SNP Discovery and Development of a High-Density Genotyping Array for Sunflower

Eleni Bachlava,Jennifer R Mandel,Christopher A Taylor,Shunxue Tang,John E Bowers,Steven J Knapp,John M Burke,Pär K Ingvarsson

doi:10.1371/journal.pone.0029814

Abstract

Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.

Highlights

Until recently, a major limitation in the genetic dissection of complex traits in both plants and animals has been the lack of availability of large numbers of genetic markers that can be assayed in an efficient manner
These platforms, which allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs) from throughout the genome, have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa
We describe the results of a large-scale sequencing and SNP discovery effort aimed at developing a high-density SNP genotyping array in one such species – sunflower (Helianthus annuus L.)

Summary

Introduction

A major limitation in the genetic dissection of complex traits in both plants and animals has been the lack of availability of large numbers of genetic markers that can be assayed in an efficient manner. When combined with rapid advances in next-generation sequencing technologies, the high levels of single nucleotide polymorphism (SNP) diversity that are present in most plant and animal gene pools (e.g., [1,2,3,4,5]) have made possible the development of high-throughput genotyping platforms. These platforms, which allow for the simultaneous interrogation of thousands of SNPs from throughout the genome, have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. The results of this work revealed a high frequency of polymorphic SNPs and relatively high levels of transferability of assays across species, making this SNP array an ideal tool for the genetic analysis of sunflower and related species

Materials and Methods

Sequencing Method

Results and Discussion