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Open Access Highly Accessed Methodology article

Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

Hindrik HD Kerstens1, Richard PMA Crooijmans1, Albertine Veenendaal1, Bert W Dibbits1, Thomas FC Chin-A-Woeng2, Johan T den Dunnen3 and Martien AM Groenen1*

Author Affiliations

1 Animal Breeding and Genomics Center, Wageningen University, Marijkeweg 40, Wageningen, 6709 PG, the Netherlands

2 Service XS, Plesmanlaan 1d, Leiden, 2333 BZ, the Netherlands

3 Leiden Genome Technology Center, Human and Clinical Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, the Netherlands

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BMC Genomics 2009, 10:479  doi:10.1186/1471-2164-10-479

Published: 16 October 2009

Abstract

Background

The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo sequence assembler and a program designed to identify variation within short reads. To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey) individuals.

Results

A total of 100 million 36 bp reads were generated, representing approximately 5-6% (~62 Mbp) of the turkey genome, with an estimated sequence depth of 58. Reads consisting of bases called with less than 1% error probability were selected and assembled into contigs. Subsequently, high throughput discovery of nucleotide variation was performed using sequences with more than 90% reliability by using the assembled contigs that were 50 bp or longer as the reference sequence. We identified more than 7,500 SNPs with a high probability of representing true nucleotide variation in turkeys. Increasing the reference genome by adding publicly available turkey BAC-end sequences increased the number of SNPs to over 11,000. A comparison with the sequenced chicken genome indicated that the assembled turkey contigs were distributed uniformly across the turkey genome. Genotyping of a representative sample of 340 SNPs resulted in a SNP conversion rate of 95%. The correlation of the minor allele count (MAC) and observed minor allele frequency (MAF) for the validated SNPs was 0.69.

Conclusion

We provide an efficient and cost-effective approach for the identification of thousands of high quality SNPs in species currently lacking a sequenced genome and applied this to turkey. The methodology addresses a random fraction of the genome, resulting in an even distribution of SNPs across the targeted genome.