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*

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

Additional files

Additional file 1:

Distribution of short read turkey contigs, turkey BES, and SNPs on chicken chromosomes. In black, short read contigs <100 bp; in blue, short read contigs ≥ 100 bp; in red, BES; in yellow, BES-short-read contigs; and in green, SNPs. On the X-axis, the chicken genome in 200 kb intervals. On the Y-axis, the frequency of mapped turkey features for a specific chicken genome interval.

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Additional file 2:

Primer sequences, PCR product sizes, and number of SNPs confirmed per amplicon for the 25 loci evaluated for genome similarity and SNPs. 1C = chicken, T = turkey. First, 13 loci were used in the determination of genome conservation between chicken and turkey. Next, 12 loci were used to validate the contig assembly and SNP detection procedure.

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Additional file 3:

Validation of candidate SNPs by genotyping a panel consisting of 96 turkeys. The 96 animals included the six turkeys from which the pooled DNA sample for SNP discovery was prepared. Listed are the 324 polymorphic SNPs out of 340 predicted SNPs that resulted in a working assay. For all SNPs, the minor allele frequencies (MAF) were calculated for the group of six turkeys from which the pooled DNA sample was prepared and for the total panel. Also, the fraction of individuals heterozygous for an SNP locus was calculated.

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