Abstract
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world’s largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
Highlights
Grapes (Vitis vinifera L.), one of the first domesticated perennials, originated in the Near East 5000–8000 years ago[1] and remain an economically and culturally important crop
We demonstrated that the primary axis of genetic structure differentiates wine from table grapes (Figures 3b and c), and that berry size is strongly correlated with the first genetic principal components (PCs) (Figure 3d)
An analysis of historical phenotype data collected over a 17-year period from the United States Department of Agriculture (USDA) grape germplasm collection revealed novel insights into patterns of grape phenotypic diversity, and enabled high-resolution genetic mapping when paired with genomic data
Summary
Grapes (Vitis vinifera L.), one of the first domesticated perennials, originated in the Near East 5000–8000 years ago[1] and remain an economically and culturally important crop. In 2015, grapevines covered 7.5 million hectares and produced 76 million tons of grapes globally.[2] Over the past millennia, human selection for traits of interest, especially those important to fruit production, have shaped the appearance of grapes. Selection for hermaphroditic flowers increased grape production, as propagating both male and female plants was no longer required. While nearly half of all grapes grown are vinified into wine, 36% are consumed fresh and the rest are dried or used for juice.[2] Desirable berry traits differ depending on the use of the grapes, and, the different breeding targets for table and wine grapes have led to differences in berry and bunch size.[3,4,5] There is evidence of selection for white berry color.[5]
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