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.

At the dairy research farm Karkendamm, the individual roughage intake was measured since 1 September 2005 using a computerised scale system to estimate daily energy balances as the difference between energy intake and calculated energy requirements for lactation and maintenance. Data of 289 heifers with observations between the 11th and 180th day of lactation over a period of 487 days were analysed. Average energy-corrected milk yield, feed intake, live weight and energy balance were 31.8kg, 20.6kg, 584 kg and 13.6 MJ NEL (net energy lactation), respectively, per day. Fixed and random regression models were used to estimate repeatabilities, correlations between cow effects and genetic parameters. The resulting genetic correlations in different lactation stages demonstrate that feed intake and energy balance at the beginning and the middle of lactation are genetically different traits. Heritability of feed intake is low with h2=0.06 during the first days after parturition and increases in the middle of lactation, whereas the energy balance shows the highest heritability with h2=0.34 in the first 30 days of lactation. Genetic correlations between energy balance and feed intake and milk yield, respectively, illustrate that energy balance depends more on feed intake than on milk yield. Genetic correlation between body condition score and energy balance decreases rapidly within the first 100 days of lactation. Hence, to avoid negative effects on health and reproduction as consequences of strong energy deficits at the beginning of lactation, the energy balance itself should be measured and used as a selection criterion in this lactation stage. Since the number of animals is rather small for a genetic analysis, the genetic parameters have to be evaluated on a more comprehensive dataset.

Tibetan Mastiff is one of the most archaic, ferocious and the largest dogs in the world. A total of 140 individuals from four geographically separated populations in China (Tibet, Gansu, Qinghai and Beijing) were sampled and genetic diversity was assessed using 10 microsatellite loci on eight different chromosomes. The mean number of alleles per locus ranged from 6 to 13. The mean observed and expected heterozygosities, polymorphism information content and allelic richness were 0.69, 0.79, 0.76 and 7.59, respectively, indicating relatively high genetic diversity in Tibetan Mastiff. However, a highly significant deficiency in heterozygote was observed within populations (mean FIS = 0.11, bootstrap 95% confidence interval (0.06, 0.17)) and total inbreeding (mean FIT = 0.12, bootstrap 95% confidence interval (0.06, 0.18)), along with strong inbreeding coefficients within populations (Fis > 0.09), all of which suggested that intense inbreeding practices occurred in Tibetan Mastiff. Therefore, effective and appropriate breeding management projects in present Tibetan Mastiff will be desirable and urgent. Low genetic differentiation was obtained with a mean FST of 0.01 (bootstrap 95% confidence interval (0.007, 0.019)). Additionally, the four Tibetan Mastiff populations showed close relationships in the neighbor-joining polygenetic tree based on the coancestral genetic distances. Tibetan Mastiff was investigated by using microsatellite loci at the first time, which could facilitate the better understanding of present situation at the molecular level, breed conservation and utilization in Tibetan Mastiff.

Lysozyme, an anti-bacterial enzyme, is mostly found in the body fluids, various tissues and secretions of animals and humans, and confers immunity against a wide range of bacterial species. The present study was carried out to elucidate the gene sequence of this enzyme in Indian Sahiwal × Holstein Friesian crossbred cattle and to explore the polymorphism of the gene as well as their association with milk production and somatic cell traits. The total length of lysozyme cDNA was found to be of 447 bp. The similarity with Bos taurus, human, pig, monkey, gorilla, mice, rat, chicken, dog and sheep was estimated as 99.1%, 85%, 81.0%, 85.2%, 84.3%, 77.9%, 77.9%, 41.4%, 40.5% and 24.6%, respectively. Polymorphism study of two fragments, extended exon1 including promoter, exon1 and partial intron1 (268 bp), and extended exon2 including partial intron1 and 2, and exon2 region (287 bp) of milk lysozyme gene was carried out by employing single-stranded conformation polymorphism (SSCP). In the extended exon1 fragment, three alleles namely A, B and C with frequencies of 0.59, 0.28 and 0.12 were observed while in the exon extended fragment, three different alleles – P, Q and R with respective frequencies of 0.61, 0.38 and 0.01 – were determined in Indian Sahiwal × Holstein Friesian cross. A total of eight haplotypes were found in this population where the most predominant one was h1 (0.52). Genotypes of exon1 extended fragment showed significant association with total milk yield, daily milk yield, peak yield and somatic cell score at P < 0.05 while that of exon2 extended fragment had significant correlation with only total lactational milk yield. Haplotype combinations also revealed significant association with total milk production where h1h1 homozygous showed highest yield during first lactation.

We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less inbreeding than minimum-coancestry mating in the hierarchical and factorial breeding schemes without any loss in genetic gain. Moreover, it generated upto 28% less inbreeding and about 3% more genetic gain than random mating. The benefits of MCAC mating over minimum-coancestry mating are worthwhile because they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should be used in breeding schemes where pedigree information is available.

Marker-assisted gene pyramiding provides a promising way to develop new animal breeds or lines, in which genes responsible for certain favorable characters identified in different breeds or lines are incorporated. In consideration of features of animal populations, we proposed five schemes for pyramiding three genes, denoted Scheme A–E, and five schemes for pyramiding four genes, denoted Scheme F–J. These schemes are representative of the possible alternatives. We also provided an algorithm to compute the population sizes needed in each generation. We compared these schemes with respect to the total population size and the number of generations required under different situations. The results show that there is no scheme that is optimal in all cases. Among the schemes for pyramiding three genes from three lines (L1, L2 and L3), Scheme D (a three-way cross between the three lines are first performed, followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) has a significant advantage over the other schemes when the recombination rate between adjacent genes ranges from 0.1 to 0.4, while Scheme A (a two-way cross between L1 and L2 and a subsequent intercross are performed, followed by a cross with L3 and a subsequent intercross to obtain the desired genotype) is optimal when recombination rate is 0.5. Among schemes for pyramiding four genes from four lines (L1, L2, L3 and L4), Scheme I (seperately, a two-way cross between L1 and L2 (L3 and L4) followed by a backcross to L1 (L3) and a subsequent intercross are performed, then the offspring from the two sides are crossed and followed by a backcross to L1 and a subsequent intercross to obtain the desired genotype) is optimal when the recombination rate ranges from 0.1 to 0.4, while Scheme F (cross and subsequent intercross between the four lines are performed successively) is the optimal when the recombination rate is 0.5. We also disscuss how the animals’ reproductive capacity, the probabilities of obtaining the desired genotypes and genetic distance between adjacent genes would affect the design of an optimal scheme.

The EU ban on in-feed antibiotics has stimulated research on weaning diets as a way of reducing post-weaning gut disorders and growth check in pigs. Many bioactive components have been investigated but only few have shown to be effective. Amongst these, organic acids (OA) have been shown to exert a bactericidal action mediated by non-dissociated OA, by lowering gastric pH, increasing gut and pancreas enzyme secretion and improving gut wall morphology. It has been postulated that they may also enhance non-specific immune responses and improve disease resistance. In contrast, relatively little attention has been paid to the impact of OA on the stomach but recent data show they can differently affect gastric histology, acid secretion and gastric emptying. Butyrate and precursors of butyric acid have received special attention and although promising results have been obtained, their effects are dependent upon the dose, treatment duration, initial age of piglets, gastrointestinal site and other factors. The amino acids (AA) like glutamine, tryptophan and arginine are supportive in improving digestion, absorption and retention of nutrients by affecting tissue anabolism, stress and (or) immunity. Glutamine, cysteine and threonine are important for maintaining mucin and permeability of intestinal barrier function. Spray-dried plasma (SDP) positively affects gut morphology, inflammation and reduces acquired specific immune responses via specific and a-specific influences of immunoglobulins and other bioactive components. Effects are more pronounced in early-weaned piglets and under poorer health conditions. Little interaction between plasma protein and antibiotics has been found, suggesting distinct modes of action and additive effects. Bovine colostrum may act more or less similarly to SDP. The composition of essential oils is highly variable, depending on environmental and climatic conditions and distillation methods. These oils differ widely in their antimicrobial activity in vitro and some components of weaning diets may decrease their activity. Results in young pigs are highly variable depending upon the product and doses used. These studies suggest that relatively high concentrations of essential oils are needed for beneficial effects to be observed and it has been assumed that these plant extracts mimic most of the effects of antibiotics active on gut physiology, microbiology and immunology. Often, bioactive substances protective to the gut also stimulate feed intake and growth performance. New insights on the effects of selected OA and AA, protein sources (especially SDP, bovine colostrum) and plant extracts with anti-bacterial activities on the gut are reported in this review.

Test-day records for average flow rate (AFR) from the routine dairy recording from Bavarian Fleckvieh cows were analysed. Two data sets with observations on approximately 20 000 cows each were sampled from the total data set. For the estimation of variance parameters, a two-step approach was applied. In a first step multiple-trait restricted maximum likelihood (REML) analyses were carried out. For each of the first three lactations, six time periods with up to 33 days were defined. An algorithm for iterative summing of expanded part matrices was applied in order to combine the estimates. In a second step covariance functions (CF) for additive-genetic variances and non-genetic animal variances were derived using second-order Legendre polynomials plus an exponential term. Estimates of test-day heritability for AFR ranged from 0.21 to 0.40, and were largest in lactation 1. For lactations 1 and 3, heritabilities decreased considerably towards the end of lactation. Genetic correlation estimates within lactation decreased as the distance between days in milk (DIM) increased. Genetic correlations between corresponding DIM in the three lactations were generally large, ranging from 0.80 to 0.99. The largest estimates were found between DIM from lactations 2 and 3. Results from this study suggest that including AFR data from second and third lactations in genetic evaluation systems could the improve accuracy of genetic selection.

Despite many recent advances in single nucleotide polymorphism (SNP) genotyping technologies, there is still the need for methodologies with a reasonable throughput. In this study, we compared three PCR-based methods for SNP detection: (1) a conventional PCR-based allele detection system with fluorescent genotyping technology, (2) a SNaPshot methodology by single nucleotide primer extension and, (3) a real-time PCR-based method by allele-specific minor groove-binder probes. These three methodologies were used to analyze 104 meat samples of a particular Italian cattle breed known for producing excellent quality meat and for a characteristic increased development of muscle mass, caused by a point mutation (C313Y) in the Myostatin gene. The analysis revealed 98 samples to be homozygous (mh/mh) and five to be heterozygous (mh/+) for the mutation whereas one sample resulted to be homozygous for the wild type (+/+). The results obtained with the three different assays were consistent. Overall, all three methodologies proved to be efficient for allelic discrimination studies; however, real-time PCR was faster and allowed to genotype up to 96 samples in a single step, minimizing the number of steps required for samples manipulation.

Bovine placental lactogen (bPL) is structurally related to prolactin (PRL) and growth hormone (GH). In synergism with steroid and thyroid hormones, bPL is crucial in stimulating the development of the mammary gland, mammary cell differentiation and function. To further explore whether bPL gene is associated with milk production traits, we herein analyzed single-nucleotide polymorphisms (SNPs) within eight regions of bPL gene, which are potentially associated with five milk production traits on 1028 Chinese Holstein cows. Among these, two SNPs, NT7409(T–C) and Nt11246(G–A), were identified. The former is within exon 2; it induces an alteration of amino acid from Val to Ala. The later is within exon 4. It is a synonymous mutation. We found that there were significant associations between NT7409(T–C) and milk and protein yield. Cows of the AA genotype yielded less milk (P = 0.001) and less protein (P = 0.003) than those of genotypes AB and BB. However, on the NT11246(G–A) locus, no significant association was observed in the five milk production traits studied. In addition, bPL has been localized near markers RM185 and CC549051 with a distance of 23.2 cR on BTA 23. It is at the same position as the region including quantitative trait loci (QTLs) affecting milk and protein yields by previous linkage analysis. In summary, our findings demonstrated that the SNP within exon 2 of bPL (NT7409(T–C)) is associated with two milk production traits, and this provided further evidence that bPL could be a major gene-controlling milk production trait in Holstein dairy cattle.

An evaluation of the European pig diversity has been carried on by several countries, with the support of the European Union over the period of 1994 to 2000. This article presents an overview of the results of this investigation, focussing on two genetic marker techniques, namely microsatellites (MS) and amplification of fragment length polymorphism (AFLP). Nearly 200 loci were characterised on about 50 individuals from each of 59 to 71 breeds, according to the marker considered. The analysis of diversity, based on genetic distances, led to similar conclusions for the two marker types (MS and AFLP), in spite of a markedly lower total diversity of AFLP compared to MS. The analysis of the MS loci showed that the allelic diversity pattern among breeds was quasi-independent from the diversity pattern based on allele frequencies. Genetic distances showed no particular clustering of local with international breeds, confirming the genetic uniqueness of the European local breeds compared to mainstream international breeds. The taxonomy of the local breeds revealed a cluster of the Iberian type breeds, in contrast with a wider dispersal of the breeds from other countries. Phylogeny often disagreed with documented breeds’ history, showing the complex migration/admixture patterns which underlie the breeds’ relationships. Methodologies developed in this investigation as well as the database and the DNA depository created should provide support for further innovative research in the field of domestic animal diversity management.

Binational genetic evaluation between Germany and France were performed for each type trait using a single-trait MACE (multiple across-country evaluation) model. Daughter yield deviations (DYD) of bulls having 30 equivalent daughter contributions or more were the data for parameter estimation. Full pedigree information of bulls was used via sire and dam relationships. In general, across-country genetic correlation estimates were in agreement with what is observed by Interbull. The estimated correlations were over 0.93 for stature, rump angle, udder depth, front teat placement, teat length and rear teat placement. These traits have been classified in both countries for a long period of time. However, some other type traits were included later in the French type classification system (most of them since 2000): chest width, body depth, angularity, rump width, rear leg rear view, fore udder and rear udder height. The estimated correlations for these traits were relatively low. In order to check changes in genetic correlations over time, data from bulls born until the end of 1995 were discarded. Higher genetic correlation estimates between both countries were obtained by using more recent data especially for traits having lower genetic correlation, e.g. body depth correlation increased from 0.55 to 0.83. Once genetic correlations were estimated, binational genetic evaluation between Germany and France were performed for each type trait using DYD of bulls. The rankings of bulls obtained from this evaluation had some differences with Interbull rankings but a similar proportion of bulls from each country was found. Finally, more computationally demanding binational evaluations were performed using yield deviations of cows for binational cow comparison. The rankings obtained were influenced by the number of daughters per bull and heritabilities used in each country.

Texel muscling quantitative trait locus (TM-QTL) is a QTL on chromosome 18, originally identified in purebred UK Texel sheep, which was reported to increase ultrasonically measured muscle depth at the third lumbar vertebra by around 4% to 7%. The objective of the present study was to comprehensively evaluate the TM-QTL and to determine whether it could provide benefits to the UK sheep industry through increased carcass meat yield in crossbred slaughter lambs. Effects of this QTL on a range of carcass traits, including those measured in vivo and by dissection, were evaluated in heterozygous carrier and non-carrier lambs produced by crossing heterozygous carrier Texel rams with non-carrier Mule (Bluefaced Leicester × Scottish Blackface) ewes from a lowland flock. The TM-QTL was found to increase loin muscling in crossbred lambs at a given live weight or carcass weight, as measured by ultrasound, X-ray computed tomography (CT) and carcass dissection. Depth of M. longissimus lumborum (MLL) was greater in TM-QTL carrier lambs compared to non-carriers as measured by both ultrasound at the third lumbar vertebra (+4.5%; P = 0.033) and CT scanning at the fifth lumbar vertebra (+6.7%; P = 0.004). Width and area of MLL measured using CT were also greater in TM-QTL carrier lambs compared to non-carriers (+3.0%; P = 0.013 and +5.1%; P = 0.047, respectively). Loin muscle volume measured using CT was greater in TM-QTL carriers than in non-carriers (+5.9%; P = 0.005) and the dissected weight of the MLL was +7.1% greater in TM-QTL carriers compared to non-carriers (P < 0.001). The proportion of the total carcass lean meat yield (LMY) that was contained within the loin region was slightly higher in TM-QTL carriers than in non-carriers (0.154 v. 0.145; P = 0.006). However, TM-QTL was found to have no significant effect on the total weight or proportion of LMY or of saleable meat yield in the carcass measured by dissection, or on muscling in the hind leg measured by CT or dissection. This work has verified that the inheritance of TM-QTL is associated with increased loin muscling in crossbred lambs, as has previously been reported for purebred Texel lambs.

As a result of the European ban of in-feed growth-promoting antibiotics, new strategies are being developed to increase the resistance to disease in farm animals. In pig production, this is of particular importance during the weaning transition when piglets are subjected to major stressful events, making them highly sensitive to digestive disorders. At this time, the development of both innate and adaptive immunity at the mucosal surface is critical in preventing the potential harmful effects of intestinal pathogenic agents. Strategies aiming at stimulating natural host defences through the use of substances able to modulate immune functions have gained increasing interest in animal research, and different bioactive components a priori sharing those properties have been the subject of in vivo nutritional investigations in pig. Among these, yeast derivates (β-glucans and mannans) are able to interact with immune cells, particularly phagocytic cells. However, studies where they have been fed to pigs have shown inconsistent results, suggesting that their ability to target the sensitive immune cells through the oral route is questionable. The plant extracts, which would benefit from a positive image in the public opinion, have also been tested. However, due to a lack of data on the bioactive components of particular plants and the large diversity of species, it has proved difficult to prepare extracts of equivalent potency and thus, the literature on their influence on pig immunity remains inconclusive. In considering piglet immunity and health benefits, the most promising results to date have been obtained with spray-dried animal plasma, whose positive effects would be provided by specific antibodies and non-specific competition of some plasma components with bacteria for intestinal receptors. The major positive effect of spray-dried animal plasma is in reducing the infiltration of gut-associated lymphoid tissue by immune cells, which is likely to be the result of a decreased colonisation by potentially harmful bacteria. This review also highlights the limitations of some of the published in vivo studies on the immunomodulatory activity of certain feed additives. Among those, the lack of standardisation of extracts and the heterogeneity of piglet-rearing conditions (e.g. exposure to pathogens) are likely the most limiting.

Adipocyte size and number are correlated with fat deposition, which is of major concern to human health and pork producers. To identify quantitative trait loci (QTL) for adipocyte size and number in pigs, a total of 341 F2 animals at 240 days in a White Duroc × Erhualian cross were measured for the area, perimeters, volume and number of adipocyte in abdominal fat. A genome scan was performed on these animals and their parents and grandparents with 183 microsatellite markers spanning the pig genome. Five chromosomal regions showed effects on the traits measured, predominantly on adipocyte size, on pig chromosome (SSC) 1, 4, 7 and 9. Neither of these QTL has been reported before this study. The QTL for adipocyte size detected in this study perfectly correspond to the previously reported QTL for fatness traits on SSC1, 4 and 7. The most significant association was evidenced at 58 cM on SSC7. At the locus, the favorable allele decreasing adipocyte size was unusually originated from the obese Erhualian breed. Only a suggestive QTL was detected for adipocyte number on SSC9. The results shed new lights on the understanding of the genetic basis of fatness traits in pigs.

The National Scrapie Plan (NSP) was launched in Great Britain in 2001, with the aim of eventually eradicating scrapie, a small ruminant transmissible spongiform encephalopathy, from the national sheep flock. Specifically, a selective breeding programme, the Ram Genotyping Scheme, was devised enabling pedigree ram breeders to reduce the number of scrapie-susceptible genotypes from their flocks. The effect of large-scale manipulation of PrP genotypes on commercially important traits within the sheep industry is, however, unknown. We have therefore examined production traits in a total of 43 968 lambs from 32 pedigree breeders across three British hill breeds, comprising 8163 North Country Cheviot (Hill), 21 366 Scottish Blackface and 14 439 Welsh Mountain lambs. Traits examined included: weights at birth, 8 and 20 weeks; ultrasonic fat and muscle depth, and average daily weight gain from 8 to 20 weeks. Linear mixed models were fitted for each trait, including animal (direct) genetic effects and up to three maternal effects. Potential associations with the PrP gene were assessed by fitting either PrP genotype or number of copies of individual alleles as fixed effects. A number of breed-specific significant associations between production traits and the PrP gene were found, but no consistent significant effects were detected across the three breeds. Breed-specific effects were as follows: (i) 0.37 kg higher birth weights (BWTs) in AHQ homozygous North Country Cheviot (Hill) lambs (P < 0.01); (ii) 0.16 kg higher BWTs in ARR homozygous Scottish Blackface lambs (P < 0.05); (iii) 0.5 kg higher 8-week weights in VRQ heterozygous Scottish Blackface lambs (P < 0.01); (iv) a 0.72 kg decrease in scan weight associated with homozygous ARR Welsh Mountain lambs (P < 0.01); (v) 0.51 mm higher ultrasonic muscle depths in AHQ homozygous Welsh Mountain lambs (P < 0.01); (vi) 0.48 mm lower ultrasonic muscle depths in Welsh Mountain lambs carrying one or more copies of the ARR allele (P < 0.05) and (vii) 0.2 mm higher ultrasonic fat depths in heterozygous VRQ Welsh Mountain lambs (P < 0.05). The use of a Bonferroni correction to define appropriate significance thresholds across the three datasets, which account for the large number of independent comparisons made, resulted in breed-specific comparisons, with P < 0.01 becoming significant at P∼0.05, and the remaining breed-specific comparisons no longer being significant. The absence of a common effect across the three breeds suggests that any true association found may be due to breed-specific alleles of neighbouring genes in linkage disequilibrium with the PrP locus.

H2A histone family, member Z (H2A.Z) is required for early mammalian development. In the present study, the 932 bp of full-length cDNA encoding a 128 amino-acid protein and the sequences of intron 2 to 4 of the porcine H2A histone family, member Z (pH2AFZ) gene were obtained. By comparative sequencing of pH2AFZ gene in Large White and Meishan pigs, a 4 bp deletion/insertion in intron 2 was detected and a PCR-Bsu15I-RFLP was established to detect this variation. In DIV (4th Dam line of Chinese lean-type new lines) pigs, the first-parity females with AA genotype had fewer piglets born alive (−2.64 and −1.83 piglets per litter) than those with AB (P < 0.01) and BB (P < 0.05) genotype. The additive allelic and dominance effect were estimated to be 0.92 (P < 0.05) and −0.87 piglets per litter (P < 0.01) for number of piglets born alive, respectively. This result suggests that the pH2AFZ gene might be a good candidate gene of litter-size trait and provides some marker information for marker-assisted selection.

Using data on age at 100 kg of three pig breeds (Large White, Landrace and Duroc) the connectedness between herds in China was evaluated by the connectedness rating (CR) method. The results show that most herds in China have low average CR (0–3.59%) with other herds. In Large White, of the 36 herds analyzed there are 20 herds, which are connected with at least one other herd. In Landrace and Duroc, of the 27 and 18 herds analyzed, only four and five herds, respectively, were found having connectedness with other herds. Generally, the connectedness exists only among two or few herds in the same region. A certain degree of connectedness between herds is a precondition for cross-herd genetic evaluation. A national or regional cross-herd genetic evaluation is not practicable at the present time in China. More intense efforts are needed to establish and enhance the connectedness between herds by means of extensively using artificial insemination (AI) in the swine industry in China.