Rapid Genomic Characterization of the Genus Vitis

Abstract

Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

“…Microsatellite and SNP markers have become in the last years the markers of choice for genetic analyses in grapevine, including genetic mapping and QTL identification (Huang et al 2012;Doligez et al 2013;Battilana et al 2013;Barba et al 2014), linkage disequilibrium and association analyses (Emanuelli et al 2010;Barnaud et al 2010;Cardoso et al 2012;Vargas et al 2013), and varietal identification (Myles et al 2010;Cabezas et al 2011;Laucou et al 2011;Migliaro et al 2012). As in many other woody plant species, genetic mapping in grapevine has been carried out using mainly the double pseudo test-cross strategy (Grattapaglia et al 1995), which is based on the study of allelic segregation of markers found in heterozygosis in one or both progenitors of an F 1 progeny.…”

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…If this situation is common throughout the genome, as suggested by studies in grapevine (Myles et al, 2010), then whole-genome scan association studies in essentially undomesticated populations will require a very large number of SNPs. It is unlikely that all necessary variants will be represented on an array in the near future.…”

“…From these surveys of LD, Kim et al (2007) estimated that B140 000 single-nucleotide polymorphisms (SNPs) would be required for the whole scan of the 125-Mb genome of Arabidopsis, whereas Yan et al (2009) estimated this number between 240 000 and 480 000 SNPs for the 2400-Mb genome of maize. A genome-wide analysis showed that LD is so low in grapevine (r 2 o0.20 even between very close sites in Vitis vinifera) that whole-genome sequencing will be required for genome-wide association analyses (Myles et al, 2010).…”

Genetic structure and domestication history of the grape

“…This susceptibility to disease, however, is not attributable to a lack of genetic diversity. Vinifera harbors levels of genetic variation an order of magnitude greater than humans and is comparable in diversity to maize (2,3), with polymorphism that dates back tens of millions of years (4). Thus, an environmentally sustainable grape-growing industry will rely on accessing and using the grape's tremendous genetic diversity to develop improved disease-resistant grape cultivars through marker-assisted breeding (5).…”

“…To this end, we recently discovered over 70,000 high-quality SNPs in the grape using next-generation DNA sequencing (4). From this SNP set, we developed and validated a 9,000-SNP genotyping array (the Vitis9kSNP array).…”