Leaf shape in plants plays important roles in water use, canopy structure, and physiological tolerances to abiotic stresses; all important traits for the future development and sustainability of grapevine cultivation. Historically, researchers have used ampelography, the study of leaf shape in grapevines, to differentiate Vitis species and cultivars based on finite leaf attributes. However, ampelographic measurements have limitations and new methods for quantifying shape are now available. We paired an analysis of finite trait attributes with a 17-point landmark survey and generalized Procrustes analysis (GPA) to reconstruct grapevine leaves digitally from five interspecific hybrid mapping families. Using the reconstructed leaves, we performed three types of quantitative trait loci (QTL) analyses to determine the genetic architecture that defines leaf shape. In the first analysis, we compared several important ampelographic measurements as finite trait QTL. In the second and third analyses, we identified significant shape variation via principal components analysis (PCA) and using a multivariate least squares interval mapping (MLSIM) approach. In total, we identified 271 significant QTL across the three measures of leaf shape and identified specific QTL hotspots in the grape genome which appear to drive major aspects of grapevine leaf shape.

Although DNA methylation has largely been shown to be stable in plants, mounting evidence indicates methylation patterns may reflect environmental sensitivity. Perennial plants experience seasonal and inter-annual environmental variation, and clonal replicates of some long-lived plants, including many perennial crops, survive in a broad range of environments. This makes perennial crops a compelling study system to investigate links between the plant epigenome and environmental variation. In this study, we used whole genome bisulfite sequencing and small RNA sequencing to characterize the epigenome in 12 clonal replicates of the winegrape cultivar ‘Chambourcin.’ We asked whether DNA methylation varied in response to a full factorial combination of irrigation and grafting treatments. We found signatures of both irrigation and grafting in the ‘Chambourcin’ epigenome, as well as compelling evidence for a unique interaction effect whereby grafting appeared to override or mitigate epigenomic changes associated with irrigation in ungrafted vines. These findings indicate that the epigenome responds to environmental and agronomic manipulations, suggesting the epigenome might be a mechanism underlying how long-lived, clonal plants respond at the molecular level to their environment. Further research is needed to assess the potential relevance of variation in DNA methylation to plant form and function, and to address the implications of environmentally-inducible patterns of DNA methylation on the adaptive capacity of long-lived woody perennials in nature and under cultivation.

Leavenworthia (Brassicaceae) has served as a model group for investigating the evolution of mating systems in plants, yet several Leavenworthia species remain understudied. One such taxon is Leavenworthia exigua var. laciniata, one of three varieties of L. exigua, a winter-annual plant endemic to the central United States. Because L. exigua var. laciniata occupies a narrow geographic range and is experiencing major habitat loss, it was recently listed as threatened; however, little is known about its genetic diversity and implications for conservation. We conducted a range-wide population genetic study of L. exigua var. laciniata and L. exigua var. exigua to understand: (1) levels of genetic diversity within and among populations, (2) whether L. exigua var. laciniata is genetically distinct from L. exigua var. exigua, and (3) implications for conservation. L. exigua var. laciniata showed identical genotypes at all 16 microsatellite loci across most of its range, fixed heterozygosity at some loci, and significant heterozygote excesses, consistent with a lack of recombination associated with an asexual mating system, which has not been documented previously in Leavenworthia. Because L. exigua var. laciniata is an annual and the same genotype occurs across multiple populations, asexuality may be caused by apomixis, asexual reproduction via seed. In contrast, most populations of L. exigua var. exigua demonstrated population genetic patterns consistent with a self-compatible mating system. Because L. exigua var. laciniata is morphologically, geographically, and genetically distinct, it should be recognized as an evolutionarily significant unit for conservation. We recommend maintaining large population sizes to conserve evolutionary potential in L. exigua var. laciniata, as the likelihood that facultative sexual reproduction may occur may be greater in larger populations. Additional research in L. exigua var. laciniata is needed to confirm the occurrence of asexuality and apomixis, clarify its reproductive isolation from other taxa, and to understand whether it exhibits residual sexual reproduction, epigenetic variation, or phenotypic plasticity to help it persist in response to environmental variation. In the future, L. exigua var. laciniata may serve as an important model in which to investigate the conservation of threatened plant species with little genetic variation in a changing climate.