QTL analysis of leaf morphology indicates conserved shape loci in grapevine

Authors: DEMMINGS, ELIZABETH - Cornell University; WILLIAMS, BRIGETTE - Missouri State University; LEE, CHENG-RUEI - National Taiwan University; BARBA, PAOLA - Instituto Nacional De Investigaciones Forestales Y Agropecuarias (INIFAP); YANG, SHANSHAN - Arizona State University; HWANG, CHIN-FENG - Missouri State University; REISCH, BRUCE - Cornell University; CHITWOOD, DANIEL - Michigan State University; Londo, Jason

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/10/2019
Publication Date: 11/15/2019
Citation: Demmings, E.M., Williams, B., Lee, C., Barba, P., Yang, S., Hwang, C., Reisch, B.I., Chitwood, D.H., Londo, J.P. 2019. QTL analysis of leaf morphology indicates conserved shape loci in grapevine. Frontiers in Plant Science. 10:1373. doi: 10.3389/fpls.2019.01373.
DOI: https://doi.org/10.3389/fpls.2019.01373

Interpretive Summary: 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. Using a standard set of measurements, such as length and width of leaves or angles between the leaf veins, ampelographers could identify specific cultivars. However, ampelographic measurements have limitations and new methods for measuring shape are now available. We combined an analysis of ampelographic measurements with with a seventeen-point landmark survey to reconstruct grapevine leaves digitally from five interspecific hybrid mapping families. Using the reconstructed leaves, we performed three types of analyses that link genetic markers to phenotypic traits in order to determine the genetic architecture that defines leaf shape. In total we identified 271 significant genomic regions in the grape genome that affect leaf shape. By combining our different methods of measuring shape, we were able to identify the 4 most important regions. These regions each explain different aspects of leaf shape but the dominant trend was that these regions affect leaf lobe shape. Breeders and researchers can now use this data to try and narrow down the genetic regions to identify the specific genes controlling leaf lobing in grapevine.

Technical Abstract: 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 seventeen-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.