Introduction Methods Results Conclusions ...

Selection Signatures in Facial Eczema Selection Flocks Hayley J

* Baird ,

Ken G Dodds, Rudiger Brauning and Sin H Phua

Agresearch Invermay, Private Bag 50034, Mosgiel, New Zealand

Introduction Facial eczema (FE) is a secondary photosensitisation disease caused by the ingestion of sporidesmin, a mycotoxin produced by the saprophytic fungus Pithomyces chartarum. The disease incurs significant costs and production losses to the New Zealand sheep and dairy industries. FE resistance is a highly heritable trait, and in 1975 FE resistant and susceptible selection lines of Romney sheep were established. Using the Illumina OvineSNP50 BeadChip a selection sweep experiment was conducted on these genetic lines. Two methods were used to evaluate the differences between the selection lines. Peddrift is a method that incorporates pedigree data in the analysis and compensates for genetic drift. The second method used was the fixation index or FST, a commonly used method to quantify the genetic differentiation between subpopulations.

P. chartarum spores

Methods The animals: The Romney rams used were selected on the basis of the liver-damage scores of their sporidesmin-dosed progeny (Morris et al., 1989; Phua et al., 1999). Since 1981 sires from within the lines were performance tested by sporidesmin dosing followed by measurement of blood gamma-glutamyl transferase (GGT) as an indicator of liver damage. The 132 animals analysed in Sporidesmin testing this work comprised of 66 resistant (male n=33, female n=33) and 66 susceptible (male n=32, female n=34). All animals were born GGT GGT between 1991 and 1995. The genotyping: High quality genomic DNA was isolated from whole blood (Montgomery & Sise, 1990). DNA samples were quantitated using the Invitrogen™ PicoGreen® dsDNA quantification kits. The DNA was Genotyping genotyped using the Illumina OvineSNP50 BeadChip Infinium II Assay according to the manufacturer’s 33 33 34 33 instructions. The statistics: Two methods were used to evaluate the allele frequency differences of the SNP markers between the selection lines. 1. Peddrift method (Dodds & McEwan, 1997) using a chi-square contingency table (line by allele) test statistic (X2); using pedigree data to provide a statistical significance value for each SNP marker and compensates for genetic drift since establishment of the lines. The method was modified to simulate drift over a range of initial minor allele frequencies and then smoothed. A conservative genome-wide 5% threshold would require P99%. 50,975 SNPs were used in the statistical analysis. The Peddrift and FST statistics were almost perfectly correlated. Fig. 1. Peddrift X2 versus minor allele frequencies (MAF) 2

Peddrift X

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Three SNPs showed highly significant allele frequency differences between the resistant and susceptible lines (P