Dario Cantu

The genetic basis of wine monoterpene variation and its sensory consequences remain poorly understood. We investigated how allelic variation at a chromosome 10 linalool QTL harboring a terpene synthase cluster, including VviTPS54, influences wine aroma in a Riesling × Cabernet Sauvignon mapping population. Twenty-six wines from progeny selected for contrasting genotypes were subjected to HS-SPME-GC-MS profiling and descriptive sensory analysis. Genotypes carrying the high-linalool Riesling allele produced substantially elevated monoterpene levels dominated by linalool. Berry and wine monoterpene profiles were significantly correlated, and berry monoterpene glycosides showed broad correlations with wine monoterpenes. High-monoterpene genotypes were more closely associated with Floral, Tropical Fruit, and Apricot/Peach attributes, though perception was modulated by matrix effects from berry pigmentation. These results demonstrate that allelic variation at a terpene synthase locus drives coordinated changes in wine monoterpene composition and linked sensory attributes, while underscoring the complexity of translating genetic variation into sensory outcomes.

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. Published avocado genomes come from type A cultivars or from accessions of unreported flowering type. 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 Dovetail Omni-C data, the assembly places 885.4 Mb, 98.8% of the expected 896 Mb genome, in 12 chromosomes with an NG50 of 84.5 Mb, a consensus quality of QV 70.02, and 99.7% complete BUSCO genes; repeats occupy 64.0% of the assembly, and 36,349 protein-coding genes were predicted. We compared Thille with the type A cultivars Hass and Puebla, a Guatemalan x Mexican hybrid, and with Unnamed Lowland, an accession of the Lowland botanical group (formerly West Indian) of unreported flowering type. The assemblies differ by large rearrangements, including a 22.6 Mb inversion on chromosome 12 specific to Hass which is most likely due to scaffolding error. Using phased reads and haplotype assemblies, we revisited and reconstructed the alleles of candidate flowering genes from the type A versus type B Fst scan from our previous work. Both Unnamed Lowland haplotypes carry the recessive SDMYB allele found in Thille; based on this study and the previous study of SDMYB, we predict Unnamed Lowland to be type B. We also observe five other genes at which two type A cultivars (Puebla and Gwen) share an allele absent from Thille and Unnamed Lowland, a pattern that requires further investigation. The genome and HiFi reads have been submitted to NCBI under BioProject PRJNA1142556. Summary: The avocado (Persea americana) is known for its synchronous dichogamous flowering system, in which cultivars are classified as Type A or Type B based on when their female and male reproductive organs mature, a timing offset that encourages cross-pollination (Stout, 1927; Davenport, 1986). While the Type A genome has been extensively studied, primarily through the widely cultivated Hass variety, this study presents the first nearly complete genome of a documented Type B avocado, derived from the Thille variety. Due to Type B being homozygous recessive (Groh et al., 2026), a Type B assembly carries only the recessive allele at the flowering-type locus. Assembling this genotype therefore avoids the allelic heterozygosity expected at that locus in Type A individuals, where the dominant and recessive haplotypes must either be phased or risk collapsing into a single consensus sequence, and it provides an unambiguous reference for the recessive haplotype. The assembly reaches 98.8% completeness, with the 12 largest scaffolds approximating pseudomolecule length and an NG50 of 84.5 Mb. Our analysis reveals structural variants, including inversions and deletions, between the Thille and Hass genomes, particularly on chromosome 10, which houses key flowering markers. This genome and its HiFi sequencing data enrich the genomic resources available for avocado, supporting breeding and further research into this agriculturally significant and resource-intensive crop (Solares et al., 2023).

Boron toxicity constrains grapevine ( Vitis ) production in irrigated arid and semi-arid regions, yet most available rootstocks are sensitive to excessive boron. Although underutilized Vitis species may harbor sources of adaptation, the genetic basis of natural variation in boron exclusion remains poorly understood, limiting the development of boron-tolerant rootstocks. We screened 267 wild Vitis accessions representing 16 species for their ability to limit leaf boron accumulation under excess boron conditions. Leaf boron concentration varied 190-fold among accessions and was highly heritable (entry-mean H² = 0.71). Its correlation with stomatal conductance was modest (r = 0.34), indicating that transpiration rate explained only a small proportion of the variation in leaf boron accumulation. Leaf boron was correlated with leaf chloride (r = 0.36), but their largely non-overlapping association profiles supported distinct genetic control. Genome-wide association analysis identified a suggestive association on chromosome 11. Independent quantitative trait locus mapping in a full-sib F ₁ population (n = 158) derived from Longii-9018 ( V. acerifolia ) × GRN3 (commercial rootstock) identified qBEx11.1 in the same syntenic region on chromosome 11, which explained 19.5% of the phenotypic variance. Positional candidate genes near the association peak included a pectinesterase and a MATE efflux transporter, suggesting roles for cell wall modification and membrane transport. Leaf spectral reflectance was associated with leaf boron concentration in both populations, particularly at visible and red-edge wavelengths, indicating potential for high-throughput phenotyping. Together, these findings identify qBEx11.1 as a priority locus for boron exclusion and support integrated genetic and spectral approaches for breeding boron-tolerant grapevine rootstocks. Plain Language Summary: Boron is needed by plants in small amounts, but too much can damage them, especially in dry regions irrigated with boron-rich water. Grapevine rootstocks, the root systems onto which fruiting grape varieties are grafted, may help limit boron uptake. We screened 267 wild grapevines and offspring from two parent vines for their ability to limit boron buildup in leaves. Leaf boron levels differed nearly 190-fold. Genetic analyses of both groups identified the same region of chromosome 11 as important for limiting leaf boron. Transpiration rate explained only a small part of this variation, and boron and chloride buildup appeared to be controlled largely by different genetic factors. Measurements of how leaves reflected light also detected boron-related changes and may allow faster screening. These findings could help breeders develop grapevine rootstocks better suited to boron-affected soils and irrigation water.

Nurseries produce tens of millions of bench-grafted grapevines ( Vitis vinifera L.) each year, yet the genetics underlying grafting success rate remain poorly understood. Here, we dissected the genetic architecture of this trait in a scion mapping population. We grafted 138 progeny from a Riesling × Cabernet Sauvignon cross, along with both parents, onto 1103P, with 40 grafts per genotype in each of three separate field blocks and grafted on separate days (16,645 grafts). Success averaged 91.1 %. Scion genotype explained 19 % of the variance among blocks (entry-mean heritability 0.42); genotype × block variance exceeded genotype variance, and a few genotypes failed almost completely in a single block. Success was uncorrelated with yield of the mother vines. QTL mapping across six phenotype definitions and four haplotype-resolved parental genome assemblies detected one modest, reproducible QTL on chromosome 7 (Cabernet Sauvignon alleles; +3.9 percentage points; 11 to 15 % of variance) and suggestive regions on chromosomes 5 and 9. Most variation in grafting success within this elite V. vinifera cross was non-genetic and attributable to events affecting entire bundles. These results set expectations for effect sizes, replication, and process control in genetic studies of grafting success.

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 × Cabernet Sauvignon F1 mapping population, revealing extensive variation and transgressive segregation consistent with multigenic control. Quantitative trait locus (QTL) mapping identified 70 significant loci associated with 48 volatile compounds and monoterpene glycosides, including two major QTLs explaining 33.6% and 33.4% 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 1-deoxy-D-xylulose-5-phosphate synthase 1 (VviDXS1) locus previously identified in Muscat cultivars. In addition, VviDXS1 expression was not correlated with terpene levels, indicating that regulatory variation within terpene synthase clusters, rather than methylerythritol phosphate 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.

The vine mealybug, Planococcus ficus, is a globally invasive pest of grapevine and a vector of leaf roll 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 4 California field individuals provided the first genome-wide baseline of nucleotide diversity for P. ficus and 132 cross-validated microsatellite markers for population monitoring. Phloem feeders secrete proteins that mediate host interaction; of 2,129 predicted secreted proteins in P. ficus, a conserved core is shared with P. citri, and each carries a lineage-specific set. 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.

Hybridization between species can contribute to parallel adaptive events. However, the prevalence of introgression is rarely measured across multiple species, meaning that it is rarely integrated with landscape-scale processes or connected to adaptive repeatability. Here we analyzed whole-genome resequencing data from 639 accessions representing 48 Vitis species. Vitis is notable for the domesticated grapevine ( Vitis vinifera ), multiple economically important North American species, and as an example of a temperate adaptive radiation. We reconstructed individual- and species-level phylogenetic frameworks for the genus and performed population genetic analyses for 19 species. The analyses uncovered widespread evidence of introgression, comprising ~14% of the average Vitis genome. Introgression was associated with the geographic distribution between species, and highly admixed individuals were more frequently found near ecological niche margins. Genetic analyses further indicated that previously recognized hybrid taxa, Vitis x doaniana and Vitis x champinii , likely represent ongoing hybrid swarms rather than distinct lineages. We assessed patterns of adaptive repeatability across eight species with denser population sampling. For six of eight species, most detected selective sweeps overlapped with sweeps in other species; on average, more recently diverged species shared more overlapping sweeps. A coalescence-based composite likelihood approach inferred that parallel sweep events were driven mostly by introgression, although a substantial fraction (~40%) was attributed to selection on ancestral standing variation. By integrating population genomic data across many species, this study highlights the central role of shared genetic variation—and the driving force of hybridization—across an adaptive radiation.

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 α-farnesene, β-ocimene, and multi-product α-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.

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.

Carménère is a widely cultivated and internationally recognised grapevine cultivar in Chile. Early studies based on SSR and AFLP markers detected limited polymorphism among clones in Chile, but these approaches interrogate only a small fraction of the genome, leaving the extent of clonal diversity unresolved. Here, we generated a near-complete chromosome-scale diploid genome assembly of Carménère FPS 02 and characterised clonal genomic diversity by sequencing 36 biological replicates representing 12 clones maintained in Chile, including heritage selections rescued from old producer vineyards by Viña 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 9000 candidate private single nucleotide variants (SNVs) and small indels per clone. A subsampling simulation showed that as few as 83 ± 2 candidate private SNVs per clone were sufficient to correctly discriminate all clones by kinship-based clustering, a level of resolution undetectable by earlier SSR and AFLP-based approaches. Most variants occurred in repetitive or intergenic regions, but a subset affected coding sequences, collectively impacting an average of 7292 genes per haplotype when variants of all predicted impact classes are considered, with genes involved in plant–pathogen interactions, transport, and secondary metabolism most frequently affected. Overall, this study provides a genome-wide characterisation of extant clonal diversity in Carménère, with implications for clonal selection and genetic resource conservation.