Inference of population structure of purebred dairy and beef cattle using high-density genotype data

Information on the genetic diversity and population structure of cattle breeds is useful when deciding the most optimal, for example, crossbreeding strategies to improve phenotypic performance by exploiting heterosis. The present study investigated the genetic diversity and population structure of the most prominent dairy and beef breeds used in Ireland. Illumina high-density genotypes (777 962 single nucleotide polymorphisms; SNPs) were available on 4623 purebred bulls from nine breeds; Angus (n=430), Belgian Blue (n=298), Charolais (n=893), Hereford (n=327), Holstein-Friesian (n=1261), Jersey (n=75), Limousin (n=943), Montbéliarde (n=33) and Simmental (n=363). Principal component analysis revealed that Angus, Hereford, and Jersey formed non-overlapping clusters, representing distinct populations. In contrast, overlapping clusters suggested geographical proximity of origin and genetic similarity between Limousin, Simmental and Montbéliarde and to a lesser extent between Holstein, Friesian and Belgian Blue. The observed SNP heterozygosity averaged across all loci was 0.379. The Belgian Blue had the greatest mean observed heterozygosity (H_O=0.389) among individuals within breed while the Holstein-Friesian and Jersey populations had the lowest mean heterozygosity (H_O=0.370 and 0.376, respectively). The correlation between the genomic-based and pedigree-based inbreeding coefficients was weak (r=0.171; P<0.001). Mean genomic inbreeding estimates were greatest for Jersey (0.173) and least for Hereford (0.051). The pair-wise breed fixation index (F_st) ranged from 0.049 (Limousin and Charolais) to 0.165 (Hereford and Jersey). In conclusion, substantial genetic variation exists among breeds commercially used in Ireland. Thus custom-mating strategies would be successful in maximising the exploitation of heterosis in crossbreeding strategies.     

Breed variation and genetic parameters for growth and body development in diverse beef cattle genotypes

Conformation scores can account for more than 20% of cattle price variation at Australian livestock sales. However, there are limited available references which define genetic factors relating objective live developmental traits to carcass composition. Weaning and post-weaning weight, height, length, girth, muscle (ratio of stifle to hip width) and fat depth of 1202 progeny from mature Hereford cows (637) mated to seven sire breeds (Jersey, Wagyu, Angus, Hereford, South Devon, Limousin and Belgian Blue) were examined for growth and development across ages. Crossbred Wagyu and Jersey were both lighter in weight and smaller in size (height, length and girth) than purebred Hereford and crossbred Angus, South Devon, Limousin and Belgian Blue. Within the five larger crossbreds, there were significant changes in relative weight from weaning to 600 days. Sire breeds differed in fat depth, with Angus being the fattest (9% on average fatter than Hereford and Wagyu), and Jersey 5% less fat than Hereford, followed by South Devon and Limousin (19% lower than Hereford) and Belgian Blue (39% lower than Hereford). Direct heritability ranged from 19 to 42% and was higher than the proportion of total phenotypic variance accounted for by maternal effects (which ranged from 0 to 17%) for most body measurement traits except for weight (38 v. 18%) and girth (36 v. 9%) traits at weaning, an indication of maternal effect on some body conformation traits at early ages. Muscularity (19 to 44%) and fat depth (26 to 43%) were moderately to highly heritable across ages. There were large differences for growth and the objective measures of body development between crossbreds with a degree of overlap among the progeny of the seven sire breeds. The variation between genetic (positive) and environmental (negative) correlations for dry versus wet season average daily gains in weight and fat, suggested the potential use of live-animal conformation traits for within breed selection of genetically superior animal in these traits across seasons.     

Selection for components related to body composition in mice: direct responses

Summary Replicated within full-sib family single-trait selection was conducted for 10 generations in mice for (1) high or low 12-week epididymal fat pad percentage (100 x epididymal fat pad weight/body weight) or (2) high or low 12-week hind carcass percentage (100 x hind carcass weight/body weight). Pooled realized heritabilities based on high, low and divergent selection were 0.66±0.09, 0.65±0.13 and 0.66±0.05 for epididymal fat pad percentage and 0.48±0.08, 0.33±0.08 and 0.40±0.04 for hind carcass percentage. The pooled realized genetic correlation (r_{G R}) between epididymal fat pad percentage and hind carcass percentage based on divergence was –0.67±0.04. Other estimates of (r_{G R}) were: epididymal fat pad percentage with body weight (0.57±0.05); epididymal fat pad percentage with epididymal fat pad weight (1.17±0.05); hind carcass percentage with body weight (–0.61±0.09); hind carcass percentage with hind carcass weight (–0.05±0.11). Indirect measures of fat and lean tissue percentages were highly heritable, and (r_{G R}) between them would be desirable from the standpoint of analogous types of traits in livestock. In the same context, undesirable (r_{G R})'s were found between epididymal fat pad percentage and body weight and between hind carcass percentage and body weight.Paper No. 10957 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, North Carolina 27695-7601, USA. The use of trade names in this publication does not imply endorsement by the North Carolina Agricultural Research Service of the products named, nor criticism of similar ones not mentioned     

Prediction of dry-cured ham weight loss and prospects of use in a pig breeding program

Large ham weight losses (WL) in dry-curing are undesired as they lead to a loss of marketable product and penalise the quality of the dry-cured ham. The availability of early predictions of WL may ease the adaptation of the dry-curing process to the characteristics of the thighs and increase the effectiveness of selective breeding in enhancing WL. Aims of this study were (i) to develop Bayesian and Random Forests (RFs) regression models for the prediction of ham WL during dry-curing using on-site infrared spectra of raw ham subcutaneous fat, carcass and raw ham traits as predictors and (ii) to estimate genetic parameters for WL and their predictions (P-WL). Visible-near infrared spectra were collected on the transversal section of the subcutaneous fat of raw hams. Carcass traits were carcass weight, carcass backfat depth, lean meat content and weight of raw hams. Raw ham traits included measures of ham subcutaneous fat depth and linear scores for round shape, subcutaneous fat thickness and marbling of the visible muscles of the thigh. Measures of WL were available for 1672 hams. The best prediction accuracies were those of a Bayesian regression model including the average spectrum, carcass and raw ham traits, with R² values in validation of 0.46, 0.55 and 0.62, for WL at end of salting (23 days), resting (90 days) and curing (12 months), respectively. When WL at salting was used as an additional predictor of total WL, the R² in validation was 0.67. Bayesian regressions were more accurate than RFs models in predicting all the investigated traits. Restricted maximum likelihood (REML) estimates of genetic parameters for WL and P-WL at the end of curing were estimated through a bivariate animal model including 1672 measures of WL and 8819 P-WL records. Results evidenced that the traits are heritable (h² ± SE was 0.27 ± 0.04 for WL and 0.39 ± 0.04 for P-WL), and the additive genetic correlation is positive and high (r_a = 0.88 ± 0.03). Prediction accuracy of ham WL is high enough to envisage a future use of prediction models in identifying batches of hams requiring an adaptation of the processing conditions to optimise results of the manufacturing process. The positive and high genetic correlation detected between WL and P-WL at the end of dry-curing, as well as the estimated heritability for P-WL, suggests that P-WL can be successfully used as an indicator trait of the measured WL in pig breeding programs.     

Selection for components related to body composition in mice: correlated responses

Summary Correlated responses were estimated in each of two replicate lines of mice selected within full-sib families for high (HF) or low (LF) 12-week epididymal fat pad weight as a percentage of body weight (epididymal fat pad percentage), or high (HL) or low (LL) 12-week hind carcass weight as a percentage of body weight (hind carcass percentage). Two replicate control lines (RC) were maintained. Correlated traits were measured in each of the 10 generations of selection. Realized (r_{G R}) and offspring-sire genetic correlations generally were in agreement. In HF and LF, 3–6 week postweaning gain (r_{G R} = 0.36±0.04) and feed intake (r_{G R} = 0.50±0.13) had positive correlated responses, but feed efficiency and feed intake/metabolic body size did not change. Positive correlated responses were found for subcutaneous fat pad percentage, body weight-adjusted subcutaneous fat pad weight and fat percentage in the hind carcass (r_{G R}'s were 1.04±0.13, 0.93±0.13 and 0.90±0.08). In the hind carcass, fat-free dry (protein + ash) percentage showed a small negative correlated response, and fat-free dry weight did not change. In HL and LL, the correlated responses for the above traits were generally opposite to those observed in HF and LF. Litter size, percentage of infertile matings, and preweaning mortality showed no consistent correlated responses in any of the lines, but an index of fitness combining the three traits showed a decrease in all four selection treatments.Paper no. 11057 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, 27695-7601. The use of trade names in this publication does not imply endorsement by the North Carolina Agricultural Research Service of the products named, nor criticisms of similar ones not mentioned     

Accuracies of genomically estimated breeding values from pure-breed and across-breed predictions in Australian beef cattle

Background

The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australian Beef Cooperative Research Center (Beef CRC) investigated these issues by deriving genomic prediction equations (PE) from a training set of animals that covers a range of breeds and crosses including Angus, Murray Grey, Shorthorn, Hereford, Brahman, Belmont Red, Santa Gertrudis and Tropical Composite. This paper presents accuracies of genomically estimated breeding values (GEBV) that were calculated from these PE in the commercial pure-breed beef cattle seed stock sector.

Methods

PE derived by the Beef CRC from multi-breed and pure-breed training populations were applied to genotyped Angus, Limousin and Brahman sires and young animals, but with no pure-breed Limousin in the training population. The accuracy of the resulting GEBV was assessed by their genetic correlation to their phenotypic target trait in a bi-variate REML approach that models GEBV as trait observations.

Results

Accuracies of most GEBV for Angus and Brahman were between 0.1 and 0.4, with accuracies for abattoir carcass traits generally greater than for live animal body composition traits and reproduction traits. Estimated accuracies greater than 0.5 were only observed for Brahman abattoir carcass traits and for Angus carcass rib fat. Averaged across traits within breeds, accuracies of GEBV were highest when PE from the pooled across-breed training population were used. However, for the Angus and Brahman breeds the difference in accuracy from using pure-breed PE was small. For the Limousin breed no reasonable results could be achieved for any trait.

Conclusion

Although accuracies were generally low compared to published accuracies estimated within breeds, they are in line with those derived in other multi-breed populations. Thus PE developed by the Beef CRC can contribute to the implementation of genomic selection in Australian beef cattle breeding.     

Visceral organ weights,digestion and carcass characteristics of beef bulls differing in residual feed intake offered a high concentrate diet

This study examined the relationship of residual feed intake (RFI) with digestion, body composition, carcass traits and visceral organ weights in beef bulls offered a high concentrate diet. Individual dry matter (DM) intake (DMI) and growth were measured in a total of 67 Simmental bulls (mean initial BW 431 kg (s.d.=63.7)) over 3 years. Bulls were offered concentrates (860 g/kg rolled barley, 60 g/kg soya bean meal, 60 g/kg molasses and 20 g/kg minerals per vitamins) ad libitum plus 0.8 kg grass silage DM daily for 105 days pre-slaughter. Ultrasonic muscle and fat depth, body condition score (BCS), muscularity score, skeletal measurements, blood metabolites, rumen fermentation and total tract digestibility (indigestible marker) were determined. After slaughter, carcasses and perinephric and retroperitoneal fat were weighed, carcasses were graded for conformation and fat score and weight of non-carcass organs, liver, heart, kidneys, lungs, gall bladder, spleen, reticulo-rumen full and empty and intestines full, were determined. The residuals of the regression of DMI on average daily gain (ADG), mid-test metabolic BW (BW^0.75) and the fixed effect of year, using all animals, were used to compute individual RFI coefficients. Animals were ranked on RFI and assigned to high (inefficient), medium or low groupings. Overall mean ADG and daily DMI were 1.6 kg (s.d.=0.36) and 9.4 kg (s.d.=1.16), respectively. High RFI bulls consumed 7 and 14% more DM than medium and low RFI bulls, respectively (P<0.001). No differences between high and low RFI bulls were detected (P>0.05) for ADG, BW, BCS, skeletal measurements, muscularity scores, ultrasonic measurements, carcass weight, perinephric and retroperitoneal fat weight, kill-out proportion and carcass conformation and fat score. However, regression analysis indicated that a 1 kg DM/day increase in RFI was associated with a decrease in kill-out proportion of 20 g/kg (P<0.05) and a decrease in carcass conformation of 0.74 units (P<0.05). Weight of non-carcass organs did not differ (P>0.05) between RFI groups except for the empty weight of reticulo-rumen, which was 8% lighter (P=0.05) in low RFI compared with high RFI bulls. Regression analysis indicated that a 1 kg DM/day increase in RFI was associated with a 1 kg increase in reticulo-rumen empty weight (P<0.05). Of the visceral organs measured, the reticulo-rumen may be a biologically significant contributory factor to variation in RFI in beef bulls finished on a high concentrate diet.     

Prediction model of a joint analysis of beef growth and carcass quality traits

A joint growth-carcass analysis was conducted to develop equations for predicting carcass quality traits associated with variation in growth path of crossbred cattle. During a four-year period (1994-1997) of the Australian "Southern Crossbreeding Project", mature Hereford cows (r = 581) were mated to 97 sires of Jersey, Wagyu, Angus, Hereford, South Devon, Limousin, and Belgian Blue breeds, resulting in 1141 calves. Data included body weight measurements of steers and heifers from birth until slaughter and four carcass quality traits: hot standard carcass weight, rump fat depth, rib eye muscle area, and intramuscular fat content. The model provides nine outputs: median and mean of carcass quality traits, predicted means, and lower and upper confidence intervals, as well as predicted intervals of carcass quality traits (95%) and economic values for domestic market and export markets. Input to the model consists of sex, sire breeds, age (in days)-weight (kg) pairs and slaughter age (500 days for heifer and 700 days for steers). The prediction model is able to accommodate different sexes across seven sire breeds and various management groups at any slaughter age. Its strength lies in its simplicity and flexibility, desirable to accommodate producers with different management schemes. In general, fat depth and intramuscular fat were found to be more affected by differences in growth rate than hot carcass weight and eye muscle area. Also, export market value was more sensitive to growth rate modifications than domestic market value. This model provides a tool by which the producer can estimate the impact of management decisions.     

Proliferation Rates of Bovine Primary Muscle Cells Relate to Liveweight and Carcase Weight in Cattle

Muscling in cattle is largely influenced by genetic background, ultimately affecting beef yield and is of major interest to the beef industry. This investigation aimed to determine whether primary skeletal muscle cells isolated from different breeds of cattle with a varying genetic potential for muscling differ in their myogenic proliferative capacity. Primary skeletal muscle cells were isolated and cultured from the Longissimus muscle (LM) of 6 month old Angus, Hereford and Wagyu X Angus cattle. Cells were assessed for rate of proliferation and gene expression of PAX7, MYOD, MYF5, and MYOG. Proliferation rates were found to differ between breeds of cattle whereby myoblasts from Angus cattle were found to proliferate at a greater rate than those of Hereford and Wagyu X Angus during early stages of growth (5–20 hours in culture) in vitro (P < 0.05). The proliferation rates of myoblasts during early stages of culture in vitro were also found to be positively related to the liveweight and carcase weight of cattle (P < 0.05). Gene expression of MYF5 was also found to be significantly down-regulated in WagyuX compared with Angus cattle (P < 0.05). These findings suggest that early events during myogenesis are important for determining liveweight and caracase weights in cattle.     

Breed-type effects on fertility traits of young bulls

Measures of fertility in young beef bulls (N=76) representative of divergent breeds and F₁ crosses were evaluated. Breed-types were straightbred Hereford and Red Poll, Hereford × Red Poll reciprocal crosses, Angus × Hereford, Angus × Charolais, Brahman × Hereford and Brahman × Angus.There was evidence of significant breed-type variation in scrotal circumference and total testicle weight, although differences were less pronounced when animal weight was taken into account. Scrotal circumference in Brahman × Hereford bulls was less (P<.05) than straightbred Hereford, Red Poll × Hereford and Angus × Hereford crosses at 8 months of age. However, at 13 months there was no difference in scrotal circumference measurements of Brahman × Hereford, Red Poll × Hereford and Angus × Hereford crosses, and all three crosses exceeded (P<.05) straightbred Herefords. Breed-type differences in semen score and presence of normal, mature sperm in the seminiferous tubules at 13 months of age approached significance at the .10 probability level. Heterosis effects on bull fertility characteristics were insignificant when body weight was included as a covariate in the analyses.     

Carcass traits of young bulls in dual-purpose cattle: genetic parameters and genetic correlations with veal calf,type and production traits

The profitability of dual-purpose breeding farms can be increased through genetic improvement of carcass traits. To develop a genetic evaluation of carcass traits of young bulls, breed-specific genetic parameters were estimated in three French dual-purpose breeds. Genetic correlations between these traits and veal calf, type and milk production traits were also estimated. Slaughter performances of 156 226 Montbeliarde, 160 361 Normande and 8691 Simmental young bulls were analyzed with a multitrait animal model. In the three breeds, heritabilities were moderate for carcass weight (0.12 to 0.19±0.01 to 0.04) and carcass conformation (0.21 to 0.26±0.01 to 0.04) and slightly lower for age at slaughter (0.08 to 0.17±0.01 to 0.03). For all three breeds, genetic correlations between carcass weight and carcass conformation were moderate and favorable (0.30 to 0.52±0.03 to 0.13). They were strong and favorable (−0.49 to −0.71±0.05 to 0.15) between carcass weight and age at slaughter. Between age at slaughter and carcass conformation, they were low and unfavorable to moderate and favorable (−0.25 to 0.10±0.06 to 0.18). Heavier young bulls tend to be better conformed and slaughtered earlier. Genetic correlations between corresponding young bulls and veal production traits were moderate and favorable (0.32 to 0.70±0.03 to 0.09), implying that selecting sires for veal calf production leads to select sires producing better young bulls. Genetic correlations between young bull carcass weight and cow size were moderately favorable (0.22 to 0.45±0.04 to 0.10). Young bull carcass conformation had moderate and favorable genetic correlations (0.11 to 0.24±0.04 to 0.10) with cow width but moderate and unfavorable genetic correlations (−0.21 to −0.36±0.03 to 0.08) with cow height. Taller cows tended to produce heavier young bulls and thinner cows to produce less conformed ones. Genetic correlations between carcass traits of young bulls and cow muscularity traits were low to moderate and favorable. Finally, genetic correlations between carcass traits of young bulls and milk production traits were low and unfavorable to moderate and favorable. These results indicate the existence for all three breeds of genetic variability for the genetic improvement of carcass traits of young bulls as well as favorable genetic correlations for their simultaneous selection and no strong unfavorable correlation with milk production traits.     

A potential association between the BM 1500 microsatellite and fat deposition in beef cattle

The obese gene was hypothesized as a candidate gene for fat characteristics in beef cattle. The BM 1500 microsatellite, near the obese gene, was characterized in 158 purebred beef bulls for which carcass trait information was available. Four breeds were included in the analyses—Angus, Charolais, Hereford, and Simmental. Four alleles were found. Lengths were approximately 138, 147, 149, and 140 bp with genotypic frequencies of 0.47, 0.44, 0.09, and 0.003 respectively. The carcass traits %rib fat, %rib lean, average fat, and grade fat were found to be significantly associated with the different alleles. The presence of the 138-bp allele in the genotype of an animal is correlated with higher levels of fat, whereas the 147-bp allele has the opposite effect. The 149-bp allele was found in low numbers, and a homozygote was never identified. Hereford and Angus bulls had the greatest frequencies of 138-bp alleles (Hereford = 0.57, Angus = 0.59), while Charolais and Simmental had a greater proportion of 147-bp alleles (Charolais = 0.54, Simmental = 0.58). This information may aid cattle producers in selecting cattle for markets that differ in the amount of fat required. Received: 27 October 1997 / Accepted: 23 January 1998     

Genetic relationships between carcass cut weights predicted from video image analysis and other performance traits in cattle

The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min r_g(MVC) = 0.35; max r_g(VHVC) = 0.69), and animal price at both weaning (min r_g(MVC) = 0.37; max r_g(VHVC) = 0.66) and post weaning (min r_g(MVC) = 0.50; max r_g(VHVC) = 0.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min r_g(HVC) = 0.34; max r_g(LVC) = 0.45), weanling quality (min r_g(MVC) = 0.12; max r_g(VHVC) = 0.49), linear scores for muscularity at both weaning (hindquarter development: min r_g(MVC) = −0.06; max r_g(VHVC) = 0.46), post weaning (hindquarter development: min r_g(MVC) = 0.23; max r_g(VHVC) = 0.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction prices and weanling quality. Total bone weight was, however, positively correlated with skeletal scores at weaning and post weaning. These results indicate that some traits collected early in life are moderate-to-strongly correlated with carcass cut weights predicted from VIA technology. This information can be used to improve the accuracy of selection for carcass cut weights in national genetic evaluations.     

Joint analysis of beef growth and carcass quality traits through calculation of co-variance components and correlations

A joint growth-carcass model using random regression was used to estimate the (co)variance components of beef cattle body weights and carcass quality traits and correlations between them. During a four-year period (1994-1997) of the Australian "southern crossbreeding project", mature Hereford cows (N = 581) were mated to 97 sires of Jersey, Wagyu, Angus, Hereford, South Devon, Limousin, and Belgian Blue breeds, resulting in 1141 calves. Data included 13 (for steers) and 8 (for heifers) body weight measurements approximately every 50 days from birth until slaughter and four carcass quality traits: hot standard carcass weight, rump fat depth, rib eye muscle area, and intramuscular fat content. The mixed model included fixed effects of sex, sire breed, age (linear, quadratic and cubic), and their interactions between sex and sire breed with age. Random effects were sire, dam, management (birth location, year, post-weaning groups), and permanent environmental effects, and their interactions with linear, quadratic and cubic growth, when possible. Phenotypic, sire and dam correlations between body weights and hot standard carcass weight and rib eye muscle area were positive and moderate to high from birth to feedlot period. Management variation accounted for the largest proportion of total variation in both growth and carcass traits. Management correlations between carcass traits were high, except between rump fat depth and intramuscular fat (r = 0.26). Management correlations between body weight and carcass traits during the pre-weaning period were positive except for intramuscular fat. The correlations were low from birth to weaning, then increased dramatically and were high during the feedlot period.     

Effects of genetic merit for carcass weight, breed type and slaughter weight on performance and carcass traits of beef × dairy steers

Crossbreeding of Holstein-Friesian dairy cows with both early maturing (e.g. Aberdeen Angus (AA)) and late maturing (e.g. Belgian Blue (BB)) beef breeds is commonly practised. In Ireland, genetic merit for growth rate of beef sires is expressed as expected progeny difference for carcass weight (EPD(CWT)). The objective of this study was to compare the progeny of Holstein-Friesian cows, sired by AA and BB bulls of low (L) and high (H) EPD(CWT) for performance and carcass traits. A total of 118 spring-born male progeny from 20 (9 AA and 11 BB) sires (8 L and 12 H) were managed together from shortly after birth to about 19 months of age. They were then assigned to one of two mean slaughter weights (560 kg (light) or 620 kg (heavy)). Following slaughter, carcasses were graded for conformation class and fat class, the 6th to 10th ribs joint was dissected as an indicator of carcass composition, and samples of subcutaneous fat and musculus longissimus were subjected to Hunterlab colour measurements. A sample of m. longissimus was also chemically analysed. Slaughter and carcass weights per day of age for AAL, AAH, BBL and BBH were 747, 789, 790 and 805 (s.e. 10.5) g, and 385, 411, 427 and 443 (s.e. 4.4) g, respectively. Corresponding carcass weight, kill-out proportion, carcass conformation class (scale 1 to 5) and carcass fat class (scale 1 to 5) values were 289, 312, 320 and 333 (s.e. 4.0) kg, 516, 522, 542 and 553 (s.e. 3.5) g/kg, 2.5, 2.4, 3.0 and 3.1 (s.e. 0.10), and 3.4, 3.5, 2.9 and 2.8 (s.e. 0.11). There were few breed type × genetic merit interactions. Delaying slaughter date increased slaughter weight, carcass weight and all measures of fatness. It also reduced the proportion of carcass weight in the hind quarter and the proportions of bone and muscle in the ribs joint. None of these effects accompanied the increase in carcass weight due to higher EPD(CWT). It is concluded that BB have superior production traits to AA. Selection of sires for higher EPD(CWT) increases growth rate, kill-out proportion and carcass weight of progeny with little effect on carcass or muscle traits. The extra carcass weight due to higher EPD(CWT) is more valuable commercially than a comparable carcass weight increment from a delay in slaughter date because it comprises a higher proportion of muscle.     

Genetic diversity and structure of natural Pinus tabulaeformis populations in North China using amplified fragment length polymorphism (AFLP)

Chinese pine (Pinus tabulaeformis carr.), endemic to China, is a conifer species with extensive and fragmented distribution in North China. In this study, the genetic diversity and structure of 20 natural populations of this species were investigated using amplified fragment length polymorphism (AFLP) markers. A total of 445 fragments were revealed with 8 pairs of primers, 379 (85.17%) of which were polymorphic. A moderate level of genetic diversity was detected at the species level (Shannon's information index I = 0.356, Nei's gene diversity H_E = 0.271) and at the population level (I = 0.219, H_E = 0.206). Most of genetic variation was within populations while a considerable level of genetic differentiation was detected (G_ST = 0.352, Ф_ST = 0.304). The high differentiation could be attributed to the complex and fragmented habitats, and a limited gene flow among populations (N_m = 0.572). The Mantel test indicated that there was significant correlation (r = 0.455, P < 0.001) between Nei's genetic distance and geographical distance among all the populations. The results suggested that proper countermeasures should be taken to prevent the habitat further deterioration and maintain the genetic diversity of this species.     

Genome-wide analyses reveal population structure and identify candidate genes associated with tail fatness in local sheep from a semi-arid area

Under a climate change perspective, the genetic make-up of local livestock breeds showing adaptive traits should be explored and preserved as a priority. We used genotype data from the ovine 50 k Illumina BeadChip for assessing breed autozygosity based on runs of homozygosity (ROH) and fine-scale genetic structure and for detecting genomic regions under selection in 63 Tunisian sheep samples. The average genomic inbreeding coefficients based on ROH were estimated at 0.017, 0.021, and 0.024 for Barbarine (BAR, n = 26), Noire de Thibar (NDT, n = 23), and Queue fine de l'Ouest (QFO, n = 14) breeds, respectively. The genomic relationships among individuals based on identity by state (IBS) distance matrix highlighted a recent introgression of QFO into the BAR and a genetic differentiation of NDT samples, possibly explained by past introgression of European gene pools. Genome-wide scan for ROH across breeds and within the BAR sample set identified an outstanding signal on chromosome 13 (46.58–49.61 Mbp). These results were confirmed using F_ST index, differentiating fat vs. thin-tailed individuals. Candidate genes under selection pressure (CDS2, PROKR1, and BMP2) were associated to lipid storage and probably preferentially selected in fat-tailed BAR animals. Our findings suggest paying more attention to preserve the genetic integrity and adaptive alleles of local sheep breeds.     

Ultra-low-density genotype panels for breed assignment of Angus and Hereford cattle

Angus and Hereford beef is marketed internationally for apparent superior meat quality attributes; DNA-based breed authenticity could be a useful instrument to ensure consumer confidence on premium meat products. The objective of this study was to develop an ultra-low-density genotype panel to accurately quantify the Angus and Hereford breed proportion in biological samples. Medium-density genotypes (13 306 single nucleotide polymorphisms (SNPs)) were available on 54 703 commercial and 4042 purebred animals. The breed proportion of the commercial animals was generated from the medium-density genotypes and this estimate was regarded as the gold-standard breed composition. Ten genotype panels (100 to 1000 SNPs) were developed from the medium-density genotypes; five methods were used to identify the most informative SNPs and these included the Delta statistic, the fixation (F_st) statistic and an index of both. Breed assignment analyses were undertaken for each breed, panel density and SNP selection method separately with a programme to infer population structure using the entire 13 306 SNP panel (representing the gold-standard measure). Breed assignment was undertaken for all commercial animals (n=54 703), animals deemed to contain some proportion of Angus based on pedigree (n=5740) and animals deemed to contain some proportion of Hereford based on pedigree (n=5187). The predicted breed proportion of all animals from the lower density panels was then compared with the gold-standard breed prediction. Panel density, SNP selection method and breed all had a significant effect on the correlation of predicted and actual breed proportion. Regardless of breed, the Index method of SNP selection numerically (but not significantly) outperformed all other selection methods in accuracy (i.e. correlation and root mean square of prediction) when panel density was ⩾300 SNPs. The correlation between actual and predicted breed proportion increased as panel density increased. Using 300 SNPs (selected using the global index method), the correlation between predicted and actual breed proportion was 0.993 and 0.995 in the Angus and Hereford validation populations, respectively. When SNP panels optimised for breed prediction in one population were used to predict the breed proportion of a separate population, the correlation between predicted and actual breed proportion was 0.034 and 0.044 weaker in the Hereford and Angus populations, respectively (using the 300 SNP panel). It is necessary to include at least 300 to 400 SNPs (per breed) on genotype panels to accurately predict breed proportion from biological samples.     

Pleiotropic Effects of Genes for Insulin Resistance on Adiposity in Baboons

Objective: Previous research has suggested a genetic contribution to the development of insulin resistance and obesity. We hypothesized that the same genes influencing insulin resistance might also contribute to the variation in adiposity. Research Methods and Procedures: A total of 601 (200 male, 401 female) adult baboons (Papio hamadryas) from nine families with pedigrees ranging in size from 43 to 121 were used in this study. Plasma insulin, glucose, C‐peptide, and adiponectin were analyzed, and homeostasis model assessment of insulin resistance (HOMA IR) was calculated. Fat biopsies were collected from omental fat tissue, and triglyceride concentration per gram of fat tissue was determined. Body weight and length were measured, and BMI was derived. Univariate and bivariate quantitative genetic analyses were performed using SOLAR. Results: Insulin, glucose, C‐peptide, and adiponectin levels, HOMA IR, triglyceride concentration of fat tissue, body weight, and BMI were all found to be significantly heritable, with heritabilities ranging from 0.15 to 0.80. Positive genetic correlations (r_Gs) were observed for HOMA IR with C‐peptide (r_G = 0.88 ± 0.10, p = 0.01), triglyceride concentration in fat tissue (r_G = 0.86 ± 0.33, p = 0.02), weight (r_G = 0.50 ± 0.20, p = 0.03), and BMI (r_G = 0.64 ± 0.22, p = 0.02). Discussion: These results suggest that a set of genes contributing to insulin resistance also influence general and central adiposity phenotypes. Further genetic research in a larger sample size is needed to identify the common genes that constitute the genetic basis for the development of insulin resistance and obesity.