A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep

Wendy Jm Smith,Eliza Collis,Tom J Dixon,Suzanne I Mortimer,Sean M Mcwilliam,Yutao Li,Antonio Reverter,Robert J Moore,Belinda J Norris,Aaron Ingham

doi:10.1186/1746-6148-6-27

Abstract

BackgroundFleece rot (FR) and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality. In addition to direct effects on fleece quality, fleece rot is a major predisposing factor to blowfly strike on the body of sheep. In order to investigate the genetic drivers of resistance to fleece rot, we constructed a combined ovine-bovine cDNA microarray of almost 12,000 probes including 6,125 skin expressed sequence tags and 5,760 anonymous clones obtained from skin subtracted libraries derived from fleece rot resistant and susceptible animals. This microarray platform was used to profile the gene expression changes between skin samples of six resistant and six susceptible animals taken immediately before, during and after FR induction. Mixed-model equations were employed to normalize the data and 155 genes were found to be differentially expressed (DE). Ten DE genes were selected for validation using real-time PCR on independent skin samples. The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP) that were genotyped across three populations for their associations with fleece rot resistance.ResultsThe majority of the DE genes originated from the fleece rot subtracted libraries and over-representing gene ontology terms included defense response to bacterium and epidermis development, indicating a role of these processes in modulating the sheep's response to fleece rot. We focused on genes that contribute to the physical barrier function of skin, including keratins, collagens, fibulin and lipid proteins, to identify SNPs that were associated to fleece rot scores.ConclusionsWe identified FBLN1 (fibulin) and FABP4 (fatty acid binding protein 4) as key factors in sheep's resistance to fleece rot. Validation of these markers in other populations could lead to vital tests for marker assisted selection that will ultimately increase the natural fleece rot resistance of Merino sheep.

Highlights

Fleece rot (FR) and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality
The current experiment investigated the genetic drivers of resistance to FR using a three-step approach: First, a skin-focussed cDNA microarray was constructed and applied to RES and SUS animals to identify differentially expressed (DE) genes; Second, a selected group of DE genes was validated via quantitative real-time PCR (qRT-PCR), and their coding regions surveyed to identify single nucleotide polymorphisms (SNP); these SNPs were genotyped across three populations with different FR characteristics to ascertain their association to FR resistance
Residual FR scores were determined at the pre-wetting and post-wetting sample collection times

Summary

Results

Analysis of phenotypic data Means (± standard error) for prewet FR scores were 0.17 ± 0.04, 1.75 ± 0.11, and 0.08 ± 0.03 for Armidale, Trangie RES and Trangie SUS flocks, respectively. The regression coefficient associated with this marker indicates that selecting animals with allele T (i.e. genotypes 1, CT, or 2, TT) would result in a reduction of FR score by 0.21 units This same SNP did not show any significant effect on FR score in post-wetting trial (Table 4), nor when the fleece rot score difference between pre- and post-wetting trials was considered (Tables 5). Significant associations for two SNPs (FABIn20237 and FABIn30360) from the same gene FABP4 (fatty acid binding protein 4) were identified for the difference between Post- and Pre-wetting FR score (P < 0.05, Table 5). They explained from 2.8% to 3.5% of the phenotypic variance. For one of them (FBLs10075), the significant association was maintained in the post-wetting trial, showing a decreasing effect (by 0.22 unit) on FR score (P < 0.05, Table 4)

Conclusions

Background

Discussion and Conclusions

Methods