A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits

Background Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos. In turn, skin wrinkle is strongly linked to susceptibility to “fly strike” (Cutaneous myiasis), which is a major welfare issue. Here, we use whole-genome sequence data in a multi-trait GWAS to identify pleiotropic putative causal variants and genes associated with changes in key wool traits and skin wrinkle. Results A stepwise conditional multi-trait GWAS (CM-GWAS) identified putative causal variants and related genes from 178 independent quantitative trait loci (QTL) of 16 wool and skin wrinkle traits, measured on up to 7218 Merino sheep with 31 million imputed whole-genome sequence (WGS) genotypes. Novel candidate gene findings included the MAT1A gene that encodes an enzyme involved in the sulphur metabolism pathway critical to production of wool proteins, and the ESRP1 gene. We also discovered a significant wrinkle variant upstream of the HAS2 gene, which in dogs is associated with the exaggerated skin folds in the Shar-Pei breed. Conclusions The wool and skin wrinkle traits studied here appear to be highly polygenic with many putative candidate variants showing considerable pleiotropy. Our CM-GWAS identified many highly plausible candidate genes for wool traits as well as breech wrinkle and breech area wool cover.

Keratin gene expression in Merino sheep with divergent wool growth

South Australian Merino sheep were selected on the basis of high or low estimated breeding values (EBV) for wool growth rate (W), but with similar bodyweight, follicle density, and mean fibre diameter. Differences in the level of expression of keratin genes were examined in the skin of these sheep to test the hypothesis that divergence in EBV for wool growth is related to the production of wool proteins differing in sulfur (S) content. Further, it was proposed that this differential gene expression would be most pronounced when the supply of S amino acids to the animal was increased. Sheep selected for high EBV (+W) produced more wool per day than low EBV sheep (–W) (on average 32.5 v. 17.7 g/day clean wool, respectively; P < 0.05) but the S content of the wool did not differ between selection groups (2.77% v. 2.87% S, respectively; P = 0.2). Expression of keratin genes including keratin-associated protein KAP 2 (a high S gene), KAP 4 (an ultra-high S gene), KAP 6 (a high glycine/tyrosine gene), and the intermediate filament gene K 2.10, did not differ significantly between +W and –W groups. KAP 2 and K 2.10 each accounted for approximately 5% of the variation in wool growth rate (WGR) but expression of none of the genes examined was significantly related to the S content of the fibre produced. This suggests that differential keratin gene expression was not the source of genetic divergence in WGR. Instead the latter likely reflects a combination of differential cellular rate and growth processes (e.g. rate of bulb cell production, hypertrophy of cortical cells), differences in the relative production of inner root sheath and fibre from the follicle bulb cell population, or differential nutrient uptake into the follicle.

Effects of abomasal protein and energy supply on wool growth in Merino sheep

The relative importance for wool growth of energy-yielding nutrients compared with amino acids required for incorporation into wool proteins was assessed in an experiment in which most nutrients were supplied via the abomasum. Nine nutritional treatments, providing three levels of protein (53, 99 and 145 g/day) to the intestines at three levels of energy (5.2, 7.5 and 9.7 MJ/day), were given to 12 Merino sheep during three consecutive periods of 3 weeks in a balanced lattice design. Abomasal nutrients consisted of varying proportions of casein, whole milk, glucose and glycerol. There was a large effect of protein supply on all components of wool growth, but there was no significant effect of energy. There was a significant interaction between the effects of protein and energy supply on diameter, length growth rate and volume of wool, but it was small relative to the main effect of protein. Extra energy appeared to enhance wool growth at the highest level of protein but reduce it at the lowest level of protein. The concentration of urea, cystine, methionine and other essential amino acids in plasma increased with protein level. Increasing energy supply reduced the concentration of urea and essential amino acids in plasma but not that of cystine or methionine. The experiment confirmed the major role of amino acid supply in controlling wool growth but indicated that there may be a small interaction with energy supply.