The effect of including genomic relationships in the estimation of genetic parameters of functional traits in pigs.

The term functionality in animal breeding is used for traits that increase the efficiency of production by lowering the input cost, such as animal health and leg weakness related to longevity. The main objective of the study was to investigate the impact of genomic information, in a multivariate variance component analysis, on some of these traits. In addition, the effect of the inclusion was studied by testing the model's prediction ability based on best linear unbiased estimates for fixed and random effects. The material in this study consists of phenotypes from 76,683 animals, of which 4933 animals are genotyped. The heritabilities for front leg conformation, stayability, osteochondrosis and arched back, estimated using the traditional pedigree, were found to be between 0.12 and 0.29. When using the combined genomic and pedigree relationship matrix, the heritabilities were between 0.14 and 0.36. The results show that the combined relationship matrix can be used for the estimation of (co)variance components, and that the predictive ability of the model in this study marginally increases with the inclusion of genomic information.

Genetic conditions of joint Nordic genetic evaluations of lifetime competition performance in warmblood sport horses.

Breeding programmes for warmblood sport horses are similar in the Nordic countries Sweden, Denmark, Finland and Norway, and stallions of same origin are used. The aim was to investigate whether a joint Nordic genetic evaluation based on lifetime competition performance is feasible and beneficial for breeding competitive sport horses in the Nordic countries. Results for almost 45,000 horses in show jumping and 30,000 horses in dressage were available. The larger populations in Sweden and Denmark contributed with 85% of the results. Heritabilities and genetic correlations between performances in the different countries were estimated, and comparisons of accuracies of estimated breeding values (EBVs) and number of stallions with EBVs based on national or joint data were studied. The heritabilities ranged between 0.25 and 0.42 for show jumping and between 0.14 and 0.55 for dressage. The genetic correlations between competition performances in the Nordic countries were estimated to 0.63-1.00. EBVs based on joint data increased accuracies for EBVs for stallions by 38-81% and increased the number of available stallions with EBVs by 40-288%, compared to EBVs based on national data only. A joint Nordic genetic evaluation for sport horses is recommended.

Genetic trends of conformation traits and genetic correlations to osteochondrosis in boars.

The objective of our study was to investigate the heritabilities and genetic correlations between traits from a linear exterior assessment system and osteochondrosis (OC) measured by computed tomography (CT), and in addition, to study the genetic trend in a population where the conformation traits have been included in the breeding goal. The data material consisted of phenotypes from a total of 4571 Norsvin Landrace test boars. At the end of the test period, all boars were subjected to a detailed exterior assessment system. Within 10 days of the assessment, the boars were CT scanned for measuring OC. The total score of osteochondrosis (OCT), used in this study, is the sum of phenotypes from the assessment on the medial and lateral condyles at the distal end of both the humerus and the femur of the right and the left leg of the boar based on images from CT. The exterior assessment traits included in the study were; 'front leg knee' (FKNE), 'front leg pasterns' (FPAS), 'front leg stance' (FSTA), 'front leg twisted pasterns' (FFLK), 'hind leg stance', 'hind leg pasterns' (HPAS), 'hind leg standing under' (HSTU), 'hind leg small inner toe', 'dipped back', 'arched back' (ARCH) and 'waddling hindquarters' (WADL). The estimation of (co)variance components and breeding values were performed using bivariate animal genetic models. Breeding values for HSTU, HPAS, FPAS, WADL and OCT traits were additional outputs from the same bivariate analyses. The lowest heritability was found for FFLK (h 2 FFLK=0.05), whereas FPAS was estimated to have the highest heritability (h 2 FPAS=0.36), and OCT demonstrating a heritability of 0.29. Significant genetic correlations were found between several traits; the strongest correlation was between FSTA and FFLK (0.94), which was followed by the correlation between FPAS and FKNE (0.69). The traits ARCH and FSTA had significant genetic correlations to OCT, whereas all other genetic correlations between OCT and the conformation traits were low and not significantly different from 0. Our study shows positive genetic trends for the conformation traits included in the breeding goal. In general, low genetic correlations between conformation traits and OC were observed in our study.

Genetic parameters for feed intake, litter weight, body condition and rebreeding success in primiparous Norwegian Landrace sows.

The aim of this study was to estimate genetic parameters for feed intake recorded as farmers' perception of young sows' appetite for the first 3 weeks of lactation (APP) and feed intake recorded for one day in the 3rd week of lactation (FEED), litter weight (LW) at 3 weeks, sow body condition at weaning (BC) and the following five reproduction traits: weaning-to-service interval of 1 to 7 days (WSI7), weaning-to-service interval of 1 to 50 days (WSI50), delayed service or not (DELAYED), pregnant on first service or not (PREGNANT) and litter size in 2nd parity (NBT2). The analyses included data on 4606 Norwegian Landrace 1st-parity sows and their litters. The Gibbs sampling method was used. The traits DELAYED and PREGNANT were analysed as threshold traits and APP, FEED, LW, BC, WSI7, WSI50 and NBT2 were analysed as linear traits. The heritability estimates for APP and FEED were low (<0.1), whereas the estimates for DELAYED and PREGNANT were rather high (0.4 and 0.3). The heritability estimate for BC was 0.2. The genetic correlations confirmed the complexity of breeding for sow performance; selection for heavy 1st litters may lead to lower body condition at weaning, which in turn leads to lower reproductive performance and smaller litters in 2nd parity. Selection for higher sow feed intake would improve body condition, but the simple way of measuring feed intake tested in this study (APP and FEED) cannot be recommended because of the low heritability obtained for these traits.

Osteochondrosis in pigs diagnosed with computed tomography: heritabilities and genetic correlations to weight gain in specific age intervals.

The aim of this study was to develop a method for scoring osteochondrosis (OC) by using information from computed tomography (CT), as well as to estimate the heritability for OC scored by means of CT (OCwCT) of the medial and lateral condyles at the distal end of the humerus or the femur of the right and left leg and the sum of these scores (OCT). In addition, we were aiming at revealing the genetic relationship between OCwCT traits and growth in different periods (days from birth to 30 kg (D30), days from 30 to 50 kg (D30_50), days from 50 to 70 kg (D50_70), days from 70 to 90 kg (D70_90), days from 90 to 100 kg (D90_100) and days from birth to 100 kg (D100)). The OCwCT was assessed for 1449 boars, and growth data were collected for these 1449 boars and additional 3779 boars tested in the same time period. All boars were tested as part of the Norsvin Landrace boar test and in the same test station. Heritabilities for OCwCT on anatomical locations varied from 0.21 (s.e. = 0.08) on the medial condyle of the right humerus to 0.06 (s.e. = 0.06) on the lateral condyle of the left femur, whereas OCT exhibited the highest heritability (h² = 0.31, s.e. = 0.09). Genetic correlations between OCT and OCwCT for the anatomical locations ranged from 0.94 (s.e. = 0.07) for OCT and OCwCT score for the medial condyle of the humerus right side to 0.26 (s.e. = 0.39) for OCT and the lateral condyle of the femur left side. Genetic correlations between D30 and OCT were medium high and unfavourable (r(g) = -0.74). As the boar gain weight, the relationship between growth rate--expressed as number of days spent growing from one interval to the next--and OCT decreased to 0.12 (s.e. = 0.19, i.e. not significantly different from zero) for the trait D90_100 kg. These changes of genetic correlation coefficients coincide with the maturing of the joint cartilage and skeletal structures. In this study, we demonstrate that CT could be used for selection against OC in breeding programmes in pigs and that the genetic correlations between growth periods and OC are decreasing over time.

Genetic diversity and admixture of indigenous cattle from North Ethiopia: implications of historical introgressions in the gateway region to Africa.

Microsatellite variation was surveyed to determine the genetic diversity, population structure and admixture of seven North Ethiopian cattle breeds by combining multiple microsatellite data sets of Indian and West African zebu, and European, African and Near-Eastern taurine in genetic analyses. Based on allelic distribution, we identified four diagnostic alleles (HEL1-123 bp, CSSM66-201 bp, BM2113-150 bp and ILSTS6-285 bp) specific to the Near-Eastern taurine. Results of genetic relationship and population structure analyses confirmed the previously established marked genetic distinction between taurine and zebu, and indicated further divergence among the bio-geographical groupings of breeds such as North Ethiopian, Indian and West African zebu, and African, European and Near-Eastern taurine. Using the diagnostic alleles for bio-geographical groupings and a Bayesian method for population structure inference, we estimated the genetic influences of major historical introgressions in North Ethiopian cattle. The breeds have been heavily (>90%) influenced by zebu, followed by African, European and the Near-Eastern taurine. Overall, North Ethiopian cattle show a high level of within-population genetic variation (e.g. observed heterozygosity = 0.659-0.687), which is in the upper range of that reported for domestic cattle and indicates their potential for future breeding applications, even in a global context. Rather low but significant population differentiation (F(ST) = 1.1%, P < 0.05) was recorded as a result of multiple introgression events and strong genetic exchanges among the North Ethiopian breeds.

Heritability of shoulder ulcers and genetic correlations with mean piglet weight and sow body condition.

The objective of this paper was to estimate the heritability for shoulder ulcers and the genetic correlations between shoulder ulcers, mean piglet weight and sow body condition. The analyses were based on information on 5549 Norwegian Landrace sows and their 7614 purebred litters. The genetic analysis was performed using the Gibbs sampling method. Shoulder ulcers were analyzed as a threshold trait. Sow body condition and mean piglet weight were analyzed as linear traits. The heritability of shoulder ulcers was estimated at 0.25 (s.d. = 0.03). The heritability for sow body condition was estimated at 0.14 (s.d. = 0.02) and that for mean piglet weight at 0.23 (s.d. = 0.02). The genetic correlation between shoulder ulcers and sow body condition was negative (-0.59, s.d. = 0.09). The genetic correlation between shoulder ulcers and mean piglet weight was positive (0.23, s.d. = 0.10) and the genetic correlation between sow body condition and mean piglet weight was negative (-0.24, s.d. = 0.10).

Genetic parameters between slaughter pig efficiency and growth rate of different body tissues estimated by computed tomography in live boars of Landrace and Duroc.

In this study, computed tomography (CT) technology was used to measure body composition on live pigs for breeding purposes. Norwegian Landrace (L; n = 3835) and Duroc (D; n = 3139) boars, selection candidates to be elite boars in a breeding programme, were CT-scanned between August 2008 and August 2010 as part of an ongoing testing programme at Norsvin's boar test station. Genetic parameters in the growth rate of muscle (MG), carcass fat (FG), bone (BG) and non-carcass tissue (NCG), from birth to ∼100 kg live weight, were calculated from CT data. Genetic correlations between growth of different body tissues scanned using CT, lean meat percentage (LMP) calculated from CT and more traditional production traits such as the average daily gain (ADG) from birth to 25 kg (ADG1), the ADG from 25 kg to 100 kg (ADG2) and the feed conversion ratio (FCR) from 25 kg to 100 kg were also estimated from data on the same boars. Genetic parameters were estimated based on multi-trait animal models using the average information-restricted maximum likelihood (AI-REML) methodology. The heritability estimates (s.e. = 0.04 to 0.05) for the various traits for Landrace and Duroc were as follows: MG (0.19 and 0.43), FG (0.53 and 0.59), BG (0.37 and 0.58), NCG (0.38 and 0.50), LMP (0.50 and 0.57), ADG1 (0.25 and 0.48), ADG2 (0.41 and 0.42) and FCR (0.29 and 0.42). Genetic correlations for MG with LMP were 0.55 and 0.68, and genetic correlations between MG and ADG2 were -0.06 and 0.07 for Landrace and Duroc, respectively. LMP and ADG2 were clearly unfavourably genetically correlated (L: -0.75 and D: -0.54). These results showed the difficulty in jointly improving LMP and ADG2. ADG2 was unfavourably correlated with FG (L: 0.84 and D: 0.72), thus indicating to a large extent that selection for increased growth implies selection for fatness under an ad libitum feeding regime. Selection for MG is not expected to increase ADG2, but will yield faster growth of the desired tissues and a better carcass quality. Hence, we consider MG to be a better biological trait in selection for improved productivity and carcass quality. CT is a powerful instrument in conjunction with breeding, as it combines the high accuracy of CT data with measurements taken from the selection candidates. CT also allows the selection of new traits such as real body composition, and in particular, the actual MG on living animals.

Simultaneous estimation of daily weight and feed intake curves for growing pigs by random regression.

In this study, random regression models were used to estimate covariance functions between feed intake and BW in boars from the two breeds: the Norwegian Landrace and the Norwegian Duroc. In total, 1476 animals of the Norwegian Landrace breed and 1300 animals of the Norwegian Duroc breed had registrations on daily feed intake and growth from 54 to 180 days of age. Random regressions on the Legendre polynomials of age were used to describe genetic and permanent environmental curves in BW (up to the second order) and feed intake (up to the first order) for both the breeds. Heritabilities on BW increased over time for the Landrace (0.18 to 0.24), but were approximately constant for the Duroc (0.33 to 0.35). Average heritabilities for feed intake were approximately the same in both the breeds (0.09 to 0.11), and the estimates decreased over time, most pronounced in Duroc. On the basis of the current data, daily feed intake was seemingly controlled by the same genetic factors throughout the test period for Duroc; however, for Landrace, genetic correlations between test days decreased with increasing distance in time. For BW, the genetic correlations between test days were in general high, and did not go below 0.8 for any of the two breeds in this study. For both feed intake and BW, permanent environmental correlations between start and end of the test were reduced with increasing difference in days, most pronounced in Duroc. This study indicates that weight of the animal at the end of the test was more closely genetically correlated to feed intake of earlier periods compared with later periods of growth for both the breeds. This may be explained by the fact that BW is the cumulative growth of an individual, which is likely to be heavily affected by the feed intake during the most intense growth period.

Genetic parameters of fat quality in pigs measured by near-infrared spectroscopy.

Subcutaneous fat from Norwegian Landrace (n=3230) and Duroc (n=1769) pigs was sampled to investigate the sources of variation and genetic parameters of various fatty acids, fat moisture percentage and fat colour, with the lean meat percentage (LMP) also included as a trait representing the leanness of the pig. The pigs were from half-sib groups of station-tested boars included in the Norwegian pig breeding scheme. They were fed ad libitum to obtain an average of 113 kg live weight. Near-infrared spectroscopy (NIRS) was applied for prediction of the fatty acids and fat moisture percentage, and Minolta was used for the fat colour measurements. Heritabilities and genetic correlations were estimated with a multi-trait animal model using average information-restricted maximum likelihood (AI-REML) methodology. Fat from Landrace pigs had considerably more monounsaturated fatty acids, polyunsaturated fatty acids (PUFAs) and fat moisture, as well as less saturated fatty acids (SFAs) than fat from Duroc pigs. The heritability estimates (s.e. 0.03 to 0.08) for the various fatty acids were as follows: Palmitic, C16:0 (0.39 and 0.51 for Landrace and Duroc pigs, respectively); Palmitoleic, C16:1n-7 (0.41 and 0.50); Steric, C18:0 (0.46 and 0.54); Oleic, C18:1n-9 (0.67 and 0.57); Linoleic, C18:2n-6 (0.44 and 0.46); α-linolenic, C18:3n-3 (0.37 and 0.25) and n-6/n-3 ratio (0.06 and 0.01). The other fat quality traits revealed the following heritabilities: fat moisture (0.28 and 0.33), colour values in subcutaneous fat: L* (whiteness; 0.22 and 0.21), a* (redness; 0.13 and 0.24) and b* (yellowness; 0.07 and 0.17) and LMP (0.46 and 0.47). LMP showed high positive genetic correlations to PUFA (C18:2n-6 and C18:3n-3), which implies that selecting leaner pigs changes the fatty acid composition and deteriorates the quality of fat. Higher concentrations of PUFA are not beneficial as the ratio of n-6 and n-3 fatty acids becomes unfavourably high. Owing to the high genetic correlation between C18:2n-6 and C18:3n-3 and a low heritability for this ratio, the latter is difficult to change through selection. However, a small reduction in the ratio should be expected if selection aims at reducing the level of C18:2n-6. Selection for more C18:1n-9 is possible in view of the genetic parameters, which are favourable for eating quality, technological quality and human nutrition. The NIRS technology and the high heritabilities found in this study make it possible to implement fat quality traits to achieve the breeding goal in the selection of a lean pig with better fat quality.

Prediction of fat quality in pig carcasses by near-infrared spectroscopy.

This study was conducted to evaluate the potential of near-infrared (NIR) spectroscopy (NIRS) technology for prediction of the chemical composition (moisture content and fatty acid composition) of fat from fast-growing, lean slaughter pig samples coming from breeding programmes. NIRS method I: a total of 77 samples of intact subcutaneous fat from pigs were analysed with the FOSS FoodScan NIR spectrophotometer (850 to 1050 nm) and then used to predict the moisture content by using partial least squares (PLS) regression methods. The best equation obtained has a coefficient of determination for cross-validation (CV; R(2)(cv)) and a root mean square error of a CV (RMSECV) of 0.88 and 1.18%, respectively. The equation was further validated with (n = 15) providing values of 0.83 and 0.42% for the coefficient of determination for validation (R(2)(val)) and root mean square error of prediction (RMSEP), respectively. NIRS method II: in this case, samples of melted subcutaneous fat were analysed in an FOSS XDS NIR rapid content analyser (400 to 2500 nm). Equations based on modified PLS regression methods showed that NIRS technology could predict the fatty acid groups, the main fatty acids and the iodine value accurately with R(2)(cv), RMSECV, R(2)(val) and RMSEP of 0.98, 0.38%, 0.95 and 0.49%, respectively (saturated fatty acids), 0.94, 0.45%, 0.97 and 0.65%, respectively (monounsaturated fatty acids), 0.97, 0.28%, 0.99 and 0.34%, respectively (polyunsaturated fatty acids), 0.76, 0.61%, 0.84 and 0.87%, respectively (palmitic acid, C16:0), 0.75, 0.16%, 0.89 and 0.10%, respectively (palmitoleic acid, C16:1n-7), 0.93, 0.41%, 0.96 and 0.64%, respectively (steric acid, C18:0), 0.90, 0.51%, 0.94 and 0.44%, respectively (oleic acid, C18:1n-9), 0.97, 0.25%, 0.98 and 0.29% (linoleic acid, C18:2n-6), 0.68, 0.09%, 0.57 and 0.16% (α-linolenic acid, C18:3n-3) and 0.97, 0.57, 0.97 and 1.22, respectively (iodine value, calculated). The magnitude of this error showed quite good accuracy using these rapid methods in prediction of the moisture and fatty acid composition of fat from pigs involved in breeding schemes.

Genetic parameters of meat quality traits in two pig breeds measured by rapid methods.

To study genetic variation in meat quality traits measured by rapid methods, data were recorded between 2005 and 2008 on samples of M. longissimus dorsi (LD) in Landrace (n = 3838) and Duroc (n = 2250) pigs included in the Norwegian pig breeding scheme. In addition, ultimate pH levels in the glycolytic LD (loin muscle) and M. gluteus medius (GM, ham muscle), and in the oxidative m. gluteus profundus (GP, ham muscle) were recorded as an extended data set (n = 16 732 and n = 7456 for Landrace and Duroc, respectively) from 1998 to 2008. Data were analysed with a multi-trait animal model using AI-REML methodology. Meat from Duroc had considerably more intramuscular fat (IMF), less moisture and protein, appeared darker with higher colour intensity and had lower drip loss than meat from Landrace. The heritability estimates (s.e. 0.01 to 0.07) for pH in LD (0.19 and 0.27 for Landrace and Duroc, respectively), GM (0.12 and 0.22) and GP (0.19 and 0.38), drip loss (0.23 and 0.33), colour values: L* (lightness) (0.41 and 0.28), a* (redness) (0.46 and 0.43), b* (yellowness) (0.31 and 0.33), IMF (0.50 and 0.62), muscle moisture (0.31 and 0.50) and muscle protein content (0.40 and 0.54) in LD all demonstrated moderate-to-high genetic variation for these traits in both breeds. Near infrared spectroscopy and EZ-DripLoss are modern technologies used in this study for the determination of chemical components and drip loss in meat. These methods gave higher heritabilities than more traditional methods used to measure these traits. The estimated genetic correlations between moisture and IMF in Duroc, and pH and drip loss in Duroc were both -0.89. Interesting differences between the two breeds in numerical value of some genetic correlations were observed, probably reflecting the differences in physiology and selection history between Landrace and Duroc. The estimated genetic correlation between drip loss and pH was much stronger in Duroc than in Landrace (-0.89 and -0.63, respectively). This might be due to the high pH in Duroc, whereas Landrace had a lower pH closer to the iso-electric point for muscle proteins. The positive genetic correlation between the L* value in meat and IMF in Duroc (0.50) was an effect of differences in visible marbling, rather than meat colour. For Landrace, this correlation was negative (-0.20). IMF content showed favourable genetic correlations to drip loss (-0.36 and -0.35 for Landrace and Duroc, respectively).

Prediction of genetic growth curves in pigs.

Genetic growth curves of boars in a test station were predicted on daily weight records collected by automated weighing scales. The data contained 121 865 observations from 1477 Norwegian Landrace boars and 108 589 observations from 1300 Norwegian Duroc boars. Random regression models using Legendre polynomials up to second order for weight at different ages were compared for best predicting ability and Bayesian information criterion (BIC) for both breeds. The model with second-order polynomials had best predictive ability and BIC. The heritability for weight, based on this model, was found to vary along the growth trajectory between 0.32-0.35 for Duroc and 0.17-0.25 for Landrace. By varying test length possibility to use shorter test time and pre-selection was tested. Test length was varied and compared with average termination at 100 kg, termination of the test at 90 kg gives, e.g. 2% reduction in accuracy of estimated breeding values (EBV) for both breeds and termination at 80 kg gives 5% reduction in accuracy of EBVs for Landrace and 3% for Duroc. A shorter test period can decrease test costs per boar, but also gives possibilities to increase selection intensity as there will be room for testing more boars.

Analysis of genetic diversity and conservation priorities for six north Ethiopian cattle breeds.

Genetic diversity and conservation potential of six indigenous cattle breeds of north Ethiopia was analysed based on 20 microsatellite markers using core set methods. Expected future diversity (assuming assigned extinction probabilities are valid for the next 20-50 years) were 0.988+/-0.011 and 0.980+/-0.010 with expected loss of diversity estimated at 0.02% and 0.74% of current level for the Maximum Variance Total (MVT) and Maximum Variance Offspring (MVO) core sets, respectively. Even though all breeds have contributed to current diversity levels, the Afar and Abergelle breeds only contributed 51% and 62% to the MVT and MVO core sets, respectively, while the Raya breed contributed only 6% and 1.5% to the MVT and MVO core set diversities, respectively. Moreover, prioritizing the six north Ethiopian cattle breeds using the conservation potential obtained from the MVT core set method seems reasonable considering the origin and migration histories of the breeds. Our results suggest that the total current genetic diversity of these breeds can be sufficiently maintained by designing a conservation strategy based on conservation potential of each breed from the MVT core set so that priority is given to lowering the extinction probabilities of breeds with high conservation potential to zero.

Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding.

An understanding of inbreeding and inbreeding depression are important in evolutionary biology, conservation genetics, and animal breeding. A new method was developed to detect departures from the classical model of inbreeding; in particular, it investigated differences between the effects of inbreeding in recent generations from that in the more distant past. The method was applied in a long-term selection experiment on first-litter size in mice. The total pedigree included 74,630 animals with approximately 30,000 phenotypic records. The experiment comprised several different lines. The highest inbreeding coefficients (F) within a line ranged from 0.22 to 0.64, and the average effective population size (N(e)) was 58.1. The analysis divided F into two parts, corresponding to the inbreeding occurring in recent generations ('new') and that which preceded it ('old'). The analysis was repeated for different definitions of 'old' and 'new', depending on length of the 'new' period. In 15 of these tests, 'new' inbreeding was estimated to cause greater depression than 'old'. The estimated depression ranged from -11.53 to -0.79 for the 'new' inbreeding and from -5.22 to 15.51 for 'old'. The difference was significant, the 'new' period included at least 25 generations of inbreeding. Since there were only small differences in N(e) between lines, and near constant N(e) within lines, the effect of 'new' and 'old' cannot be attributed to the effects of 'fast' versus 'slow' inbreeding. It was concluded that this departure from the classical model, which predicts no distinction between this 'old and 'new' inbreeding, must implicate natural selection and purging in influencing the magnitude of depression.

Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis.

Ethiopia is considered to be a putative migratory corridor for both Near-East Bos taurine and Arabian and Indian B. indicus cattle into East Africa. African pastoralism, which is associated with adaptation to specific habitats and farming systems, has contributed to the composite constitution of Ethiopian cattle. We analyse, for the first time, five Y-chromosome microsatellite markers from seven north Ethiopian cattle populations, using a European Holstein-Friesian population as a reference, to assess the paternal gene pool and to explore the mechanisms behind the genetic structure. Our results reveal that the indicine alleles predominate in the present populations, with only one animal in the Arado carrying the taurine alleles. The north Ethiopian cattle populations with one exception (Abergelle) are characterized by a general low Y-chromosome haplotype diversity, as well as by a reduced interpopulation variance (Phi(ST)=4.0%), which can be a result of strong male-mediated selective sweeps. Population structure revealed by multidimensional-scaling analysis differentiates two populations (Arado and Abergelle) from the rest. Analysis of molecular variance does not lend support to the traditional classification for the populations, which is mainly based on physical characteristics. A network analysis indicates two closely related founding haplotypes accounting for a large proportion (50.0% in Abergelle and 85.0-94.7% in others) of north Ethiopian cattle Y-chromosomes. Our findings point to a common, but limited, paternal origin of the north Ethiopian cattle populations and strong male-mediated gene flow among them. The findings also provide insight into the historical immigration of cattle into East Africa.

Long-term responses, changes in genetic variances and inbreeding depression from 122 generations of selection on increased litter size in mice.

Data on mice selected for litter size over 122 generations have been analysed in order to reveal the effect of long-term selection on responses and changes in variances over a long selection period. Originally, three lines were established from the same base population, namely an H line selected for large litter size, an L line selected for small litter size and a K line without selection. In generation 122, the mean number of pups born alive (NBA) was 22 for the H line and 11 for the K line. Phenotypic response to selection is reduced over generations, but crossing of plateaued lines increased responses and realized heritabilities. Both realized heritabilities and heritabilities from residual maximal likelihood (REML) analyses were, in general, calculated from generation (-1)-44 (period 1), 45-70 (period 2) and 71-122 (period 3) separately. Realized heritabilities were in general smaller than heritabilities estimated from mixed model analysis. An overall estimate of heritability for NBA was found to be 0.19 (+/- 0.01) by REML analysis. Additive variance is constant over all periods in the high line and the control line, but is reduced over periods in the low line. The reduction of additive variance in the low line could probably be explained by changes in gene frequencies. In all lines, environmental variances increased over periods. Inbreeding reduced the mean litter size by 0.72 (+/- 0.10) pups per 10% increase in inbreeding, with substantial variance between periods and lines.

Genetic analysis of age at first service, return rate, litter size, and weaning-to-first service interval of gilts and sows.

The aim of this study was to estimate genetic parameters of seven traits related to sow reproductive performance. Data on all Norwegian Landrace pigs (NL) born in nucleus herds and raised in nucleus or multiplying herds from 1990 to 2000 were extracted from the Norwegian national recording scheme. Reproductive traits investigated were age at first service (AFS), return rate in gilts (RRg), age at first farrowing (AFF), live-born piglets in the first litter (NBA1), interval from weaning to first service after first litter (WTS1), return rate after first litter (RR1), live-born piglets in the second litter (NBA2), and interval from weaning to first service after second litter (WTS2). After editing, the data set comprised 12,583 to 56,042 records, depending on the trait. A mixed linear and a joint linear threshold animal model were used to estimate (co)variance components. A full Bayesian approach via Gibbs sampling was adopted. The statistical model used for analysis included contemporary groups of herd-year (-season), purebred or crossbred litter, single or double insemination, mating type, parity in which the animal was born, a regression on lactation length, and an additive genetic effect. Neither the estimated heritabilities nor the genetic correlations differed much between the two approaches, but there was a tendency for higher genetic correlations using the joint linear threshold model approach. Average heritabilities were as follows: AFS = 0.31; RRg = 0.03; RR1 = 0.02; NBA1 = 0.12; NBA2 = 0.14; WTS1 = 0.08; and WTS2 = 0.03. The highest genetic correlations were estimated between NBA1 and NBA2 (r(g) = 0.95), RR1 and WTS1 (r(g) = 0.93), and between WTS1 and WTS2 (r(g) = 0.78). The estimated genetic correlation between NBA and WTS were close to zero. Selection for increased NBA will slightly increase AFS and reduce the probability of a return. Selection for decreased AFS will have a favorable effect on WTS intervals; however, selection for decreased AFS seems to have an unfavorable effect on return rate both on gilts and sows. Conversely, selection for decreased WTS intervals will reduce the probability of a return. Potential selection candidates to include in a multivariate fertility index are AFS, NBA, and WTS1. Due to the low heritability and low, but favorable, genetic correlations to NBA and WTS, RR is not recommended as a selection candidate.

Genetic correlations between reproduction and production traits in swine.

Genetic correlations between reproduction and production traits were estimated in swine. Reproduction traits investigated were age at first service (AFS), number of live-born piglets in the first litter (NBA1), interval from weaning to first service after first litter (WTS1), number of live-born piglets in the second litter (NBA2), and interval from weaning to first service after the second litter (WTS2). Females generating the data were Norwegian Landrace born in nucleus herds between 1990 and 2000, and the number of records ranged from 13,792 to 56,932. Genetic correlations were estimated among the main production traits in the breeding goal: adjusted age at 100 kg live weight (A100), percentage of lean meat content (LMC), individual feed consumption from 25 to 100 kg (FC), and bacon side quality (BSQ). Average adjusted backfat thickness (BF) was included as a production trait. The A100 and BF traits were recorded on gilts on-farm with 190,454 records, whereas LMC, BSQ, and FC were recorded on-station with the number of records ranging from 12,487 to 12,992. Analyses were carried out with a multivariate animal model using average information restricted maximum likelihood procedures by first running each reproduction trait with A100 and BF, followed by each reproduction trait with LMC, BSQ, and FC. Average heritabilities for reproduction traits were as follows: AFS (0.38), NBA1 (0.11), WTS1 (0.06), NBA2 (0.12), and WTS2 (0.03); and for production traits: A100 (0.30), BF (0.44), FC (0.22), LMC (0.58), and BSQ (0.23). The highest genetic correlation was estimated between A100 and AFS (r(g)= 0.68), also resulting in a positive genetic correlation between FC and AFS. Growth (A100) was negatively (i.e., unfavorably) genetically correlated to NBA1 and NBA2 (r(g) = 0.60 and rg = 0.42 respectively), and so the genetic correlation to FC also became unfavorable (r(g)= 0.23 and r(g) = 0.20). Single-trait selection for enhanced LMC would also affect NBA1 and NBA2 unfavorably (r(g)= -0.12 and r(g)= -0.24). Correlations between BF at 100 kg live weight and reproduction traits were close to zero; however, a low genetic correlation between BF and WTS1 was obtained (r(g)= -0.12), indicating that selection toward reduced BF at 100 kg live weight may have an unfavorable impact on WTS1.

Genetic analysis of litter size, parturition length, and birth assistance requirements in primiparous sows using a joint linear-threshold animal model.

The aim of this study was to investigate whether selection for number of live born piglets has led to prolonged parturition and increased requirement for birth assistance, resulting in increased numbers of stillborn piglets. Data were collected from 6,718 primiparous Norwegian Landrace sows farrowing between 2001 and 2003. The need for birth assistance was recorded as a binary response. Physical intervention in the birth of piglets and/or hormonal treatment by the farmer was recorded as birth assistance. The duration of the parturition was analyzed as a binary trait (<4 h and >4 h). The statistical model used for analysis included contemporary groups of herd-year, litter breed, season of farrowing, parity in which the sow was born, a regression on the age of sow at farrowing, an additive genetic effect, and a service sire effect. A full Bayesian approach via Gibbs sampling was adopted to estimate the genetic relationships between these four traits. A total chain length of 100,000 iterations was run. The first 10,000 samples were discarded as burn-in, and the remaining 90,000 iterations were retained without thinning for post-Gibbs analysis. The highest direct heritability was estimated for the number of live-born piglets (h2 = 0.07), followed by the duration of farrowing (h2 = 0.05), the need for birth assistance (h2 = 0.05), and the number of stillborn piglets (h2 = 0.04). The genetic correlations revealed that the number of live and stillborn piglets was uncorrelated; however, the number of live piglets born had a moderate genetic correlation to the need for birth assistance (rg = 0.24 +/- 0.01) and duration of farrowing (rg = -0.20 +/- 0.01), whereas the number of stillborn piglets was highly correlated to the need for birth assistance (rg = 0.74 +/- 0.01) and the duration of parturition (rg = 0.66 +/- 0.01). The duration of farrowing and the need for birth assistance were genetically highly correlated (rg = 0.89 +/- 0.00). For all traits, the service sire variance was approximately one quarter in magnitude compared with its respective genetic variance. The results showed that selection for the number of live born piglets is not expected to influence the number of stillborn piglets. Increasing the number of live piglets born through selection should have a slight negative effect on farrowing duration and a minor increase in the need for birth assistance. Sows with a high genetic potential for birth assistance and prolonged parturition were more likely to give birth to greater numbers of stillborn piglets.