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Holistic analyses of various levels of the genotype-phenotype-map, particularly of the genome and transcriptome and their integration contribute to the elucidation of the molecular basis of inheritance and trait expression. The individual variation of the genome, transcriptome, proteome, and metabolome are put into relation with each other and with the appearance of the animal. Towards balanced livestock breeding functional traits become increasingly important and lead to the adaptation of the breeding objectives. The data collected by the application of omics techniques provides new molecular phenotypes that contribute to our understanding of complex relationships between production and functional traits and environmental factors. Biomarkers can be derived from these molecular phenotypes and serve as indicators of the state of an organism. Biomarkers provide information on appropriate management or treatment measures, serve as a new trait for complex organismal traits and contribute to the identification of trait-associated genes and alleles for the marker-/gene-assisted selection. As new molecular traits biomarker are tools for animal breeding and animal husbandry, which is exemplified in this paper. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) and mRNAs establish a complex regulatory network influencing diverse biological pathways including muscle development and growth. Elucidating miRNA-dependent regulatory networks involved in muscle development could provide additional insights into muscle traits largely predefined during prenatal development. The present study aimed to determine differentially expressed transcripts and functional miRNA- mRNA relationships associated with different stages of skeletal muscle development in two pig breeds, German Landrace and Pietrain, distinct in muscle characteristics. A comparative transcriptional profiling of longissimus dorsi muscle tissues from fetuses at 35, 63 and 91 days post-conception as well as adult pigs (180 days postnatum) was performed using the Affymetrix GeneChip porcine genome microarray. Differential expression patterns were identified to be associated with muscularly developmental stages and breed types. The integration of miRNA expression data and ingenuity pathways analysis (ipa) pathway analysis revealed several miRNA-dependent regulatory networks related to muscle growth and development. The present results provide insights into muscle biology for further improvement of porcine meat quality. [ABSTRACT FROM AUTHOR]

Pre-slaughter stress has a negative impact on animal welfare and on meat quality. Aggressive behaviour when pigs are mixed together for transportation to, or on arrival at, the abattoir is an important factor in pre-slaughter stress. Aggressiveness of pigs varies between individuals in the population, and this study investigated its effects on stress and meat quality at slaughter. We mixed pigs at a young age to identify individuals of high (H) or low (L) aggressive temperament using the previously validated approach of lesion scoring. To contrast extremes of social stress single-sex groups of eight pigs were mixed according to their aggressiveness in HH, HL or LL combinations or left unmixed (U) prior to transport and slaughter (n=271). Each treatment was replicated in at least two groups in each of four slaughter batches. Mixing per se had little effect, but mixed groups composed of aggressive pigs (HH) had more carcass skin lesions and higher levels of plasma cortisol at slaughter and had loin muscle samples with higher pH at 24 h, and lower redness (a*) and yellowness (b*) compared to the other treatments. Females had higher levels of plasma cortisol at slaughter, a more rapid decline in pH post-slaughter and greater lean content of meat. Lactate and creatine kinase (CK) levels and meat pH were affected by the interaction of sex and treatment. Genetic factors, dam and sire line composition, and halothane locus (ryanodine receptor 1, RYR1) genotype, also affected a number of production and meat quality parameters as expected. Additionally, 'commercially normal' levels of social stress were studied in four further slaughter batches with no manipulation of group composition (n=313). In these pigs, the proportion of unfamiliar pigs and group size of lairage groups explained limited variation in lesion scores at slaughter, but earlier aggressiveness did not. High numbers of skin lesions on the carcass were associated with high levels of cortisol and lactate and low glucose at slaughter, but not with meat quality measures. When stress and meat quality measures were compared for all pigs, high lactate was associated with low early pH and high drip loss, while high cortisol and CK were associated with high pH at 24 h and changes in meat colour. In conclusion, mixing pigs of above average aggressiveness resulted in greater aggression and stress, and changes in meat quality parameters, consistent with the effects of pre-slaughter stress on muscle chemistry. [ABSTRACT FROM AUTHOR]

Ten genes ( ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain × (Landrace × Large White), Duroc × (Landrace × Large White) as well as in an experimental F2 population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human–porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of ≤ 0.05; PDGFRA revealed no association reaching the P ≤ 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical–genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations. [ABSTRACT FROM AUTHOR]

We performed a genome-wide QTL scan for production traits in a line cross between Duroc and Pietrain breeds of pigs, which included 585 F2 progeny produced from 31 full-sib families genotyped with 106 informative microsatellites. A linkage map covering all 18 autosomes and spanning 1987 Kosambi cM was constructed. Thirty-five phenotypic traits including body weight, growth, carcass composition and meat quality traits were analysed using least square regression interval mapping. Twenty-four QTL exceeded the genome-wide significance threshold, while 47 QTL reached the suggestive threshold. These QTL were located at 28 genomic regions on 16 autosomal chromosomes and QTL in 11 regions were significant at the genome-wide level. A QTL affecting pH value in loin was detected on SSC1 between marker-interval S0312- S0113 with strong statistical support ( P < 3.0 × 10−14); this QTL was also associated with meat colour and conductivity. QTL for carcass composition and average daily gain was also found on SSC1, suggesting multiple QTL. Seventeen genomic segments had only a single QTL that reached at least suggestive significance. Forty QTL exhibited additive inheritance whereas 31 QTL showed (over-) dominance effects. Two QTL for trait backfat thickness were detected on SSC2; a significant paternal effect was found for a QTL in the IGF2 region while another QTL in the middle of SSC2 showed Mendelian expression. [ABSTRACT FROM AUTHOR]

Mannose-binding lectin (MBL) mediates activation of the complement system via the lectin pathway. Two forms of MBL, MBL-A and MBL-C, were characterized in rodents, rabbits, bovine and rhesus monkeys, whereas only one form was identified in humans, chimpanzees and chickens. The two forms are encoded by two distinct genes named MBL1 and MBL2, which have been identified in many species including the pig. In this report, we studied the two porcine genes MBL1 and MBL2. The porcine MBL genes had higher identities to bovine rather than primate and rodent sequences. Both genes were assigned to chromosome 14 by radiation hybrid panel and linkage mapping. Both MBL genes were highly expressed in liver. MBL1 was also found to be expressed in the lung, testis and brain, whereas low expression of MBL2 was detected in the testis and kidney. New single nucleotide polymorphisms of porcine MBL2 gene were found and genotyped in an experimental F2 pig population, together with a previously reported SNP of MBL1. MBL1 genotypes differed in C3c serum concentration, i.e. in vivo complement activity, at P < 0.1. Correspondingly, linkage analysis revealed a quantitative trait locus for C3c serum level close to the position of the MBL genes. The study thus promotes the porcine MBL genes as functional and positional candidate gene for complement activity. [ABSTRACT FROM AUTHOR]

β-actin ( ACTB) was examined as a direct functional candidate gene for the possible association with sperm concentration, motility (MOT), semen volume per ejaculate, plasma droplet rate, abnormal sperm rate (ASR) and the fertility traits, non-return rate and number of piglets born alive (NBA). Three polymorphisms in intron 3 (T>C) and one polymorphism in exon 4 (T>C) of porcine ACTB gene were identified by comparative sequencing of animals of the breeds Pietrain and Hampshire. Association analysis revealed that haplotypes affected the variation of the traits MOT, ASR and NBA. The beneficial haplotypes may provide considerable improvement of sperm quality and fertility in the tested commercial boar population. [ABSTRACT FROM AUTHOR]

The porcine corticotropin-releasing hormone (CRH) gene is a functional–positional candidate for quantitative tract loci on porcine chromosome 4 with major effects on growth and carcass composition. In addition, the central role of CRH in the neuroendocrine response to stress implicates the CRH gene as a functional candidate for meat quality. Association of a single nucleotide polymorphism (SNP) in the promoter region of the porcine CRH gene (g.233C>T) with several growth, carcass and meat quality traits was examined using more than 2000 individuals from four commercial lines: German Landrace (LR), Pietrain (Pi), German Large White × German Landrace (F1) and the German commercial fattening pig cross of Pietrain × F1 (PiF1). Significant association of the CRH SNP was found with feed conversion ratio in the PiF1 line, with carcass length in the LR line and with lean content in the F1, LR and Pi lines. Moreover, significant association with meat colour was found in the Pi and LR lines; however, the effects were in opposite directions. The presented results indicate that sequence variation in the porcine CRH gene has no major effect on growth and carcass composition in commercial pig lines, although it may significantly contribute to variation in meat quality. The g.233C>T SNP may be in incomplete linkage disequilibrium with causal mutations and/or exhibit effects in the context of DNA variation at other interacting loci. [ABSTRACT FROM AUTHOR]

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc × Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes. [ABSTRACT FROM AUTHOR]

α-Actinins (ACTN1andACTN4) andγ-actin (ACTG2), were investigated as candidate genes on the basis of their known functions, for their possible association with sperm concentration, motility, semen volume per ejaculate, plasma droplets rate, abnormal sperm rate and the fertility traits, non-return rate and number of piglets born alive. Polymorphisms were identified in intron 18 (G>A) of the porcineACTN1gene and in exon 22 (A>C) of the porcineACTN4gene by comparative sequencing of animals from the Pietrain (PI) and Hampshire (HA) breeds. Pietrain (n = 244) and crossbreed PI × HA (n = 112) boars from an artificial insemination boar station were genotyped for the single nucleotide polymorphisms (SNPs) withinACTN1andACTN4as well as for a previously described microsatellite withinACTG2. The study provides evidence for effects ofACTN1on fertility and ofACTG2on sperm quality traits, while no indication of impact ofACTN4on any of these traits was found. [ABSTRACT FROM AUTHOR]

Retinoid X receptors are frequently implicated in their role in embryonic development. However, there is no report regarding their expression in embryos with different qualities. In this study, expression pattern and levels of retinoid X receptor transcripts in different qualities and stages ofin vitro-produced pre-implantation bovine embryos were examined using real-time polymerase chain reaction (PCR) techniques. Four independent cDNA pools per sample were prepared from mRNAs isolated from different developmental-stage embryos, after classifying them to be of good and bad quality. Primers were also designed to amplify products with PCR. Based on analysis, except retinoid X receptor gamma (RXRG) transcripts, the remaining two types (alpha and beta forms) were expressed in all samples with significantly higher (p ≤ 0.05) levels until the eight-cell stage compared with the stages thereafter. However, the transcript levels for bad-quality embryos were consistently lower in all cases in comparison with good-quality embryos. RXRG was identified in 39% of the samples, but all in the pre-embryonic genome activation development stage. Therefore, strong expression patterns of these transcripts in earlier stages indicates their possible role during the maternal phase of embryo development, and the variations of copy number in embryos with different qualities substantiates their possible candidacy as potential quality markers. Moreover, identifying the transcript variations in different qualities and expression of RXRG at these stages is a novel input to the pre-implantation-stage knowledge. [ABSTRACT FROM AUTHOR]

This study was carried out to examine the temporal variation in the relative abundance of transcripts during the post-fertilization stages of bovine embryos derived fromin vitroorin vivoculture. For this purpose, cumulus–oocyte complexes obtained from ovaries from slaughterhouses were matured, fertilized and culturedin vitro. Thein vitroculture was carried out using CR1 medium.In vivoembryos were derived from superovulated and artificially inseminated Simmental heifers and cows. Embryos were recovered from both systems approximately at day 1 (two-cell), day 2 (four-cell), day 3 (eight-cell), day 4 (16-cell), day 5 (morula) and day 7 (blastocyst) after insemination. Relative abundance of target transcripts was performed using real-time PCR. The transcripts studied were the nucleosome assembly protein, mRNA for alivin 1, Pleckstrin homology Sec7 coiled domain, polyadenylate binding protein, NADH dehydrogenase subunit 2, high-mobility group transcription factor, cytokine-like nuclear factor, NY-REN-58 antigen mRNA, mRNA for KIAA1764 and one novel transcript. These transcripts were derived from our previous study conducted using mRNA differential display reverse transcription-polymerase chain reaction (DDRT-PCR) betweenin vitro-produced bovine eight-, 16-cell, morula and blastocyst-stage embryos. The results of the present study have demonstrated the temporal variation in the relative abundance of these transcripts betweenin vitroandin vivoculture systems. Such variation in the relative abundance of transcripts during the post-fertilization developmental stages ofin vitroandin vivoembryos may reflect the effect of thein vitroculture condition on the transcriptional activity thereby on the developmental competence of the resulting embryos. [ABSTRACT FROM AUTHOR]

Twenty expressed sequence tags (ESTs) derived from cDNA libraries of different developmental stages of embryos were mapped using a whole genome bovine hamster radiation hybrid panel. These include 14 markers representing genes, most of which have not so far been mapped in cattle, with another three being novel in both cattle and human. The markers were placed on specific chromosomes with high LOD scores and except two all localizations fit the current human and cattle comparative map. The assignment of these genes further enriches the cattle genome map and also contributes to the international effort of generating comparative maps. [ABSTRACT FROM AUTHOR]

Increasing the number of mapped genes will facilitate (1) the identification of potential candidate genes for a trait of interest within quantitative trait loci regions and (2) comparative mapping. The metabolic activities of the liver are essential for providing fuel to peripheral organs, for regulation of amino acid, carbohydrate and lipid metabolism and for homoeostasis of vitamins, minerals and electrolytes. We aimed to identify and map genes coding for enzymes active in the liver by somatic cell genetics in order to contribute to the improvement of the porcine gene map. We mapped 28 genes of hepatic metabolic pathways including six genes whose locations could be confirmed and 22 new assignments. Localization information in human was available for all but one gene. In total 24 genes were assigned to in the expected chromosomal regions on the basis of the currently available information on the comparative human and pig map while for four genes our results suggest a new correspondence or extended regions of conservation between porcine and human chromosomes. [ABSTRACT FROM AUTHOR]

Summary The genetic variability of various local chicken populations derived from Bolivia, India, Nigeria and Tanzania was evaluated with 22 microsatellites. Between two and 11 alleles per locus were detected. All populations showed high levels of heterozygosity with the lowest value of 45% for the population named Aseel from India and the highest value of 67% for Arusha from Tanzania. A dendrogram was constructed based on CHORD distance by upgma analysis. Within this tree the populations were assorted according to their geographical origin. Bootstrapping values within the dendrogram were between 37 and 99%. The contribution of the determination of genetic variability with genetic markers to the decision on conservation and/or further use of the populations in crossbreeding programs designed to create genetic stocks with improved adaptability and productivity in tropical countries is discussed. [ABSTRACT FROM AUTHOR]

Presents a study on the estimation of genetic variation based on deoxyribosenucleic acid (DNA) fingerprinting and microsatellites in samples of chicken lines. Details on the breeds; Detection of microsatellites; Measures of genetic variation; Description of genetic distance between populations.

Presents information on a study in which a deoxyribonucleic acid (DNA) fingerprinting technique was used to assess the extent of genetic variation within and between twelve lines of chickens of different origin. Materials and methods used to conduct this study; Measures of genetic variation within populations; Comparison of representative banding patterns of all twelve populations of chickens; Discussion of the study.