Search

Context There has been a lot of interest in recent years in developing estimated breeding values (EBVs) to reduce methane emissions from the livestock sector. However, while a major limitation is the availability of high-quality methane phenotypes measured on individual animals required to develop these EBVs, it has been recognised that selecting for improved efficiency of milk production, longevity, feed efficiency and fertility may be an effective strategy to genetically reduce methane emissions in dairy cows. Aim Applying carbon dioxide equivalents (CO2-eq) weights to these EBVs, we hypothesise that it is possible to develop a genetic tool to reduce greenhouse-gas emissions (GHG). Methods We calculated the effect of an EBV unit change in each trait in the Balanced Performance Index on CO2-eq emissions per cow per year. The estimated environmental weights were used to calculate a prototype index of CO2-eq emissions. The final set of EBVs selected for inclusion in the GHG subindex were milk volume, fat yield and protein yield, survival and feed saved, as these traits had an independent effect on emissions. Feed saved is the Australian feed efficiency trait. A further modification was to include a direct methane trait in the GHG subindex, which is a more direct genomic evaluation of methane estimated from measured methane data, calculated as the difference between actual and predicted emissions, for example, a residual methane EBV. Key results The accuracy of the GHG subindex (excluding residual methane EBV) is ~0.50, calculated as the correlation between the index and gross methane (using 3-day mean gross methane phenotypes corrected for fixed effects, such as batch and parity and adjusting for the heritability). The addition of the residual methane EBV had a minimal effect with a correlation of 0.99 between the indexes. This was likely to be due to limited availability of methane phenotypes, resulting in residual methane EBVs with low reliabilities. Conclusions We expect that as more methane data becomes available and the accuracy of the residual methane trait increases, the two GHG subindexes will become differentiated. When the GHG subindex estimates are applied to bull EBVs, it can be seen that selecting for bulls that are low emitters of GHG can be achieved with a small compromise in the BPI of ~20 BPI units (standard deviation of BPI = 100). Implications Therefore, selection for more sustainable dairy cattle, both economic and environmental, may be promptly implemented until sufficient data are collected on methane.

Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P P P FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.

Background Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. Results GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. Conclusions The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended.

Additional file 4. Analyses of variants located around previously reported wool and hair genes. A set of variants in and close to 453 previously reported genes associated with wool/fur/hair traits across mammals (Published-Gene set) were identified including 1619 coding variants and 11,712 variants up- and down-stream of the genes. A BayesR fine-mapping analysis identified which of these variants were most associated with wool traits and a GBLUP tested the proportion of genetic variance that the sequence variant set explained for each of the wool traits.

Additional file 2: Table S1. STAR parameters used for alignment.

Additional file 4: Table S2. RNA-seq library information. Mean, minimum, maximum and median values of the number of read pairs that pass trimming and filtering (clean reads), and are uniquely mapped reads, and the proportion of clean reads that map uniquely to the genome in liver and muscle samples. The distribution of the proportion of clean reads that are uniquely mapped in liver and muscle samples is also shown.

Background One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. Results Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise FST between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. Conclusions Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0216-x) contains supplementary material, which is available to authorized users.