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Understanding the genetic basis of leaf size and shape is essential for evaluating and selecting for plant adaptability and performance in variable and shifting climatic conditions. This study maps the leaf size and shape phenotypic variation as influenced by the genetic architecture of a rootstock population and its conferred influence on these traits in a common scion. The influence of the root system genotype was studied using two different presentations of an F1 rootstock population (F1_Vruprip;V. rupestrisScheele ‘B38’ (USDA PI#588160) XV. ripariaMichx. ‘HP1’ (USDA PI#588271)); 1) the F1_Vruprip grapevine progeny on their own roots and 2) a F1_Vruprip cohort that was grafted with the common scion scion 'Marquette'. Three leaf positions (apical, middle, and basal) were sampled in both presentations at two timepoints in two consecutive growing seasons. A twenty-one-point leaf morphological landmark coordinate analysis was conducted, and ten leaf size and six derived shape phenotypes were used for QTL mapping. Genetic analysis identified five distinct hotspots associated with size-related leaf area attributes in own-rooted and grafted vines. The identification of multiple leaf-growth-associated pathways in these hotspot regions strengthened the correlation between genetics and phenotypic traits. Shape related QTL accounted for 12-48% of the shape phenotypic variation but did not cluster as QTL hotspots. Three QTL hotspots captured the genetic influence of the rootstock conferred onto the scion leaf area traits. The results showed that the leaf position and the rootstock population’s genetic composition significantly impacted leaf morphological attributes and that there was a measurable rootstock genotype influence conferred on the grafted scion leaves. This reveals the genetic loci and gene pathways underlying leaf morphological phenotypes in own-rooted progeny and also verifies the potential of rootstock genetics to confer modulation of scion canopy features, providing greater potential to select for climate-resilient grapevines. 

Abstract BackgroundCapturing 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. ResultsHere we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are 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 Pierce’s 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. ConclusionsThis study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research. 

Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine ( Vitis vinifera L. ssp. vinifera ). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine. 

Grapevine 3D inflorescence architecture was comprehensively characterized among 10 wild Vitis species to reveal new phenotypic and evolutionary relationships.