Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back‐cross cattle finished on pasture or feedlot

A QTL study of live animal and carcass traits in beef cattle was carried out in New Zealand and Australia. Back‐cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. This paper reports on weights of eight organs (heart, liver, lungs, kidneys, spleen, gastro‐intestinal tract, fat, and rumen contents) and 12 fat composition traits (fatty acid (FA) percentages, saturated and monounsaturated FA subtotals, and fat melting point). The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. For organ weights and fat composition traits, 10 and 12 significant QTL locations (P < 0.05), respectively, were detected on a genome‐wide basis, in combined‐sire or within‐sire analyses. Seven QTL significant for organ weights were found at the proximal end of chromosome 2. This chromosome carries a variant myostatin allele (F94L), segregating from the Limousin ancestry, and this is a positional candidate for the QTL. Ten significant QTL for fat composition were found on chromosomes 19 and 26. Fatty acid synthase and stearoyl‐CoA desaturase (SCD1), respectively, are positional candidate genes for these QTL. Two FA QTL found to be common to sire groups in both populations were for percentages of C14:0 and C14:1 (relative to all FAs) on chromosome 26, near the SCD1 candidate gene.     

Quantitative trait loci with additive effects on growth and carcass traits in a Wagyu-Limousin F2 population

A whole-genome scan for carcass traits [average daily gain during the pre-weaning, growth and finishing periods; birth weight; hot carcass weight and longissimus muscle area (LMA)] was performed on 328 F(2) progeny produced from Wagyu x Limousin-cross parents derived from eight founder Wagyu bulls. Nine significant (P Limousin breeds.     

Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot

A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant ( P  <   0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.     

Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population

A whole-genome scan was conducted on 328 F(2) progeny in a Wagyu x Limousin cross to identify quantitative trait loci (QTL) affecting palatability and fatty acid composition of beef at an age-constant endpoint. We have identified seven QTL on five chromosomes involved in lipid metabolism and tenderness. None of the genes encoding major enzymes involved in fatty acid metabolism, such as fatty acid synthase (FASN), acetyl-CoA carboxylase alpha (ACACA), solute carrier family 2 (facilitated glucose transporter) member 4 (SLC2A4), stearoyl-CoA desaturase (SCD) and genes encoding the subunits of fatty acid elongase, was located in these QTL regions. The present study may lead to a better-tasting and healthier product for consumers through improved selection for palatability and lipid content of beef.     

Genetic correlation estimations between artificial insemination sire performances and their progeny beef traits both measured in test stations

In France, beef traits of artificial insemination (AI) beef bulls are improved through the sequential selection for their own performances and for their male progeny performances, both being recorded in test stations. The efficiency of such programmes mainly depends on the genetic correlations between sire performances and progeny beef traits. Such correlations were independently estimated, using the multivariate REML (restricted maximum likelihood) method in a Limousin and a Charolais programme. In both breeds, high genetic correlations were observed between sires and progeny analogous morphology scores (from 0.64 to 0.82). Genetic correlations estimated between sires and progeny growth (from 0.41 to 0.70) were lower probably due to the difference of diet in central and progeny stations. Correlations between sire muscling scores and progeny skeletal frames (and vice-versa) were negative (from -0.05 to -0.58). The genetic correlations of sire traits with progeny dressing percentage (DP_p) and carcass fatness score (CF_p) were only low to moderate. These results show that the selection of bulls at the end of performance testing in test stations may be efficient in improving progeny growth and morphology. However, such a selection is insufficient in improving their dressing percentage and carcass composition.     

Detection of selection signatures in Limousin cattle using whole-genome resequencing

Limousin, a renowned beef breed originating from central France, has been selectively bred over the last 100 years to improve economically important traits. We used whole-genome sequencing data from 10 unrelated Limousin bull calves to detect polymorphisms and identify regions under selection. A total of 13 943 766 variants were identified. Moreover, 311 852 bi-allelic SNPs and 92 229 indels located on autosomes were fixed for the alternative allele in all sequenced animals, including the previously reported missense deleterious F94L mutation in MSTN. We performed a whole-genome screen to discover genomic regions with excess homozygosity, using the pooled heterozygosity score and identified 171 different candidate selective sweeps. In total, 68 candidate genes were found in only 57 of these regions, indicating that a large fraction of the genome under selection might lie in non-coding regions and suggesting that a majority of adaptive mutations might be regulatory in nature. Many QTL were found within candidate selective sweep regions, including QTL associated with shear force or carcass weight. Among the putative selective sweeps, we located genes (MSTN, NCKAP5, RUNX2) that potentially contribute to important phenotypes in Limousin. Several candidate regions and genes under selection were also found in previous genome-wide selection scans performed in Limousin. In addition, we were able to pinpoint candidate causative regulatory polymorphisms in GRIK3 and RUNX2 that might have been under selection. Our results will contribute to improved understanding of the mechanisms and targets of artificial selection and will facilitate the interpretation of GWASs performed in Limousin.     

Effects of quantitative trait loci and the myostatin locus on trace and macro elements (minerals) in bovine liver,muscle and kidney

A quantitative trait locus (QTL) study of the concentrations of 14 trace and macro elements (minerals) in tissues of beef cattle was conducted in New Zealand. Back‐cross calves with Jersey and Limousin ancestry (202 heifers and 211 steers) were generated using first‐cross sires. This paper reports on testing for effects of QTL on the concentrations of minerals in liver, kidney and muscle in cattle at slaughter, following a growth phase during which rearing and finishing stages were on pasture. Fifteen QTL were identified (P < 0.05) on a genome‐wide basis in combined‐sire and within‐sire analyses. In addition, the possible effect of the Limousin myostatin F94L allele was tested by fitting each calf's myostatin genotype, and 16 QTL were identified. Twelve were in common with those QTL identified previously, comprising six affecting the liver (copper and zinc, on two chromosomes each; plus iron and molybdenum), three affecting the kidney (calcium, copper and iron), and three affecting muscle (iron, strontium and zinc).     

Increasing the accuracy of genomic prediction in pure‐bred Limousin beef cattle by including cross‐bred Limousin data and accounting for an F94L variant in MSTN

Explicitly fitting effects for major genes or QTL that account for a large percentage of variation in a whole genomic prediction model may increase prediction accuracy. This study compared approaches to account for a major effect of an F94L variant in the MSTN gene within the genomic prediction using bovine whole‐genomic SNP markers. Among the beef cattle breeds, Limousin have been known to have an F94L variant that is not present in Angus. The reference population in this study consisted of 3060 beef cattle including pure‐bred Limousin (PL), cross‐bred Limousin with Angus (LF) and pure‐bred Angus, genotyped using a BovineSNP50 BeadChip and directly for the MSTN‐F94L variant. We compared prediction accuracies in PL animals using the three datasets from only the PL population, admixed PL and LF (AL) or multibreed analysis using all of the PL, LF and Angus (MB) population according to four‐fold cross‐validation after K‐means clustering. The MSTN‐F94L variant was the most strongly associated with five traits (birth weight, calving ease direct, milk, weaning weight and yield grade) among the 13 measured traits in PL and AL populations. Fitting the MSTN‐F94L variant as a random effect, the genomic prediction accuracies for birth weight increased by 2.7% in PL, by 2.2% in AL and by 3.2% in MB. Prediction accuracies for five traits increased in the MB analysis. Fitting MSTN‐F94L as a fixed effect in PL, AL and MB analyses resulted in increased prediction accuracy in PL for eight traits. Prediction accuracies can be improved by including a causal variant in genomic evaluation compared with simply using whole‐genome SNP markers. Fitting the causal variant as a fixed effect along with markers fitted as random effects resulted in greater prediction accuracies for most traits. Causal variants should be genotyped along with SNP markers.