Open Access Research article

Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of featherless chickens

Kirsty L Wells1, Yair Hadad2, Danny Ben-Avraham2, Jossi Hillel2, Avigdor Cahaner2* and Denis J Headon1*

Author Affiliations

1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom

2 Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O Box 12, Rehovot, 76100, Israel

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BMC Genomics 2012, 13:257  doi:10.1186/1471-2164-13-257

Published: 19 June 2012

Additional files

Additional file 1 :

Table S1. Results from sequencing of candidate mutations inEFHA2andSLC7A2.The polymorphisms identified in sc/sc were found to be carried by a number of WTs. The nucleotide numbers given for the EFHA2 c.144 and SLC7A2 c.1211 SNPs refer to the NCBI coding sequences; the nucleotide numbers given for the SLC7A2 polymorphisms between c.1159 and c.1164 refer to the ENSEMBL coding sequence. The letter/number codes given for each wild type sample are our identifiers for specific individuals within the diverse chicken DNA collection. Table S2 Raw data obtained from mapping of thesclocus. Names, position on chromosome 4, intensity values and absRAFdif for each SNP located within the 1.25 Mb mapped region depicted in Figure 2 are shown, together with the location of each of the 11 genes in the region (shaded). The 3 SNPs with absRAFdif values above 0.45 are highlighted in red. See Methods for explanation of data processing.

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Additional file 2 :

Figure S1.Genotyping assay to discriminateFGF20 c.535A andFGF20 c.535T alleles. Agarose gel analysis of undigested dCAPS PCR product, and WT, sc/+, and sc/sc products after digestion with NlaIII. The undigested PCR product is 249 bp. Upon digestion, the WT product yields 198 bp and 51 bp bands, while the sc product yields 151 bp, 51 bp and 47 bp bands. The sc/+ genotype is identified by the presence of both the 198 bp and 151 bp bands.

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