Body weight and body measurements are commonly used to represent growth and measured at several growth stages in beef cattle. Those economically important traits should be genetically improved. To achieve breeding programs, genetic parameters are prerequisite, as they are needed for designing and predicting outcomes of breeding programs, as well as estimating of breeding values. (Co)variance components were estimated for BW and body measurements on Brahman cattle born between 1990 and 2016 from 17 research herds across Thailand. The traits measured were BW, heart girth (GR), hip height (HH) and body length (BL) and were measured at birth, 200 days, 400 days and 600 days of age. The number of records varied between traits from 18 890 for birth BW to 876 for GR at 600 days. Estimation of variance components was performed using restricted maximum likelihood using univariate and multivariate animal models. Pre-weaning traits were influenced by genetic and/or permanent environmental effects of the dam, except for BL. Heritability estimates from birth to 600 days of age ranged from 0.28±0.01 to 0.50±0.06 for BW, 0.27±0.01 to 0.43±0.09 for GR, 0.28±0.01 to 0.58±0.08 for HH and 0.34±0.01 to 0.51±0.08 for BL using univariate analysis. Heritability estimates for the traits studied increased with age. A similar trend was observed for the phenotypic and genetic correlations between subsequent BW and body measurements. A positive correlation was observed between different traits measured at a similar age, ranging from 0.22±0.01 to 0.72±0.01 for the phenotypic correlation and 0.25±0.04 to 0.97±0.11 for the genetic correlation. Also, a positive correlation was observed for similar traits across different age classes ranging from 0.07±0.03 to 0.76±0.02 for the phenotypic correlation and 0.24±0.11 to 0.92±0.05 for the genetic correlation. Therefore, all correlations between body measurements at the same age and across age classes were positive. The results show the potential improvement of growth traits in Brahman cattle, and those traits can be improved simultaneously under the same breeding program.

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.

Background: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene. Low-density genotypes of these animals were imputed to the Illumina Ovine high-density (600k) chip and the 1.78-kb insertion polymorphism in RXFP2 was included in the imputation process to whole-genome sequence. We evaluated the mode of inheritance and validated models by a fivefold cross-validation and across- and between-family prediction.

Results: The most significant SNPs for prediction of P/NP and H/NH were OAR10_29546872.1 and OAR10_29458450, respectively, located on chromosome 10 close to the 1.78-kb insertion at 29.5 Mb. The mode of inheritance included an additive effect and a sex-dependent effect for dominance for P/NP and a sex-dependent additive and dominance effect for H/NH. Models with the highest prediction accuracies for H/NH used either single SNPs or 3-SNP haplotypes and included a polygenic effect estimated based on traditional pedigree relationships. Prediction accuracies for H/ NH were 0.323 for females and 0.725 for males. For predicting P/NP, the best models were the same as for H/NH but included a genomic relationship matrix with accuracies of 0.713 for females and 0.620 for males.

Conclusions: Our results show that prediction accuracy is high using a single SNP, but does not reach 1 since the causative mutation is not genotyped. Incomplete penetrance or allelic heterogeneity, which can influence expression of the phenotype, may explain why prediction accuracy did not approach 1 with any of the genetic models tested here. Nevertheless, a breeding program to eradicate horns from Merino sheep can be effective by selecting genotypes GG of SNP OAR10_29458450 or TT of SNP OAR10_29546872.1 since all sheep with these genotypes will be non-horned.