these findings provide valuable genomic resources for Fraxinus salt-resistance breeding and the research community.

SoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3 908 408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3 437 115 CRISPR guide sequences, 212 395 transcription factors and 19 086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.

Advances in the molecular mechanism of grapevine resistance to fungal diseases

Grapevine is an important economic fruit tree worldwide, but grape production has been plagued by a vast number of fungal diseases, which affect tree vigor and the quality and yield of berries. To seek remedies for such issues, researchers have always been committed to conventional and biotechnological breeding. In recent years, increasing progress has been made in elucidating the molecular mechanisms of grape-pathogenic fungi interactions and resistance regulation. Here, we summarize the current knowledge on the molecular basis of grapevine resistance to fungal diseases, including fungal effector-mediated susceptibility and resistance, resistant regulatory networks in grapevine, innovative approaches of genetic transformation, and strategies to improve grape resistance. Understanding the molecular basis is important for exploring and accurately regulating grape resistance to fungal diseases.

Comprehensive insights on association mapping in perennial fruit crops breeding - Its implications, current status and future perspectives

In order to provide food and nutritional security for the world's rapidly expanding population, fruit crop researchers have identified two critical priorities: increasing production and preserving fruit quality during the pre- and post-harvest periods. The genetic basis of these complex, commercially important fruit traits which are uniquely regulated by polygenes or multi-allelic genes that interact with one another and the environment can be analyzed with the aid of trait mapping tools. The most interesting trait mapping approach that offers the genetic level investigation for marker-trait associations (MTAs) for these complex fruit traits, without the development of mapping population, is association mapping. This approach was used during the genetic improvement program, emphasizing the obstacles (breeding strategies adopted, generation interval, and their genomic status) pertaining to perennial fruit crops. This method of studying population diversity and linkage disequilibrium in perennial fruit crops has been made possible by recent developments in genotyping, phenotyping, and statistical analysis. Thus, the purpose of this review is to provide an overview of different trait mapping techniques, with a focus on association mapping (method, essential components, viability, constraints, and future perspective) and its advantages, disadvantages, and possibilities for breeding perennial fruit crops.

Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era

Crop wild relatives of perennial fruit crops have a wealth of untapped genetic diversity that can be utilized for cultivar development. However, barriers such as linkage drag, long juvenility, and high heterozygosity have hindered their utilization. Advancements in genome sequencing technologies and assembly methods, combined with the integration of chromosome conformation capture have made it possible to construct high-quality reference genomes. These genome assemblies can be combined into pan-genomes, capturing inter- and intraspecific variations across coding and non-coding regions. Pan-genomes of perennial fruit crops are being developed to identify the genetic basis of traits. This will help overcome breeding challenges, enabling faster and more targeted development of new cultivars with novel traits through breeding and biotechnology.

Genome sequencing of 'Fuji' apple clonal varieties reveals genetic mechanism of the spur-type morphology

Somatic variations can give rise to bud sports with advantageous traits, serving as the foundation for bud sport breeding in perennial plants. Here, we report a fully phased genome assembly of 'Fuji' apple, enabling comprehensive identification of somatic variants across 74 clonally propagated 'Fuji' varieties. Phylogenetic analysis indicates that spur-type and early-maturation traits in 'Fuji' sport varieties arise from multiple independent events. Several putative functional somatic variants have been identified, including a spur-type-specific deletion in the promoter of the TCP transcription factor gene MdTCP11. DNA methylation level of the deletion-associated miniature inverted-repeat transposable element is lower in spur-type varieties compared to standard-type varieties, while the expression of MdTCP11 is significantly higher. Overexpression of MdTCP11 in apple decreases plant height, highlighting its important role in the development of spur-type apple varieties. This study sheds light on the cloning history of 'Fuji' and provides valuable resources for apple breeding.

Advancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples

Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern United States, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis, generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these 2 genomes and previously published genome of M. angustifolia, and lower relatedness with M. fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.

Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes

Advances in next-generation sequencing (NGS) have significantly reduced the cost and improved the efficiency of obtaining single nucleotide polymorphism (SNP) markers, particularly through restriction site-associated DNA sequencing (RAD-seq). Meanwhile, the progression in whole genome sequencing has led to the utilization of an increasing number of reference genomes in SNP calling processes. This study utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana, a tropical tree of the walnut family (Juglandaceae), with SNP calling conducted using the STACKS pipeline. We aimed to compare both reference-based approaches, namely, employing a closely related species as the reference genome versus the species itself as the reference genome, to evaluate their respective merits and limitations. Our findings indicate a substantial discrepancy in the number of obtained SNPs between using a closely related species as opposed to the species itself as reference genomes, the former yielded approximately an order of magnitude fewer SNPs compared to the latter. While the missing rate of individuals and sites of the final SNPs obtained in the two scenarios showed no significant difference. The results showed that using the reference genome of the species itself tends to be prioritized in RAD-seq studies. However, if this is unavailable, considering closely related genomes is feasible due to their wide applicability and low missing rate as alternatives. This study contributes to enrich the understanding of the impact of SNP acquisition when utilizing different reference genomes.

Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening

Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.

Technology-enabled great leap in deciphering plant genomes

Plant genomes provide essential and vital basic resources for studying many aspects of plant biology and applications (for example, breeding). From 2000 to 2020, 1,144 genomes of 782 plant species were sequenced. In the past three years (2021-2023), 2,373 genomes of 1,031 plant species, including 793 newly sequenced species, have been assembled, representing a great leap. The 2,373 newly assembled genomes, of which 63 are telomere-to-telomere assemblies and 921 have been generated in pan-genome projects, cover the major phylogenetic clades. Substantial advances in read length, throughput, accuracy and cost-effectiveness have notably simplified the achievement of high-quality assemblies. Moreover, the development of multiple software tools using different algorithms offers the opportunity to generate more complete and complex assemblies. A database named N3: plants, genomes, technologies has been developed to accommodate the metadata associated with the 3,517 genomes that have been sequenced from 1,575 plant species since 2000. We also provide an outlook for emerging opportunities in plant genome sequencing.