Intramuscular adipogenesis in cattle: Effects of body fat distribution and macrophage infiltration.

Ectopic fat is defined by the deposition of adipose tissue within non-adipose tissue such as skeletal muscle. Japanese Black cattle (Wagyu) are characterized by the ability to accumulate high amounts of intramuscular adipose tissue. Obese conditions enhance the accumulation of ectopic fat. This review shows the effects of subcutaneous and visceral fat distribution on Wagyu intramuscular adipogenesis. Obese conditions also stimulate the macrophage infiltration into adipose tissues. Adipose tissue macrophages have reported to regulate adipose tissue growth and ectopic fat accumulation in humans and rodents. Wagyu is characterized by the higher capacity for intramuscular adipogenesis than Holsteins. This review discusses the depot-specific effects of macrophage infiltration among subcutaneous, visceral, and intramuscular adipose tissue on intramuscular adipogenesis in Wagyu and Holstein cattle. Recently, metabolome analysis has been used to identify obesity-related biomarkers by comparing the biological samples between lean and obese patients. This review introduces the metabolomic profiles of plasma and intramuscular adipose tissue between Wagyu and Holsteins.

Developmental programming: Adipose depot-specific changes and thermogenic adipocyte distribution in the female sheep.

Prenatal testosterone (T)-treated female sheep exhibit an enhanced inflammatory and oxidative stress state in the visceral adipose tissue (VAT) but not in the subcutaneous (SAT), while surprisingly maintaining insulin sensitivity in both depots. In adult sheep, adipose tissue is predominantly composed of white adipocytes which favor lipid storage. Brown/beige adipocytes that make up the brown adipose tissue (BAT) favor lipid utilization due to thermogenic uncoupled protein 1 expression and are interspersed amidst white adipocytes, more so in epicardiac (ECAT) and perirenal (PRAT) depots. The impact of prenatal T-treatment on ECAT and PRAT depots are unknown. As BAT imparts a metabolically healthy phenotype, the depot-specific impact of prenatal T-treatment on inflammation, oxidative stress, differentiation and insulin sensitivity could be dictated by the distribution of brown adipocytes. This hypothesis was tested by assessing markers of oxidative stress, inflammation, adipocyte differentiation, fibrosis and thermogenesis in adipose depots from control and prenatal T (100  mg T propionate twice a week from days 30-90 of gestation) -treated female sheep at 21 months of age. Our results show prenatal T-treatment induces depot-specific changes in inflammation, oxidative stress state, collagen accumulation, and differentiation with changes being more pronounced in the VAT. Prenatal T-treatment also increased thermogenic gene expression in all depots indicative of increased browning with effects being more prominent in VAT and SAT. Considering that inflammatory and oxidative stress are also elevated, the increased brown adipocyte distribution is likely a compensatory response to maintain insulin sensitivity and function of organs in the proximity of respective depots.

Genome-wide association studies revealed candidate genes for tail fat deposition and body size in the Hulun Buir sheep.

Fat-tailed sheep have a unique characteristic of depositing fat in their tails. In the present study, we conducted genome-wide association studies (GWAS) on traits related to tail fat deposition and body size in the Hulun Buir sheep. A total number of 300 individuals belonging to two fat-tailed lines of the Hulun Buir sheep breed genotyped with the Ovine Infinium HD SNP BeadChip were included in the current study. Two mixed models, one for continuous and one for binary phenotypic traits, were employed to analyse ten traits, that is, body length (BL), body height (BH), chest girth (CG), tail length (TL), tail width (TW), tail circumference (TC), carcass weight (CW), tail fat weight (TF), ratio of CW to TF (RCT) and tail type (TT). We identified 7, 6, 7, 2, 10 and 1 SNPs significantly associated with traits TF, CW, RCT, TW, TT and CG, respectively. Their associated genomic regions harboured 42 positional candidate genes. Out of them, 13 candidate genes including SMURF2, FBF1, DTNBP1, SETD7 and RBM11 have been associated with fat metabolism in sheep. The RBM11 gene has already been identified in a previous study on signatures of selection in this specific sheep population. Two more genes, that is, SMARCA5 and GAB1 were associated with body size in sheep. The present study has identified candidate genes that might be implicated in tail fat deposition and body size in sheep.

Effects of rearing systems on growth performance, carcass yield, meat quality, lymphoid organ indices, and serum biochemistry of Wannan Yellow chickens.

This study was conducted to investigate the effects of free-range system (FRS) and conventional cage-rearing system (CRS) on growth performance, carcass yield, meat quality, lymphoid organ indices, and serum biochemistry of Wannan Yellow chickens. At 56 days of age, a total of 640 male chickens were randomly allocated to FRS and CRS groups, each of which included 4 replicates with 80 chickens in each replicate. The experiment lasted from 56 to 112 days of age. The results showed that CRS chickens exhibited better final body weight, average daily feed intake, average daily gain, and feed conversion ratio, whereas FRS chickens showed better breast and leg yields, shear force, meat color, lower drip loss, and decreased abdominal fat deposition. Moreover, the absolute thymus weight and thymus to body weight ratio of FRS birds were significantly higher than those of CRS birds (p < 0.05). Additionally, FRS chickens had significantly reduced glucose, total protein, triglyceride, and cholesterol contents, but enhanced levels of high-density lipoprotein cholesterol (p < 0.05). In conclusion, the FRS has advantages in breast and leg yields, meat quality, and some serum biochemical parameters of Wannan Yellow chickens, whereas it has negative effects on growth performance.

Apoptosis during the development of the hepatic steatosis in force-fed ducks and cooking yield implications.

Mule ducks were force-fed for 12 d to determine whether or not signs of apoptosis could occur during the development of the hepatic steatosis induced by the huge quantities of corn ingested twice daily by the birds. Presence of apoptosis in hepatocytes was assessed through the measurements of increased activities of capsase-3 +-7, -8, and -9. From d 0 of the force-feeding period until d 8, activities of the different caspases remained at a low level. On the contrary, at d 10 and d 12, activities of all measured caspases dramatically increased, indicating that apoptosis occurred at this stage, which corresponds to the time of accumulation of large quantities of lipids in the hepatic cells.The melting level of the liver issued from force-feeding ("foie gras") during cooking is a point of interest for processors because it could degrade the quality of this delicate dish. In this study, we used the levels of caspases activities to improve the predictability of foie gras cooking, in addition to other parameters usually used, such as its weight or lipid content. From this improvement, we suggest that part of the variability of melting during cooking of fatty livers could reside in more or less intense activity of hepatic proteases.

Correlated responses to selection for intramuscular fat in several muscles in rabbits.

The aim of this study was to evaluate the effect of six generations of selection for intramuscular fat (IMF) in muscle Longissimus thoracis et lumborum (LTL) at 9 wk. in IMF and fatty acid (FA) composition of muscles with diverse metabolic profile in rabbits. Direct response to selection was 0.33 g of IMF/ 100 g of LTL, around 0.4 SD per generation. A positive correlated response was observed in IMF of Biceps femoris, Supraspinatus and Semimembranosus proprius muscles at 9 wk., representing around 0.2 SD of the trait per generation. Selection affected similarly the FA composition of all muscles at 9 wk., high-IMF line showing greater monounsaturated but lower polyunsaturated FA percentages than low-IMF line, whereas no differences were observed for saturated FA. Traits were also measured at 13 wk. and correlated responses were in the same direction. Our results suggest a common genetic background for IMF and FA composition in muscles with different metabolic profile in rabbits.

Eating quality traits of shoulder roast and stir fry cuts outperformed loin and silverside cuts sourced from entire and immunocastrated male pigs.

This study investigated the effects of ageing period (2 or 7days), endpoint temperature (70 or 75°C), cut type (loin (M. longissimus thoracis et lumborum), silverside (M. biceps femoris), blade (M. triceps brachii) and chuck tender (M. supraspinatus)), cooking method (roast and stir fry (all cuts) and steak (loin only)) on eating quality attributes of pork from entire and immunocastrated male pigs. Higher intramuscular fat levels were found in all cuts from immunocastrated males compared with entire males. Of the seven cut type×cooking method combinations evaluated, shoulder cuts had the lowest fail rate (P<0.001) and loin steak and silverside cuts scored lowest (P<0.001) for tenderness, juiciness, overall liking, quality grade and re-purchase intention. Although no differences in sensory scores due to gender were observed, boar taint was identified in 10% of entire males. Minimising adverse risks in eating quality due to boar taint in males remains a key industry issue to ensure consistent delivery of high quality pork.

Differential expression of extracellular matrix and integrin genes in the longissimus thoracis between bulls and steers and their association with intramuscular fat contents.

This study was performed to compare expression of genes for extracellular matrix (ECM) components, ECM degrading factors, and integrin subunits in the longissimus thoracis (LT) between bulls and steers. Steers had lower (P<0.05) ECM component collagen type 1 α1 and collagen type 3 α1 mRNA levels than did bulls, but they had higher (P<0.05) thrombospondin 1 mRNA and protein levels. Steers had higher (P<0.01) matrix metalloproteinase (MMP) 9 mRNA levels than did bulls. Steers had higher (P<0.05) integrin α5 mRNA levels but lower (P<0.05) integrin ß6 mRNA and protein levels; however, expression levels of several other integrin subunits were not different between steers and bulls. MMP9 mRNA levels were positively correlated (P<0.05) with intramuscular fat content in bull group. In conclusion, these results demonstrate that castration has moderate effects on expression of ECM components, ECM degrading factors, and integrin subunit genes in the LT.

Dietary fibre alleviates hepatic fat deposition via inhibiting lipogenic gene expression in meat ducks.

This study investigated the effect of dietary fibre (DF) supplementation on hepatic fat deposition of Cherry Valley meat ducks. A total of 600 1-d-old ducks were randomly allotted to five dietary fibre diets (1.46 (basal diet), 3.09, 4.15, 6.18 and 7.52% (analysed)) for 14 days. Growth performance decreased with increasing DF concentrations, when the DF level more than 6.18% the average daily gain (ADG) and feed conversion ratio (F/G) markedly decreased in meat ducks. Meat ducks supplemented over 4.15% DF had lower percentage of liver reported to live weight, liver lipid contents, hepatic triglyceride and total cholesterol concentrations as well as decreased serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) concentrations at 14 days. The transcription of fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC) and sterol-regulatory element-binding protein-1 (SREBP-1) in liver was significantly reduced by DF, while no any significant difference was found about the effect of DF on hepatic peroxisome proliferator-activated receptor α (PPARα), adipose triglyceride lipase (ATGL), transcription as well as caecal digesta short-chain fatty acids (SCFA). Data suggested that dietary fibre supplementation decreased hepatic lipid deposition and improved characteristics of liver health via inhibiting hepatic FAS, ACC and SREBP-1 expression in meat ducks.

Use of ractopamine during compensatory gain of finishing pigs on carcass and meat performance and quality / Uso de ractopamina durante ganho compensatório de suínos em terminação sobre o desempenho e a qualidade da carcaça e de carne

The objective of this study was to evaluate the effects of compensatory gain associated with the use of 10ppm ractopamine after a period of feed restriction in finishing pigs on performance, carcass and meat quality. Twenty castrated males and 20 females, at 110 days of age and 66.137±6.13kg live weight, were submitted to four treatments using a 2 x 2 factorial design (fed ad libitum or with 20% restriction between 0(21 days of age and fed with or without 10ppm ractopamine for 22(42 days of experimentation), with 10 replicates (animals). There was no interaction between the factors for any of the evaluated parameters. Animals treated with ractopamine presented better weight gain (1.083 versus 1.259kg), feed conversion (2.910 versus 2.577), warm and cold carcass weight (86.08 versus 89.00 and 83.46 versus 87.20kg, respectively), loin depth (63.02 versus 68.40mm), loin eye area (41.43 versus 46.59mm2) and muscle fiber diameter (27.48 versus 35.85µm). Animals submitted to feed restriction followed by ad libitum feed presented compensatory gain without losses to carcass and meat characteristics, but with a reduction in the ethereal extract (2.19 versus 1.64%) and lower water loss due to thawing in the meat (11.35 versus 9.42%). The effects of compensatory gain after food restriction and ractopamine are independent of the parameters evaluated.(AU)

Objetivou-se avaliar os efeitos do ganho compensatório associado ao uso de 10ppm de ractopamina após um período de restrição alimentar, em suínos em terminação, sobre características de desempenho, carcaça e qualidade de carne. Foram utilizados 20 machos castrados e 20 fêmeas, com 110 dias de idade e 66,137±6,13kg de peso vivo, submetidos a quatro tratamentos, fatorial 2 x 2 (alimentação à vontade ou com 20% de restrição entre zero e 21 dias de experimentação; e alimentação à vontade, sem ou com 10ppm de ractopamina, durante 22 a 42 dias de experimentação), com 10 repetições, sendo o animal a repetição. Não houve interação entre os fatores para nenhum dos parâmetros avaliados. Animais tratados com ractopamina apresentaram melhor ganho de peso (1,083 versus 1,259kg), conversão alimentar (2,910 versus 2,577), peso da carcaça quente e fria (86,08 versus 89,00 e 83,46 versus 87,20kg, respectivamente), profundidade do lombo (63,02 versus 68,40mm), área de olho de lombo (41,43 versus 46,59mm2) e diâmetro de fibras musculares (27,48 versus 35,85µm). Animais submetidos à restrição alimentar seguida de arraçoamento ad libitum apresentaram ganho compensatório sem prejuízos às características de carcaça e à carne, mas com redução do extrato etéreo (2,19 versus 1,64%) e menor perda de água por descongelamento na carne (11,35 versus 9,42%) Os efeitos do ganho compensatório após a restrição alimentar e da ractopamina mostram-se independentes sobre os parâmetros avaliados.(AU)

Contemporary group estimates adjusted for climatic effects provide a finer definition of the unknown environmental challenges experienced by growing pigs.

Environmental descriptors derived from mean performances of contemporary groups (CGs) are assumed to capture any known and unknown environmental challenges. The objective of this paper was to obtain a finer definition of the unknown challenges, by adjusting CG estimates for the known climatic effects of monthly maximum air temperature (MaxT), minimum air temperature (MinT) and monthly rainfall (Rain). As the unknown component could include infection challenges, these refined descriptors may help to better model varying responses of sire progeny to environmental infection challenges for the definition of disease resilience. Data were recorded from 1999 to 2013 at a piggery in south-east Queensland, Australia (n = 31,230). Firstly, CG estimates of average daily gain (ADG) and backfat (BF) were adjusted for MaxT, MinT and Rain, which were fitted as splines. In the models used to derive CG estimates for ADG, MaxT and MinT were significant variables. The models that contained these significant climatic variables had CG estimates with a lower variance compared to models without significant climatic variables. Variance component estimates were similar across all models, suggesting that these significant climatic variables accounted for some known environmental variation captured in CG estimates. No climatic variables were significant in the models used to derive the CG estimates for BF. These CG estimates were used to categorize environments. There was no observable sire by environment interaction (Sire×E) for ADG when using the environmental descriptors based on CG estimates on BF. For the environmental descriptors based on CG estimates of ADG, there was significant Sire×E only when MinT was included in the model (p = .01). Therefore, this new definition of the environment, preadjusted by MinT, increased the ability to detect Sire×E. While the unknown challenges captured in refined CG estimates need verification for infection challenges, this may provide a practical approach for the genetic improvement of disease resilience.

Polymorphisms of RDH16 and VEGFR1 influence M. trapezius steatosis in Japanese Black carcass.

The exact cause of steatosis, one of defects in Japanese beef carcasses, has not been elucidated to date, because it is very difficult to diagnose cyclopedically with certain reproducibility due to the bias in the outbreak. Therefore, the objective of this study was to assess the influence of polymorphisms in retinol dehydrogenase 16 (RDH16), myoferlin (MYOF) and vascular endothelial growth factor receptors 1 and 2 (VEGFR1, VEGFR2) on carcass-graded Musculus trapezius steatosis. For logistic regression analysis, 646 carcasses shipped from 29 farms in Miyazaki, Japan, were used. The GG genotype in RDH16 showed significant odds ratios against AA and AG. In VEGFR1, CT had a significant odds ratio against CC. After evaluating for interaction, highly significant odds ratios were observed in the combinations that included the GG risk genotype in RDH16. It is noteworthy that there was no steatosis in the combination GG (RDH16) and CC (VEGFR1). It may be concluded that there is a possibility that steatosis can be suppressed by the CC genotype in VEGFR1. The current study revealed the influence of genetic polymorphisms on M. trapezius steatosis that had not been reported until now, and may help elucidate the cause of steatosis.

Refining genomewide association for growth and fat deposition traits in an F pig population.

The identification of genomic regions that affect additive genetic variation and contain genes involved in controlling growth and fat deposition has enormous impact in the farm animal industry (e.g., carcass merit and meat quality). Therefore, a genomewide association study was implemented in an F pig population using a 60,000 SNP marker panel for traits related to growth and fat deposition. Estimated genomic EBV were linearly transformed to calculate SNP effects and to identify genomic positions possibly associated with the genetic variability of each trait. Genomic segments were then defined considering the markers included in a region 1 Mb up- and downstream from the SNP with the smallest -value and a false discovery rate < 0.05 for each trait. The significance for each 2-Mb segment was tested using the Bonferroni correction. Significant SNP were detected on SSC2, SSC3, SSC5, and SSC6, but 2-Mb segment significant effects were observed on SSC3 for weight at birth (wt_birth) and on SSC6 for 10th-rib backfat and last-rib backfat measured by ultrasound at different ages. Furthermore, a 6-Mb segment on SSC6 was also considered because the 2-Mb segments for 10 different fat deposition traits were overlapped. Although the segment effects for each trait remain significant, the proportion of additive variance explained by this larger segment was slightly smaller in some traits. In general, the results confirm the presence of genetic variability for wt_birth on SSC3 (18.0-20.2 Mb) and for fat deposition traits on SSC6 (133.8-136.0 Mb). Within these regions, fibrosin () and myosin light chain, phosphorylatable, fast skeletal muscle () genes could be considered as candidates for the wt_birth signal on SSC3, and the SERPINE1 mRNAbinding protein 1 gene () may be a candidate for the fat deposition trait signals on SSC6.

Evaluation of sire by environment interactions for growth rate and backfat depth using reaction norm models in pigs.

Reaction norm models for sires were used to evaluate genotype by environment interactions for lifetime average daily gain (ADG) and backfat depth (BF) in pigs recorded at 143 days. Data for ADG and BF were available for 265 103 pigs recorded in Australia between 2000 and 2010 in nine herds. The full data set and two subsets based on minimum numbers of progeny per sire of 50 and 100 were analysed. The environmental descriptor was quantified as least square means of herd-by-birth month (HBM) contemporary groups which varied from 540 to 738 g/day for ADG and from 8.2 to 13.8 mm for BF. Several models were evaluated for estimation of variance components in terms of predictive ability for sire intercepts and slopes. The accuracy of genetic parameter estimates was improved by increasing family size, fitting models with a fixed regression coefficient on the environmental descriptor instead of fixed HBM effects and heterogeneous residual variances. Significant sire by environment interactions were found for ADG but not for BF. Heritability estimates for ADG ranged from approximately 0.21 in average environments to approximately 0.30 in the most unfavourable environments. Estimates of sire intercepts and slopes varied by 98.5 g/day and 0.253 g/day per g/day for ADG, respectively. Lowly negative correlations between sire intercept and slope do not support the hypothesis that high growth is associated with larger environmental sensitivity.

Selection against abdominal fat percentage may increase intramuscular fat content in broilers.

Excessive abdominal fat content (AFC) has negative impacts on feed efficiency and carcass quality. Unlike AFC, intramuscular fat content (IMFC) could be a favourable trait, which has a positive impact on meat quality. To meet consumers' needs, a long-term goal of broiler breeders is to decrease AFC and improve the IMFC simultaneously. The current study was designed to investigate the relationship between AFC and IMFC and to compare IMFC, including the pectoral major muscle fat content (PIMFC) and intramuscular fat content of leg muscle (LIMFC), between two broiler lines divergently selected for abdominal fat percentage over 17 generations. The results showed that there was a significant difference in PIMFC and LIMFC between the two lines in all five generation populations used. The birds in the lean line had significantly lower AFC but higher PIMFC and LIMFC than the birds in the fat line. We also detected differences in the liver fat content (LFC) between the two lines and the results showed that birds in the fat line had significant higher LFC than birds in the lean line. Our results indicated that a desirable broiler line with higher IMFC but lower AFC could be obtained by genetic selection.

Divergent selection on intramuscular fat in rabbits: Responses to selection and genetic parameters.

A divergent selection experiment on intramuscular fat (IMF) was performed in rabbits. The aim of this study is to estimate the response to selection, the correlated responses in carcass and meat quality traits, and their genetic parameters. Selection criterion was the averaged phenotypic value of IMF measured at 9 wk of age in 2 full-sibs of the candidate. Traits considered were IMF, BW, chilled carcass weight, reference carcass weight, scapular and perirenal fat weights, carcass and meat color, pH, protein and fatty acid composition of meat. Total direct response to selection for IMF was 2.6 phenotypic SD of the trait, around 5% of the mean (1.09 g/100 g) per generation, with both lines following a symmetrical trend. Heritability of IMF was high (0.54), and in general, all traits related to carcass fat depots and IMF fatty acid composition showed high heritabilities (dissectible fat of the carcass, 0.70; MUFA percentage, 0.61; PUFA percentage, 0.45; and PUFA:SFA ratio, 0.42), except SFA percentage (0.09). The other carcass and meat quality traits showed moderate to low heritabilities. Intramuscular fat and dissectible fat percentage showed a low genetic correlation (0.34). Intramuscular fat was positively correlated with MUFA percentage (0.95) and negatively correlated with PUFA percentage (-0.89) and PUFA:SFA ratio (-0.98), corroborated with high correlated responses to selection. The rest of the traits did not show any substantial correlated response except protein content, which was greater in the high-IMF line than in the low-IMF line.

Signatures of selection identify loci associated with fat tail in sheep.

Identification of genomic regions that have been targets of selection for phenotypic traits is one of the most challenging applications of dense marker panels in animal genetics. In this study, a genomewide scan using approximately 50,000 SNP was performed in an attempt to identify genomic regions associated with fat deposition in sheep, the importance of this not only being limited to livestock facing future climate changes but also for elucidating the physiology of lipid metabolism. The genotyping results obtained with the Ovine SNP50K BeadChip in 2 fat tail breeds were compared with those obtained in 13 thin tail breeds. Direct sequencing of the annotated genes located in proximity to the markers with opposite allele frequency in thin tail vs. fat tail sheep gave additional SNP of interest. To further confirm the results of the genomewide scan, we genotyped the SNP within these genes in the 2 groups of sheep. A missense mutation in the gene, with different allele frequency in the 2 groups, was detected. The results indicated and as the most probable genes involved in the fat tail phenotype.

Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations.

Intramuscular fat (IMF) content is an important trait affecting the quality of pork. Two Duroc populations, one under positive selection for IMF and the other selected for decreased backfat but under stabilizing selection for IMF, were used to identify signatures of selection associated with IMF using 60,000 single-nucleotide polymorphism data. The effects of selection were analyzed between 2 lines or groups representing selected and control animals within each population using a discriminant analysis of principal components and Wright's fixation index (FST). Moreover, extended haplotype homozygosity-based approaches were used to examine the changes in haplotype frequency due to recent selection. Each statistical method identified 10­20 selection signatures. A few haplotype-based signatures of selection agreed with results from a genome-wide association study (GWAS), while FST measures showed a better agreement with GWAS results. Agreement of marker-trait associations and signatures of selection was limited, and further examination will be necessary to understand the effect of selection on IMF and why some regions identified by GWAS did not appear to respond to the selection practiced. The genes in 21 consensus selection signatures were examined. Several genes with an effect on overall fatness were identified, but further research is needed to assess whether or not some of them could have a specific effect on IMF.

A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle.

The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.

Genome-wide detection of signatures of selection in Korean Hanwoo cattle.

The Korean Hanwoo cattle have been intensively selected for production traits, especially high intramuscular fat content. It is believed that ancient crossings between different breeds contributed to forming the Hanwoo, but little is known about the genomic differences and similarities between other cattle breeds and the Hanwoo. In this work, cattle breeds were grouped by origin into four types and used for comparisons: the Europeans (represented by six breeds), zebu (Nelore), African taurine (N'Dama) and Hanwoo. All animals had genotypes for around 680 000 SNPs after quality control of genotypes. Average heterozygosity was lower in Nelore and N'Dama (0.22 and 0.21 respectively) than in Europeans (0.26-0.31, with Shorthorn as outlier at 0.24) and Hanwoo (0.29). Pairwise FST analyses demonstrated that Hanwoo are more related to European cattle than to Nelore, with N'Dama in an intermediate position. This finding was corroborated by principal components and unsupervised hierarchical clustering. Using genome-wide smoothed FST , 55 genomic regions potentially under positive selection in Hanwoo were identified. Among these, 29 were regions also detected in previous studies. Twenty-four regions were exclusive to Hanwoo, and a number of other regions were shared with one or two of the other groups. These regions overlap a number of genes that are related to immune, reproduction and fatty acid metabolism pathways. Further analyses are needed to better characterize the ancestry of the Hanwoo cattle and to define the genes responsible to the identified selection peaks.