Biology subjects

Figueroa-Balderas, R.

Publications and source records attributed to Figueroa-Balderas, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Thille, a chromosome-level type B avocado genome, and the structural and allelic variation at candidate flowering-type loci

Avocado (Persea americana Mill.) is heterodichogamous: each flower opens first as female and then as male, and cultivars fall into two complementary flowering types, A and B, determined by the transcription factor SDMYB, whose dominant allele confers type A. Avocado genomes have so far come from type A cultivars. Here we report a chromosome-level genome of Thille, a type B cultivar used in breeding. From 72.2 Gb of PacBio HiFi reads (81x coverage) and Omni-C data, the assembly places 859.8 Mb, 96% of the expected 896 Mb genome, in 12 chromosomes with an NG50 of 84.5 Mb, a consensus quality of QV 69.95, and 97.3% complete BUSCO genes; repeats occupy 64.0% of the assembly, and 35,386 protein-coding genes were predicted. We compared Thille with the type A cultivars Hass and Puebla, a predominantly Guatemalan hybrid, and with a West Indian (WI) accession, a Lowland botanical group variety of unreported flowering type. The assemblies differ by large rearrangements, including an 18.8 Mb inversion on chromosome 12 specific to Hass. Using phased reads and haplotype assemblies, we reconstructed the alleles of candidate flowering genes from a type A versus type B Fst scan. Both WI haplotypes carry the recessive SDMYB allele found in Thille; based on this study and the previous study of SDMYB, we predict the WI accession to be type B. Six genes, including SDMYB, carry an allele shared by all three type A cultivars and absent from Thille and WI. The genome and HiFi reads are available under BioProject PRJNA1142556.

genomics↗

bioRxiv2026

TPS Expression, Not Copy Number, Explains Aroma Diversity among Grapevine (Vitis vinifera L.) Cultivars

Terpenoids are major contributors to grapevine berry and wine aroma, with mono- and sesquiterpenoids exhibiting substantial variation among cultivars. However, the genetic basis of cultivar-specific terpenoid profiles remains only partially understood due to gene duplications that expanded the terpenoid synthase (TPS) gene family across different cultivars. Here, we compared haplotype-resolved genome assemblies for seven cultivars to analyze copy number variation and expression profiles of terpenoid biosynthesis genes and terpenoid accumulation throughout flower and berry development. These assemblies resolved duplicated TPS loci at the haplotype level, revealing extensive copy number variation across cultivars and between haplotypes within a cultivar, with up to 44 mono-TPS genes on a single haplotype. We identified eight specific monoterpenoids as key drivers of cultivar-specific profiles in ripe berries. Total TPS transcript abundance correlated strongly with total terpenoid accumulation over time. In contrast, TPS copy number was largely decoupled from both expression and terpenoid accumulation, indicating that expression regulation, rather than gene dosage, underlies aroma differences among cultivars. Transcript-metabolite network analysis revealed both expected correlations between specific TPS genes and putative products as well as novel associations. We functionally validated selected candidate TPS in Nicotiana benthamiana, characterizing -farnesene, {beta}-ocimene, and multi-product -terpineol synthases. The in vivo characterization demonstrated that minor sequence variations can alter catalytic activity and product profile. Together, these findings show that the extensive duplication of TPS genes in grapevine does not itself determine terpenoid output; instead, cultivar-specific aroma arises from how these genes are expressed and from sequence differences that shape enzyme activity.

plant biology↗

bioRxiv2026

Genomic compartmentalization of pervasive sex-biased gene expression in the vine mealybug Planococcus ficus

The vine mealybug, Planococcus ficus, is a globally invasive pest of grapevine and a vector of leafroll viruses. Like other mealybugs, it reproduces through paternal genome elimination, a sex-determination system that operates without sex chromosomes and is associated with extreme sexual dimorphism. To characterize genome organization and sex-biased expression in this species, we generated a long-read reference genome spanning 369 Mb with 23,489 annotated genes and macrosynteny conserved with the citrus mealybug, Planococcus citri. Resequencing of four California field individuals yielded a first whole-genome estimate of nucleotide diversity and 132 microsatellite markers for population monitoring. Among 2,129 candidate secreted proteins, a conserved core is shared with P. citri, but each species carries a distinct set of lineage-specific effectors. Comparing adult male and female transcriptomes, we found sex-biased expression to be pervasive and skewed toward females: 41% of tested genes differed between the sexes, with female-biased genes both more numerous and showing larger fold changes. These female-biased genes were not randomly distributed but concentrated in discrete blocks of coordinately expressed, tandemly duplicated gene families, a pattern not previously described in a mealybug. Male- and female-biased secreted proteins also differed in origin, with male-biased proteins drawn from a conserved repertoire shared with P. citri and female-biased proteins spanning a more lineage-specific pool. Together, these results reveal a female-skewed, spatially clustered architecture of sex-biased expression in a mealybug that lacks sex chromosomes, and provide genomic resources for managing an invasive vineyard pest.

genomics↗

bioRxiv2026

Botrytis cinerea infection reshapes the grape berry microbiome during noble rot

Noble rot, caused by Botrytis cinerea, profoundly alters grape berry physiology and is essential to produce botrytized wines. In this study, we profiled bacterial and fungal communities associated with Vitis vinifera cv. Semillon berries across four stages of noble rot development and four consecutive vintages using 16S rRNA gene and ITS1 amplicon sequencing. Noble rot stage significantly impacted the structure of bacterial communities across vintages, while fungal communities showed more variable vintage-dependent responses. Bacterial alpha diversity increased consistently at advanced stages of infection (S3), coinciding with a marked shift from Pseudomonas-dominated communities toward acetic acid bacteria, particularly Gluconobacter, which was significantly enriched at S3 in all vintages. Fungal communities remained dominated by Sclerotiniaceae throughout infection, consistent with pervasive B. cinerea colonization, while non-Botrytis fungal taxa shifted from filamentous fungi such as Cladosporium and Alternaria toward fermentative yeasts including Hanseniaspora and Lachancea. Co-occurrence network analysis revealed a positive association between Gluconobacter and these fermentative yeasts, suggesting coordinated enrichment of oxidative and fermentative microorganisms at advanced noble rot stages. Together, these results reveal a reproducible stage-associated microbial succession during noble rot progression and identify acetic acid bacteria as consistent markers of advanced infection.

microbiology↗

bioRxiv2026

Cell-type-specific transcriptional plasticity in a multi-organ atlas reveals organ-independent companion cell regulatory programs in grapevine

Plants comprise both cell types shared across organs and those restricted to specific tissues. How the transcriptional programs defining cell identity are maintained or remodeled across organ contexts remains poorly understood, particularly in long-lived perennials, for which cell type-resolved transcriptomic data remain scarce. We generated a multi-organ single-nucleus transcriptomic atlas of the dwarf grapevine cultivar Pixie, comprising over 220,000 nuclei from nine organs, including roots, green stems, pre-anthesis flowers, dormant buds, young and old leaves, and berries at three developmental stages, each sampled in duplicates. We annotated 46 distinct cell types, reconstructed developmental trajectories within selected cell types, and inferred gene regulatory networks at cell type resolution. Broadly distributed cell types, including epidermis, xylem parenchyma, and phloem parenchyma, exhibited pronounced organ-dependent transcriptional divergence, with organ identity accounting for 65% of regulon activity variance across the atlas. In contrast, companion cells maintained organ-independent regulatory programs, representing the stable end of a continuum of transcriptional plasticity that spans shared cell types. We identified cell-type-specific transcription factor expression and inferred gene regulatory networks using motif-based regulon analysis, revealing candidate regulators of cell identity and tissue specialization. Together, this atlas provides a reference framework for cell type-resolved functional genomics in a perennial woody crop.

genomics↗

bioRxiv2026

Haplotype-specific expression of a terpene synthase underlies linalool variation in the grapevine cultivar Riesling

Grapevine cultivars vary widely in monoterpenoid content, yet the genetic and regulatory mechanisms underlying this variation remain poorly characterized beyond highly aromatic Muscat types. We profiled free volatiles and monoterpenoid glycosides in a Riesling x Cabernet Sauvignon F1 mapping population, revealing extensive variation and transgressive segregation consistent with multigenic control. QTL mapping identified 59 significant loci associated with 47 volatile compounds and monoterpene glycosides, including two major QTLs explaining 33.8% and 32.4% of phenotypic variance in (3S)-linalool accumulation. Integration of haplotype-resolved transcriptomics with metabolite data, enabled by a chromosome-scale diploid Riesling genome assembly, resolved a (3S)-linalool/nerolidol synthase cluster on chromosome 10 and identified VviTPS54 as the strongest candidate underlying linalool variation. VviTPS54 exhibited haplotype-specific expression strongly correlated with (3S)-linalool accumulation across genotypes, while no QTL was detected at the VviDXS1 locus and VviDXS1 expression was not correlated with terpene levels, indicating that regulatory variation within terpene synthase clusters, rather than methylerythritol phosphate (MEP) pathway flux, drives monoterpenoid composition in this population. These results establish regulatory variation of terpene synthases as a key mechanism underlying monoterpenoid diversity in grapevine and demonstrate that resolving such variation requires haplotype-phased genome assemblies coupled with haplotype-resolved transcriptomics to detect allele-specific expression differences at complex, heterozygous loci.

plant biology↗

bioRxiv2026

Genome-wide characterization of extant clonal diversity in Chilean Carmenere

Carmenere is a widely cultivated and internationally recognized grapevine cultivar in Chile, yet genetic variation among its clones remains poorly characterized. Early studies based on SSR and AFLP markers detected limited polymorphism, but these approaches interrogate only a small fraction of the genome, leaving the extent of clonal diversity unresolved. Here, we generated an improved chromosome-scale diploid genome assembly of Carmenere FPS clone 02 and characterized clonal genomic diversity by sequencing 36 biological replicates representing 12 clones maintained in Chile, including heritage selections rescued from old producer vineyards by Vina Santa Carolina as part of its Bloque Herencia conservation program, and commercial nursery-derived clones. Focusing on low-frequency variants and using replicate-aware consensus calling, we identified more than 9,000 private single nucleotide variants (SNVs) and small indels per clone, providing high-resolution markers for clonal identification. Although most variants were located in repetitive or intergenic regions, a subset affected coding sequences, with genes involved in plant-pathogen interactions, transport, and secondary metabolism most frequently impacted. While variant-affected genes associated with wine anthocyanin content, TA, pH, and alcohol percentage were identified, broader phenotypic characterization will be required to assess their biological significance. Overall, this study provides a genome-wide characterization of extant clonal diversity in Carmenere, with implications for clonal selection and genetic resource conservation.

genomics↗

bioRxiv2025

Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's Disease in Vitis arizonica and its hybrids

Previous genetic mapping studies indicate that multiple haplotypes of the Pierces disease (PD) Resistance 1 (PdR1) locus occur in Vitis arizonica and its hybrids. To characterize sequence diversity at this locus, we assembled chromosome-scale diploid genomes for four PD-resistant (PD-R) accessions: b43-17 (PdR1a/PdR1b), the backcross 07744-094 (PdR1c/PdR1-), b46-43 (PdR1e/PdR1f), and b42-26 (PdR1-/PdR1-), which displays quantitative PD resistance not associated with PdR1. Haplotype resolution of PdR1a, PdR1b, PdR1c, and PdR1e revealed substantial variation in intergenic repeat content and gene composition between PdR1 and their alternative haplotype at the PdR1 locus not associated with PD resistance phenotype (PdR1-), as well as among PdR1 haplotypes, demonstrating extensive sequence diversity at the PdR1 locus. Sequence graph analysis uncovered substantial structural divergence concentrated in approximately one quarter of the locus, together with smaller-scale variation across haplotypes. This analysis identified PdR1-specific graph nodes, showing that PdR1a and PdR1b share most of their PdR1-specific features, whereas PdR1c contains the highest number of private nodes, followed by PdR1e. Integration of sequence graph features with gene expression data further refined a set of defense-related candidate genes within PdR1c. Together, these results identify candidate genes for functional validation and indicate that multiple resistance determinants co-localized within the PdR1 locus may contribute to PD resistance, highlighting opportunities for targeted genetic improvement strategies.

genomics↗

bioRxiv2025

Dual single-nucleus gene expression atlas of grapevine and Erysiphe necator during early powdery mildew infection

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and Erysiphe necator, the causal agent of powdery mildew, at one and five days post-infection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei, and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key E. necator structures, including appressoria, haustoria, and hyphae, and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in E. necator laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue.

plant biology↗

bioRxiv2025

Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires

Phytophthora theobromicola is an emerging cacao pathogen recently identified in Brazil as an aggressive agent of black pod rot. We generated genome assemblies for two P. theobromicola isolates using long-read sequencing and five additional isolates using short reads. Comparative analysis revealed a genome size and predicted gene content comparable to P. citrophthora, a closely related species with a broad host range that includes both citrus and cacao. An intraspecies sequence-graph analysis revealed a highly dynamic genome structure with high proportion of variable effectors. Syntenic orthology analysis across 13 Phytophthora species identified orthologous gene groups conserved only in cacao pathogens and others specific to P. theobromicola. RxLR effectors and CAZymes were particularly enriched among lineage-specific syntenic groups, with RxLRs preferentially located near transposable elements and within gene-sparse, repeat-rich regions. Transcriptome analysis of infected cacao tissues showed that 88% of predicted effectors were expressed, with pods exhibiting the highest number of upregulated genes. Notably, several RxLRs classified as P. theobromicola-specific syntenic orthologs were highly expressed in infected tissues, suggesting that these lineage-specific effectors may play key roles in host-pathogen interactions unique to cacao. Together, our findings highlight the dynamic architecture and functional plasticity of the P. theobromicola genome, providing foundational insights into its virulence strategies and supporting future studies on host adaptation and effector evolution in emerging cacao pathogens.

genomics↗

bioRxiv2025

Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid

Epigenetic modifications, such as DNA methylation, regulate transcription and influence key biological traits. While many efforts were made to understand their stability in annual crops, their long-term persistence in clonally propagated plants remains poorly understood. Grapevine (Vitis vinifera) provides a unique model, with cultivars vegetatively propagated for centuries. Here, we assembled the phased genomes of Cabernet Sauvignon and its parental lineages, Cabernet Franc and Sauvignon Blanc, using HiFi long-reads and a gene map tenfold denser than existing maps. Using three clones per cultivar, we quantifyied methylation with very consistent short- and long-read sequencing and ensured both varietal representativeness and assessment of clonal variability. We leveraged the parent-progeny sequence graph to highlight allele-specific methylation and conserved transcriptomic patterns for genes and small RNA. Such a format was essential to integrate multi-omics data and revealed that despite less clonal conservation than genetic polymorphisms, methylation marks were remarkably inherited. By further demonstrating the linear-reference limitations, we determined the correct representation of genetic variants by the sequence graph is crucial for the accurate allelic quantification of the methylome. These findings reveal the remarkable stability of epigenetic marks in a model propagated by asexual reproduction. Using a phased sequence graph, we introduce a scalable framework that accounts for genomic variation, accurately quantifies allele-specific methylation, and supports multi-omics integration such as our evaluation of the transcriptional impact of epigenetic inheritance. This approach has broad implications for perennial crops, where epigenetic variation could influence traits relevant to breeding, adaptation, and long-term agricultural sustainability.

genomics↗

bioRxiv2025

Integration of diploid T2T parental genomes with progeny genomes and transcriptomes identifies resistance genes in the grape powdery mildew resistance loci Ren6 and Ren7 of Vitis piazeskii

The Chinese grape accession Vitis piasezkii DVIT2027 carries two loci associated with powdery mildew (PM) resistance loci, Ren6 and Ren7, which differ in timing and strength of response to Erysiphe necator. Both loci are consistent with recognition by intracellular immune receptors. To identify the underlying nucleotide-binding leucine-rich repeat (NLR) genes, we assembled chromosome-scale diploid genomes of DVIT2027 and the susceptible V. vinifera F2-35, parents of a segregating F1 population. We integrated these assemblies with deep resequencing data from eight F1 sib-lines carrying different Ren6/Ren7 combinations and generated trio-binned, parent-phased genomes for six progeny. This resolved both PM-resistant (PMR) and PM-susceptible (PMS) haplotypes at Ren6 and Ren7. Comparative analyses revealed extensive structural variation and complete haplotype specificity among NLRs, with several candidate genes lacking allelic counterparts in PMS haplotypes. Expression profiling across PMR sib-lines identified four and two CC-NBS-LRR genes potentially associated with Ren6 and Ren7, respectively. Sequence graph reconstruction of these loci across multiple V. piasezkii accessions revealed broad intraspecific diversity and DVIT2027-specific nodes, including within candidate NLR genes. These results provide a high-resolution view of Ren6 and Ren7 and support the identification of resistance gene candidates for functional validation and grapevine breeding.

plant biology↗

bioRxiv2025

The Genetic Basis of Microbiome Recruitment in Grapevine and its Association with Fermentative and Pathogenic Taxa

O_LIWhile grapevine is an exceptional perennial model for studying host-microbiome interactions, the host genomes role in microbiome assembly is often masked by environmental factors. This research provides a first insight into the genetic mechanisms shaping berry-associated microbial communities. C_LIO_LIUsing QTL mapping in a newly established population of 140 F1-progeny grapevine genotypes in a complete random block design, we were able to control abiotic effects and investigate how the host genome influences grape berry-associated bacterial and fungal communities. C_LIO_LIWe identify significant associations between various microorganisms and the grape genome, including pathogenic fungi such as Botrytis spp. and fermentative yeasts such as Saccharomyces cerevisiae. Many of these taxa map to the same genetic loci associated with plant immune responses, suggesting that specific genetic loci broadly influence microbial community assembly in fruits. C_LIO_LIOur findings demonstrate that grapevine genetics significantly shape the microbiome, even under varying environmental conditions; moreover, that broad, rather than known symbiont-specific mechanisms control microbial colonization of fruit, revealing an emergent "domino" effect with implications for plant-fungal-bacterial interactions. We provide a framework for understanding genotype-microbiome interactions in perennial plants, enabling future targeted experiments to establish causal relationships in microbiome recruitment and offer a potential avenue for breeding programs advancing sustainable viticulture. C_LI

microbiology↗

bioRxiv2025

Smoke exposure triggers rapid transcriptional changes and reveals glycosyltransferases linked to smoke taint in ripening grape berries

With the increasing frequency of wildfires, vineyards are more often exposed to smoke, resulting in a higher risk of smoke taint in wine. This taint imparts undesirable "smoky" and "ashy" aromas and causes significant economic losses. Smoke-derived volatile phenols (VPs) in grape berries, metabolized into stable, non-volatile glycoconjugates via glycosyltransferases (GTs), underlie smoke taint formation. Here, we present the dwarf grapevine cultivar Pixie as a model system for smoke taint research. We generated a phased, telomere-to-telomere diploid genome using HiFi long-read sequencing, along with an expression atlas spanning 30 replicated samples across various tissues and developmental stages. We also constructed a second telomere-to-telomere assembly for Pinot Noir to assess GT expression during berry ripening in the field. Controlled smoke-exposure experiments profiled GT expression and enabled transcriptome-wide analyses at multiple time points. We measured VPs in both smoke-exposed and control samples, revealing 12 GT1 genes significantly upregulated by smoke, named Vitis vinifera smoke-inducible UGTs (VviSIUGTs). Their expression peaked one day post-exposure and declined by day three, mirroring glycoside accumulation dynamics. Gene co-expression network analyses highlighted stress-responsive modules enriched in these VviSIUGTs, while transcription factor binding site analyses pinpointed stress-related regulatory elements in their promoters. These findings provide new insights into the molecular basis of smoke taint and identify potential targets for breeding and biotechnological interventions aimed at developing grapevine cultivars with reduced susceptibility to smoke damage.

plant biology↗

bioRxiv2024

Evolutionary history of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae

Dioecy, defined by the presence of either female or male flowers on separate individual plants, is rare in angiosperms. However, it has independently evolved multiple times from hermaphroditic ancestors. In Vitis spp., flower sex is determined by a [~]200-kbp region with five genes involved in flower development and sexual identity. This study traces the evolutionary history of the Vitis sex-determining region (SDR) to assess whether it evolved in a conserved flowering-related locus. We analyzed the conservation of the Vitis SDR across 42 plant genomes and found collinearity in all 39 angiosperms, but not in non-flowering plants. The number of collinear genes and their rank-normalized gene conservation score were higher in the Vitis SDR compared to the rest of the genome, indicating its importance for flowering. We further explored SDR conservation within the Vitaceae family by long-read sequencing and haplotype phasing of eight species, including the outgroup Leea coccinea. Similarly, the Vitis SDR was highly conserved across the Vitaceae genomes, although variations in region size, primarily attributed to differences in repetitive elements, were observed. Interestingly, no recombination suppression was found in the dioecious Tetrastigma, suggesting a different sex determination mechanism. In Muscadinia rotundifolia, linkage disequilibrium analysis, haplotype comparison, and gene expression profiling showed that muscadine grapes have similar SDR boundaries and candidate sex-determining genes as Vitis. These results suggest that dioecy emerged in a common ancestor of the two grape genera at a locus associated with flower morphology and fertility, highly conserved in flowering plants.

evolutionary biology↗

bioRxiv2023

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

The permanent organs of grapevines (V. vinifera L.), like other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection, and recent gene-family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes in E. lata and P. minimum glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.

genomics↗

bioRxiv2023

A reference-unbiased super-pangenome of the North American wild grape species (Vitis spp.) reveals genus-wide association with adaptive traits

Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierces disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.

genomics↗

bioRxiv2022

The grape powdery mildew resistance loci Ren2, Ren3, Ren4D, Ren4U, Run1, Run1.2b, Run2.1, and Run2.2 activate different transcriptional responses to Erysiphe necator

Multiple grape powdery mildew (PM) genetic resistance (R) loci have been found in wild grape species. Little is known about the defense responses associated with each R locus. In this study, we compare the defense mechanisms associated with PM resistance in interspecific crosses segregating for a single R locus from Muscadinia rotundifolia (Run1, Run1.2b, Run2.1, Run2.2), Vitis cinerea (Ren2), V. romanetii (Ren4D and Ren4U), and the interspecific hybrid Villard blanc (Ren3). By combining optical microscopy, visual scoring, and biomass estimation, we show that the eight R loci confer resistance by limiting infection at different stages. We assessed the defense mechanisms triggered in response to PM at 1 and 5 days post inoculation (dpi) via RNA sequencing. To account for the genetic differences between species, we developed for each accession a diploid synthetic reference transcriptome by incorporating into the PN40024 reference homozygous and heterozygous sequence variants and de novo assembled transcripts. Most of the R loci exhibited a higher number of differentially expressed genes (DEGs) associated with PM resistance at 1 dpi compared to 5 dpi, suggesting that PM resistance is mostly associated with an early transcriptional reprogramming. Comparison of the PM resistance-associated DEGs showed a limited overlap between pairs of R loci, and nearly half of the DEGs were specific to a single R locus. The largest overlap of PM resistance-associated DEGs was found between Ren3+, Ren4D+, and Ren4U+ genotypes at 1 dpi, and between Ren4U+ and Run1+ accessions at 5 dpi. The Ren3+, Ren4D+, and Ren4U+ were also found to have the highest number of R locus-specific DEGs in response to PM. Both shared and R locus-specific DEGs included genes from different defense-related categories, indicating that the presence of E. necator triggered distinct transcriptional responses in the eight R loci.

genetics↗