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.
Highlights
The aim of genetic mapping studies is to identify loci that underlie phenotypic variation
We show that the Vitis9KSNP array provides sufficient high-quality genotypes to successfully capture the genetic structure within and between the V. vinifera cultivars and wild Vitis species
Our analyses suggest that the use of single nucleotide polymorphisms (SNPs) arrays for WGA studies will be inadequate for high-diversity plant species in which linkage disequilibrium (LD) decays rapidly, as in the grapevine
Summary
The aim of genetic mapping studies is to identify loci that underlie phenotypic variation. The first step towards GWA and GS is to discover large numbers of genetic markers, generally single nucleotide polymorphisms (SNPs), across the genome. This initial step of large-scale SNP discovery is already underway in several organisms. SNP discovery using nextgeneration sequence data is still in its infancy, but several studies have already demonstrated that large numbers of high quality SNPs can be identified in a cost effective manner using next-generation sequence data [5,6,7,8,9]. RRLs are generated by digesting each sample with a common restriction enzyme before sequencing and they have been useful for large-scale SNP discovery in several organisms [8,9,10,11]
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