Genetics of cattle temperament and its impact on livestock production and breeding – a review

Abstract. Cattle temperament, which describes individual behaviour differences with regard to a stressor or environmental challenge, is known for its impact on working safety, adaptability to new housing conditions, animal productivity and for evaluation of animal welfare. However, successful use of temperament in animal breeding and husbandry to improve keeping conditions in general or animal welfare in particular, requires the availability of informative and reproducible phenotypes and knowledge about the genetic modulation of these traits. However, the knowledge about genetic influences on cattle temperament is still limited. In this review, an outline is given for the interdependence between production systems and temperament as well as for the phenotyping of cattle temperament based on both behaviour tests and observations of behaviour under production conditions. In addition, the use of temperament as a selection criterion is discussed.

Transcriptional profiling and miRNA-dependent regulatory network analysis of longissimus dorsi muscle during prenatal and adult stages in two distinct pig breeds

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.

Integrating expression profiling and whole-genome association for dissection of fat traits in a porcine model

Traits related to fatness, important as economic factors in pork production, are associated with serious diseases in humans. Genetical genomics is a useful approach for studying the effects of genetic variation at the molecular level in biological systems. Here we applied a whole-genome association analysis to hepatic gene expression traits, focusing on transcripts with expression levels that correlated with fatness traits in a porcine model. A total of 150 crossbred pigs [Pietrain × (German Large White × German Landrace)] were studied for transcript levels in the liver. The 24K Affymetrix expression microarrays and 60K Illumina single nucleotide polymorphism (SNP) chips were used for genotyping. A total of 663 genes, whose expression significantly correlated with the trait "fat area," were analyzed for enrichment of functional annotation groups as defined in the Ingenuity Pathways Knowledge Base (IPKB). Genes involved in metabolism of various macromolecules and nutrients as well as functions related to dynamic cellular processes correlated with fatness traits. Regions affecting the transcription levels of these genes were mapped and revealed 4,727 expression quantitative trait loci (eQTL) at P < 10⁻⁵, including 448 cis-eQTL. In this study, genome-wide association analysis of trait-correlated expression was successfully used in a porcine model to display molecular networks and list genes relevant to fatness traits.

The spatial expression pattern of antimicrobial peptides across the healthy bovine udder

Antimicrobial peptides are key molecules in local host defense. With the aim to better understand the possible involvement of these peptides in the prevention of bovine mastitis, we determined, for the first time to our knowledge, the spatial pattern of constitutive expression of 5 bovine beta-defensins and bovine psoriasin (S100A7) across 5 localizations of the bovine mammary gland applying a quantitative real-time PCR approach. We observed 3 different expression patterns in the healthy udder: 1) constitutive expression of the lingual and tracheal antimicrobial peptides (LAP and TAP), as well that of bovine neutrophil beta-defensins 4 and 10 (BNBD4 and BNBD10), is essentially restricted to the mammary lymph node; 2) bovine beta-defensin 1 (DEFB1) is mainly expressed in the cisternal epithelium and the Rosette of Fürstenberg; 3) strong constitutive mRNA expression of the calcium-binding protein S100A7, which is also known as psoriasin and which has been reported to be highly active against Escherichia coli, was detected in the streak canal. These results indicate a crucial role of S100A7 in the early-stage prevention of coliform mastitis, and the analyzed beta-defensins might be regarded as inducible weapons against already invading pathogens.

Analysis of key molecules of the innate immune system in mammary epithelial cells isolated from marker-assisted and conventionally selected cattle

Mastitis is the most prevalent infectious disease in dairy herds. Breeding programs considering mastitis susceptibility were adopted as approaches to improve udder health status. In recent decades, conventional selection criteria based on phenotypic characteristics such as somatic cell score in milk have been widely used to select animals. Recently, approaches to incorporate molecular information have become feasible because of the detection of quantitative trait loci (QTL) affecting mastitis resistance. The aims of the study were to explore molecular mechanisms underlying mastitis resistance and the genetic mechanisms underlying a QTL on Bos taurus chromosome 18 found to influence udder health. Primary cell cultures of mammary epithelial cells from heifers that were selected for high or low susceptibility to mastitis were established. Selection based on estimated pedigree breeding value or on the basis of marker-assisted selection using QTL information was implemented. The mRNA expression of 10 key molecules of the innate immune system was measured using quantitative real-time PCR after 1, 6, and 24 h of challenge with heat-inactivated mastitis pathogens (Escherichia coli and Staphylococcus aureus) and expression levels in the high and low susceptibility groups were compared according to selection criteria. In the marker-assisted selection groups, mRNA expression in cells isolated from less-susceptible animals was significantly elevated for toll-like receptor 2, tumor necrosis factor-alpha, IL-1beta, IL-6, IL-8, RANTES (regulated upon activation, normal t-cell expressed and secreted), complement factor C3, and lactoferrin. In the estimated pedigree breeding value groups, mRNA expression was significantly elevated only for V-rel reticuloendotheliosis viral oncogene homolog A, IL-1 beta, and RANTES. These observations provide first insights into genetically determined divergent reactions to pathogens in the bovine mammary gland and indicate that the application of QTL information could be a successful tool for the selection of animals resistant to mastitis.

Effects of threshold choice on the results of gene expression profiling, using microarray analysis, in a model feeding experiment with rats

Abstract. Global gene expression studies using microarray technology are widely employed to identify biological processes which are influenced by a treatment e.g. a specific diet. Affected processes are characterized by a significant enrichment of differentially expressed genes (functional annotation analysis). However, different choices of statistical thresholds to select candidates for differential expression will alter the resulting candidates list. This study was conducted to investigate the effect of applying a False Discovery Rate (FDR) correction and different fold change thresholds in statistical analysis of microarray data on diet-affected biological processes based on a significantly increased proportion of differentially expressed genes. In a model feeding experiment with rats fed genetically modified food additives, animals received a supplement of either lyophilized inactivated recombinant VP60 baculovirus (rBV-VP60) or lyophilized inactivated wild type baculovirus (wtBV). Comparative expression profiling was done in spleen, liver and small intestine mucosa. We demonstrated the extent to which threshold choice can affect the biological processes identified as significantly regulated and thus the conclusion drawn from the microarray data. In our study, the combined application of a moderate fold change threshold (FC≥1.5) and a stringent FDR threshold (q≤0.05) exhibited high reliability of biological processes identified as differentially regulated. The application of a stringent FDR threshold of q≤0.05 seems to be an essential prerequisite to reduce considerably the number of false positives. Microarray results of selected differentially expressed molecules were validated successfully by using real-time RT-PCR.

Cytogenetic and radiation hybrid mapping of the bovine <i>interleukin 4 induced 1 (IL4I1)</i> gene to cattle chromosome 18 (Brief Report)

Abstract. The interleukin 4 induced 1 (IL4I1) gene, also known as FIG1, encodes a lysosomal protein in B cells with L-amino oxidase (EC 1.4.3.2) property and a high preference for aromatic amino acid substrates implicating a fundamental role in antigene processing and presentation (MANSON et al. 2004). In human, IL4I1 has been assigned to chromosome 19q13.3-19q13.4, a hot spot for susceptibility to several autoimmune diseases (CHAVAN et al. 2002). Based on comparative genome data between human and cattle (GOLDAMMER et al. 2002), an assignment of IL4I1 to Bos taurus chromosome 18 (BTA18) has been predicted within a quantitative trait locus for somatic cell score (KÜHN et al. 2003). This prediction is supported by the putative bovine sequence for IL4I1, LOC520692, which has been assigned to BTA18 close to 56.1 megabases within the annotated bovine sequence (NCBI build Btau-4.0). Therefore, we started positional cloning of bovine IL4I1, as a candidate gene related to adaptive immunity, i.e. during udder infections in cattle. Here we present the physical assignment of the bovine IL4I1 gene by fluorescence in situ hybridization (FISH) and radiation hybrid (RH) mapping.

Association of ZYX polymorphisms with carcass and meat quality traits in commercial pigs

Zyxin (ZYX) is one of the proteins in focal adhesions along the actin fibers playing a role in actin organization and signal transduction. By radiation hybrid and genetic mapping we assigned ZYX to porcine chromosome 18 in the area of quantitative traits loci for carcass and meat quality and muscle fiber traits and hence considered ZYX a functional positional candidate gene. Analysis of a newly detected SNPs (c.+279 C>T, c.+399 A>G, c.+522 A>G) in pigs from different commercial breeds (Pietrain [Pi], German Landrace [LR], German Large White x German Landrace [F1] and PiF1) revealed a significant association with carcass traits (including: side- and backfat thickness, loin weight and carcass lean content) and meat quality traits (including: pH, color and drip loss). However, the lack of consistent association across all pig populations in this study indicates that the association of the SNPs may be depending on causal mutations in linkage disequilibrium and/or interactions with other loci.

Marker assisted selection of heifers improved milk somatic cell count compared to selection on conventional pedigree breeding values

Abstract. Although mastitis in cattle is an important factor for dairy economy and animal welfare and although udder health parameters have a substantial genetic variability, in many countries there is little or no improvement of udder health in the conventional commercial breeding programs. Strategies implementing information about Quantitative trait loci (QTL) via genetic marker information seem to offer new prospects to improve this situation. In a proof-of-principle approach, we show that selection of German Holstein heifers prior to first calving based on marker information regarding a confirmed QTL affecting somatic cell score (SCS) on bovine chromosome 18 (BTA18) (MAS strategy) indeed enabled prediction of halfsibs with a high (q) or a low (Q) number of somatic cells in milk already early in the first lactation. Compared to a strategy relying on conventional breeding values only (CON strategy), selection including marker information resulted in a stronger discrimination between and a higher uniformity within the MAS-Q and -q groups compared to the CON-Q and – q groups selected by conventional selection strategies. The selected heifers, which are clinically unaffected, however genetically different in their capacity of mammary gland protection against pathogens, will serve as tools for a comprehensive expression analysis to highlight molecular processes underlying a different genetic predisposition to mastitis susceptibility. Thus, functional mechanisms resulting in a decreased susceptibility of the Q individuals can be identified to further improve selection on udder health in cattle.

Staphylococcus aureus and Escherichia coli cause deviating expression profiles of cytokines and lactoferrin messenger ribonucleic acid in mammary epithelial cells

Pathogens invading the mammary gland cause a complex signaling network that activates the early immune defense and leads to an outcome of inflammation symptoms. To examine the importance of mammary epithelial cells in these regulations and interactions resulting in a pathogen-related course of mastitis, we characterized the mRNA expression profile of key molecules of the innate immune system by quantitative real-time PCR. Mammary gland epithelial cells isolated on d 42 of lactation from 28 first-lactation Holstein dairy cows were cultured separately under standardized conditions and treated for 1, 6, and 24 h with heat-inactivated gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria. Both pathogens increased mRNA expression patterns of proteins involved in pathogen recognition such as Toll-like receptors and nuclear factor-kappa B, whereas gram-negatives acted as a stronger stimulus. Furthermore, this could be confirmed by the expression profile of the proinflammatory cytokines tumor necrosis factor alpha, IL-1 beta, IL-6, and chemokines such as IL-8 and RANTES (regulated upon activation, normal T-cell expressed and secreted). Remarkably, at a low level of mRNA expression after 1 h of treatment these cytokines and chemokines were expressed at a significantly higher level in Staphyloccocus aureus than in Escherichia coli affected cells. Lactoferrin showed a deviating expression pattern to pathogen stimulation (i.e., at the 1-h measuring point Escherichia coli induced a higher mRNA expression, whereas the highest level was reached after 24 h of stimulation with Staphylococcus aureus). Complement factor 3 was the only measured factor that responded equally to both microorganisms. Our data emphasize the role of mammary epithelial cells in the immune defense of the udder and confirm their contribution to pathogen-related different courses of mastitis.

Trait-associated expressed hepatic and intestine genes in cattle of different metabolic type--putative functional candidates for nutrient utilization

The present study aimed at identifying bovine hepatic and intestinal DNA sequences expressed breed specifically as potential functional candidate genes for nutrient transformation. Transcript levels of 29 expressed sequence tags (ESTs) were analysed comparatively in the liver and intestine of growing Charolais and German Holstein bulls by real-time RT-PCR. In previous studies, these ESTs were characterized as differentially displayed in mRNA differential display of cows varying in metabolic type and harbouring single nucleotide polymorphisms. Breed-specific gene expression levels indicate significantly increased hepatic metabolic activity in Charolais and increased intestinal metabolic activity in German Holstein bulls. Transcript levels of six functional genes measured in liver (NDUFB8, NACA, UAP1, SAH) and intestine (FUS/TLS, APOC3), respectively, support this assumption. The observed coincidence of metabolic type-specific expressed ESTs with variant ESTs showing breed-specific allele distribution points to functional genetic variants located in the vicinity of the analysed sequences. In addition, location of most of the breed specifically expressed ESTs within chromosome regions known to be affecting carcass and growth traits in cattle supports the putative candidate gene character of the ESTs identified.

Confirmation of quantitative trait loci for somatic cell score on bovine chromosome 18 in the German Holstein

Abstract. Fifty-one half-sib families with 2768 sires were selected for this study to confirm a quantitative trait locus (QTL) detected within a previous project initiated by the German Cattle Breeders Federation (ADR). The data based on a granddaughter design were divided into two parts and were analysed using linear models and paternal half sib regression methods. The results strongly support the hypothesis that the chromosomal region around marker TGLA227 at the telomeric end of chromosome 18 harbours a QTL for somatic cell score (SCS) in the German Holstein population. Using a two-QTL model the analysis showed evidence for another QTL for SCS in that region on chromosome 18. Further fine mapping studies should be carried out to decide on the two QTL hypothesis.

YAC/BAC contig spanning the MHC class III region of cattle

A contig of the class III region of the bovine major histocompatibility complex (MHC) was established from bacterial and yeast artificial chromosomes using PCR and BAC-end sequencing. The marker content of individual clones was determined by gene and BAC-end specific PCR, and the location of genes and BAC-ends was confirmed analyzing somatic hybrid cells. A comparative analysis indicated that the content and order of MHC class III genes is strongly conserved between cattle and other mammalian species. Fluorescence in situ hybridization localized the bovine class III region to BTA23q21-->q22. The results show that the collection of sequenced BAC-ends is a powerful resource for generating high-resolution comparative chromosome maps.

Mapping of quantitative trait loci for lactation persistency traits in German Holstein dairy cattle

A whole genome scan to map quantitative trait loci (QTL) for persistency of milk yield (PMY), persistency of fat yield (PFY), persistency of protein yield (PPY) and persistency of milk energy yield (PEY) was performed in a granddaughter design in the German Holstein dairy cattle population. The analysis included 16 paternal half-sib families with a total of 872 bulls. The analysis was carried out for the first lactation and for the first three lactations combined using univariate weighted multimarker regression. Controlling the false discovery rate across traits and data sets at a level of 0.15 and treating the four persistency traits as different traits revealed 27 significant QTL. A total of 12 chromosomes showed significant QTL effects on a chromosomewise basis. The DGAT1 effect was highly significant for PPY and protein yield. A haplotype analysis using results of previous studies of the same design revealed a co-segregation of various persistency QTL and QTL affecting health traits like dystocia and stillbirth and functional traits like non-return rate 90 and somatic cell score.

Identification of genetic variants in differentially expressed sequences in cattle of different metabolic type – potential genetic markers of nutrient utilization

Abstract. Two cattle breeds serve as a model to identify genes and genetic variants, respectively, that are potentially associated with nutrient transformation: Holsteins bred for high milk production mainly, and Charolais bred for high body weight with outstanding muscular growth. The major differences between Charolais and Holstein regarding many general body parameters originate from differences in pathways and deposition of nutrients. In an initial experiment, expressed sequence tags (ESTs) differentially displayed between both cattle breeds were isolated by mRNA differential display in liver and intestine. Of the in total identified 277 ESTs, 79 showing the most prominent differences, were screened for single nucleotide polymorphisms (SNPs). Thirty four SNPs were detected in 30 ESTs In a direct sequencing approach based on the comparative sequencing of the corresponding amplicons generated by PCR from genomic DNA pools of 20 animals each of both cattle breeds,. Eighteen of these SNPs showed breed specific distribution of allelic variants. Occurrence of ESTs with a breed specific SNP distribution and localisation of the respective ESTs to chromosome regions known to be affecting carcass and growth traits in cattle suggest a trait association of the respective SNPs. The polymorphic nature of the SNP markers suggests that they will be useful for evaluating whether variation in these genomic regions influences nutrient pathways in cattle.

Clarifications on breakpoints in HSAX and BTAX by comparative mapping of F9, HPRT, and XIST in cattle

The coagulation factor IX gene (F9), the hypoxanthine phosphoribosyl transferase 1 gene (HPRT1), and the X-inactive specific transcript gene (XIST) were physically assigned in cattle to analyze chromosomal breakpoints on BTAX recently identified by radiation hybrid (RH) mapping experiments. Whereas the FISH assignment of XIST indicates a similar location on the q-arm of the human and cattle X chromosomes, the locus of HPRT1 supported the assumption of a chromosome rearrangement between the distal half of the q-arm of HSAX and the p-arm of BTAX identified by RH mapping. F9 previously located on the q-arm of BTAX was assigned to the p-arm of BTAX using RH mapping and FISH. The suggested new position of F9 close to HPRT1 supports the homology between HSAXq and BTAXp. The F9 locus corresponds with the gene order found in the homologous human chromosome segment. XIST was assigned on BTAXq23, HPRT1 and F9 were mapped to BTAXp22, and the verification of the location of F9 in a 5000 rad cattle-hamster whole genome radiation hybrid panel linked the gene to markers URB10 and HPRT1.

The DGAT1 K232A mutation is not solely responsible for the milk production quantitative trait locus on the bovine chromosome 14

The gene, acyl-CoA:diacylglycerol acyltransferase1 (DGAT1), was recently identified as the one underlying the quantitative trait locus (QTL) for milk production traits in the centromeric region of the bovine chromosome 14. Until now, 2 alleles, the lysine variant (increasing fat yield, fat and protein percentage) and the alanine variant (increasing protein and milk yield), were postulated at DGAT1. This study investigated whether the diallelic DGAT1 polymorphism is responsible for all the genetic variation at the centromeric region of this chromosome for milk, fat, and protein yield and fat and protein percentage. A statistical model was applied to a granddaughter design to analyze 16 German Holstein families. The model included the diallelic DGAT1 effect and the QTL transition probability estimated for each chromosomal position by a multiple marker approach. Because the regression coefficient of this probability was corrected for the diallelic DGAT1 polymorphism, it represented a putative conditional QTL effect. The effect of the DGAT1 gene was always highly significant. The conditional QTL effect was significant genomewise for fat percentage at the proximal end of the chromosome and for protein percentage at a more distal chromosomal region. Additional chromosomewise significance was found for fat and protein yield. Our results suggest an additional source of genetic variance on this chromosome for these traits; either one or more additional alleles segregating at DGAT1 that were not previously detected, a second quantitative trait locus affecting these traits, or both.

Mapping of QTL for Body Conformation and Behavior in Cattle

Genome scans for quantitative trait loci (QTL) in farm animals have concentrated on primary production and health traits, and information on QTL for other important traits is rare. We performed a whole genome scan in a granddaughter design to detect QTL affecting body conformation and behavior in dairy cattle. The analysis included 16 paternal half-sib families of the Holstein breed with 872 sons and 264 genetic markers. The markers were distributed across all 29 autosomes and the pseudoautosomal region of the sex chromosomes with average intervals of 13.9 cM and covering an estimated 3155.5 cM. All families were analyzed jointly for 22 traits using multimarker regression and significance thresholds determined empirically by permutation. QTL that exceeded the experiment-wise significance threshold (5% level) were detected on chromosome 6 for foot angle, teat placement, and udder depth, and on chromosome 29 for temperament. QTL approaching experiment-wise significance (10% level) were located on chromosome 6 for general quality of feet and legs and general quality of udder, on chromosome 13 for teat length, on chromosome 23 for general quality of feet and legs, and on chromosome 29 for milking speed. An additional 51 QTL significant at the 5% chromosome-wise level were distributed over 21 chromosomes. This study provides the first evidence for QTL involved in behavior of dairy cattle and identifies QTL for udder conformation on chromosome 6 that could form the basis of recently reported QTL for clinical mastitis.

Genetic predisposition for productive life is associated with functional inactivation of a AP2-binding site in the promoter of the stress protein 70.1-encoding gene in cattle

Abstract. The complex pattern of action for cell viability makes the heat shock protein (HSP) loci to potential candidate genes for stress susceptibility. In the bovine hsp70.1 gene a functional AP2 box variant affecting a significant decrease of cellular stress response, was described. To monitor the distribution of this promoter variant in phenotypically different populations a diagnostic PCR-RFLP assay was developed. As an indicator for individual stress susceptibility the phenotypic trait "productive life" was measured based on the assumption that animals having longer "productive life" might be superior in coping with stress during lifetime. Association of the observed promoter variant with the estimated breeding value "productive life time" was studied in a Holstein sire population and a granddaughter design. Our observations suggest that this polymorphism affects productive life in cattle. Animals with a normal AP2 box are characterised by an increased stress tolerance concluded from their prolonged productive life. These results are supported by the observed different distribution of the hsp70.1 promoter variant in cows of different lactation numbers and degree of selection. Frequency of the mutant hsp70.1-AP2 box allele is significantly lower in cows selected as dams of sires and in cows with an increased lactation number. Additionally, cows with a mutant hsp70.1-AP2 box variant exhibited an increased hazard for culling.

Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits

The bovine CSN1S1 5' flanking region (CSN1S1-5') was screened for polymorphisms in different cattle breeds. Single-strand conformation polymorphisms (SSCP) and sequence analyses revealed four alleles (1-4), two of them being new allelic forms (3 and 4). Sequences were deposited in GenBank with accession numbers AF549499-502. In alleles 1 and 4, potential transcription factor binding sites are altered by the mutations. Using SSCP analysis, all four alleles were identified in German Holsteins. Six intragenic haplo-types comprising CSN1S1-5' (alleles 1, 2, 3, 4) and exon 17 (CSN1S1*B and C) genotypes were found. Linkage mapping using half-sib families from the German QTL project positioned CSN1S1 between the markers FBN14 and CSN3, with 5.6 cM distance between CSN1S1 and CSN3. Variance analysis, using family and CSN1S1 promoter genotypes as fixed effects, of breeding values and deregressed proofs for milk production traits (milk, fat, and protein yield and also fat and protein percentage) revealed significant effects on protein percentage when all families and genotypes were considered. Contrast calculations assigned a highly significant effect to genotype 24, which was associated with highest LS-means for protein percentage breeding values. As CSN1S1 is one of the main caseins in milk, this could be an effect of mutations in regulatory elements in the promoter region. An effect on milk yield breeding values was indicated for genotype 12, but is probably caused by a linked locus.

Quantitative trait loci mapping of functional traits in the German Holstein cattle population

A whole-genome scan to detect quantitative trait loci (QTL) for functional traits was performed in the German Holstein cattle population. For this purpose, 263 genetic markers across all autosomes and the pseudoautosomal region of the sex chromosomes were genotyped in 16 granddaughter-design families with 872 sons. The traits investigated were deregressed breedingvalues for maternal and direct effects on dystocia (DYSm, DYSd) and stillbirth (STIm, STId) as well as maternal and paternal effects on nonreturn rates of 90 d (NR90m, NR90p). Furthermore, deregressed breeding values for functional herd life (FHL) and daughter yield deviation for somatic cell count (SCC) were investigated. Weighted multimarker regression analyses across families and permutation tests were applied for the detection of QTL and the calculation of statistical significance. A ten percent genomewise significant QTL was localized for DYSm on chromosome 8 and for SCC on chromosome 18. A further 24 putative QTL exceeding the 5% chromosomewise threshold were detected. On chromosomes 7, 8, 10, 18, and X/Yps, coincidence of QTL for several traits was observed. Our results suggest that loci with influence on udder health may also contribute to genetic variance of longevity. Prior to implementation of these QTL in marker assisted selection programs for functional traits, information about direct and correlated effects of these QTL as well as fine mapping of their chromosomal positions is required.

Comparative mapping of five coding DNA sequences on cattle chromosomes 7 and 25

Comparative mapping of four genes and one unknown coding DNA sequence in breakpoint positions of bovine chromosomes (BTA) 7 and 25 are presented. Performing a genome data base search five bovine expressed sequence tags from the MARC library matched with human genes coding for the general transcription factor IIIC polypeptide 1 (GTF3C1), the hypothetical protein KIAA0556, the interleukin 4 receptor (IL4R), the regulatory factor X-associated ankyrin-containing protein (RFXANK), and with an unknown human coding sequence partially homologous to the genomic cosmid clone R30923. Loci for these sequences were COMPASS predicted on BTA7 or BTA18 and to BTA18 or BTA25. Mapping was performed in a cattle-hamster somatic hybrid cell panel and a cattle-hamster 5000 rad whole genome radiation hybrid panel. GTF3C1, KIAA0556 and IL4R were assigned to the centromere region of BTA25 and RFXANK and R30923 close to the centromere of BTA7. The assignments contribute to the identification of evolutionary chromosome break points between human chromosomes 16 and 19 and BTA7, BTA18, and BTA25.

Mapping of the bovine blood group systems J, N', R', and Z show evidence for oligo-genetic inheritance

Genes determining the bovine erythrocyte antigens were mapped by linkage analysis. In total 9591 genotypes of 20 grandsire families with 1074 sires from a grand-daughter design were elucidated for the genes determining the erythrocyte antigens EAA, EAB, EAC, EAF, EAJ, EAL, EAM, EAN', EAR', EAS, EAT', and EAZ according to standard paternity testing procedures in the blood typing laboratories. Linkage analyses were performed with 248 microsatellite markers, eight SSCP markers and four polymorphic proteins and enzymes covering the 29 autosomes and the pseudoautosomal region of the sex chromosomes. The number of informative meioses for the blood group systems ranged from 76 to 947. Blood group systems EAM and EAT' were non-informative. Most of the erythrocyte antigen loci showed significant linkage to a single chromosome and were mapped unequivocally. The genes determining erythrocyte antigen EAA, EAB, EAC, EAL, and EAS were mapped to chromosomes 15, 12, 18, 3, and 21, respectively. Lod-score values ranged from 11.43 to 107.83. Moreover, the EAF system could be mapped to chromosome 17. However, the EAN' system previously known as part of the EAF system could be mapped to chromosome 5. In addition, the blood group systems EAJ, the new EAN', EAR', and EAZ, showed significant linkage to microsatellite markers on various chromosomes and also to other blood groups. The appearance of a single blood group system might be therefore either dependent on the existence of other blood group systems or because of an interaction between different loci on various chromosomes as is known in humans and in pigs.

Functional promoter variants of highly conserved inducible hsp70 genes significantly affect stress response

Promoter variants differing in potential cis-acting elements and showing impaired binding of corresponding transcription factors are described in the inducible porcine hsp70.2 gene (GC box; initiator-like region, InR) and in its bovine homologue (AP2 site), respectively. Interestingly, all these promoter variants are stable established in the analysed populations in spite of significant negative effects on transcriptional activity and indications of not neutral behaviour in response to breeding selection. Moreover, in pigs they are likely to be evolutionary fixed as suggested by their presence in recent breeds and in wild boars as well. Compensation of the effect of the observed 'down'-mutations by further yet unknown gene variants is assumed.

Expression of the aromatase cytochrome P450 encoding gene in cattle and sheep

During this report the tissue-specific expression and promoter usage of the aromatase cytochrome P450 encoding gene, Cyp19, are compared between cattle and sheep. In addition, data will be presented on the identification of cis-acting regulatory sequences located in the bovine placenta-specific promoter 1.1. In cattle and sheep Cyp19 is mainly expressed in the foetal placental layer and ovarian granulosa cells but also in other organs as brain or testis. Differently spliced transcripts of Cyp19 which include an invariable coding region but a variable 5'-untranslated region could be detected in tissues of both species. However, in contrast to ovary and brain which express homologous transcript variants, different transcripts are present in placentae suggesting that also different placenta-specific promoter regions are active in cattle and sheep. The analysis of the chromatin structure of the main placental promoter 1.1 in different bovine tissues revealed that hypomethylation and the occurrence of DNaseI hypersensitive sites (HS) within this region are associated with promoter activity. Active regulatory elements were identified in reporter gene studies in JEG-3 choriocarcinoma cells. The co-localisation of an E-box element within one of the placenta-specific HS suggests that this element is important for Cyp19 expression in the bovine placenta.

Sex determination in cattle based on simultaneous amplification of a new male-specific DNA sequence and an autosomal locus using the same primers

A PCR-based method for sex determination of bovine DNA samples and embryo biopsies is presented. Using only one primer pair both the male-specific sequence FBNY (127 bp) and a sex-independent control PCR-fragment, the microsatellite marker FBN17 (136-140 bp) are generated in the same PCR reaction. Synteny mapping assigned the male-specific sequence to bovine chromosome Y (BTA Y), whereas FBN17 was mapped to bovine chromosome 2. Localisation of FBNY on BTA Y was confirmed by fluorescence in hybridisation of two BAC clones containing the male-specific sequence. There was no amplification of the male-specific target sequence FBNY in sheep, pig, goat, mice, man, and several wild species of the tribe Bovini. The bovine male-specific fragment was detected in dilutions containing as little as 10 pg genomic DNA and in blastomeres from embryo biopsies. The PCR assay presented here does require neither restriction endonuclease digestion of the PCR product nor additional nested PCR steps. Owing to the advantage of parallel amplification of the autosomal locus FBN17 no additional control fragment is necessary to detect PCR failure. The results of sex determination in embryo biopsies using FBNY were in agreement with the outcome from a reference assay used in commercial breeding programs.

A whole genome scan for differences in recombination rates among three Bos taurus breeds

Twenty paternal half-sib families of a granddaughter design were genotyped for 265 genetic markers, most of them microsatellites. These were 16 Holstein families, 3 Simmental families, and 1 Brown Swiss family. The number of sires per breed was 872, 170, and 32, respectively. Two-point recombination rates were estimated both jointly for all breeds and each single breed separately. Of 1168 marker intervals, 865 provided estimates for at least two breeds. Differences between breeds were tested by likelihood ratio tests. Four marker intervals, representing three genomic regions on BTA19, BTA24, and BTA27, show a significant impact of the breed at a false discovery rate of 0.23 and indicate a genetic component of observed heterogeneity of recombination. The variability of recombination rates between cattle breeds might not be a common feature of the whole genome, but rather might be restricted to certain chromosomal segments. Thus, attention should be paid to heterogeneities when pooling data of such regions from different breeds.

A mammary gland EST showing linkage disequilibrium to a milk production QTL on bovine Chromosome 14

As part of a genome scan, ESTs derived from mammary gland tissue of a lactating cow were used as candidate genes for quantitative trait loci (QTL), affecting milk production traits. Resource families were genotyped with 247 microsatellite markers and 4 polymorphic ESTs. It was shown by linkage analysis that one of these ESTs, KIEL_E8, mapped to the centromeric region of bovine Chromosome (Chr) 14. Regression analysis revealed the presence of a QTL, with significant effect on milk production, in this chromosome region, and analysis of variance showed no significant interaction of marker genotype and family. The estimated significant differences between homozygous marker genotypes were 140 kg milk, -5.02 kg fat yield, and 2.58 kg protein yield for the first 100 days of lactation. Thus, there was strong evidence for a complete or nearly complete linkage disequilibrium between KIEL_E8 and the QTL. To identify the biological function of KIEL_E8, we extended the sequence for 869 bp by 5'-RACE. A 560-bp fragment of this shows a 90.9% similarity to a gene encoding a cysteine- and histidine-rich cytoplasmic protein in mouse. Although such a protein may have a regulatory function for lactation and a linkage disequilibrium between the EST marker and the QTL has been observed, it remains to be elucidated whether they are identical or not. Nevertheless, KIEL_E8 will be an efficient marker to perform marker-assisted selection in the Holstein-Friesian population.

Molecular genome analysis in livestock at the beginning of the new millennium

Prerequisites, current status, further challenges and limitations in the application of molecular approaches for genome analysis in livestock are reviewed. Aspects of the utilization of mapped 'quantitative trait loci' (QTL) in breeding programmes and of the final identification cloning of the corresponding candidate genes are discussed.

Isolation and characterization of hepatic and intestinal expressed sequence tags potentially involved in trait differentiation between cows of different metabolic type

mRNA differential display was applied to identify hepatic and intestinal expressed sequence tags (ESTs) in lactating cows of different metabolic types (milk type, meat/milk type, meat type) that are potentially associated with energy turnover and involved in the regulation of these processes. Altogether, 277 ESTs (liver: 161, intestine: 116) were identified. For 150 transcripts (liver: 99, intestine: 51), the sequences showed similarity to previously described genes and ESTs. Many of these homologous sequences are reported to be involved in hepatic metabolism. Ninety-four ESTs (liver: 43, intestine: 51) did not match with any database entries. Semi-quantitative RT-PCR revealed quantitative differences in transcript represented by randomly chosen ESTs in liver samples of animals of the Holstein and Charolais breeds. One hundred twenty-two ESTs were mapped physically by using a bovine-hamster somatic cell hybrid panel (SCP) and a 5000-rad bovine whole genome radiation hybrid panel (WGRH). These ESTs were assigned to the bovine syntenic groups and positioned in the recently established RH-based ordered comparative map of the cattle and human genomes. The mapped, differentially expressed sequence tags are a useful prerequisite for cloning of genetic variation underlying economic traits.

Genome-wide search for loci controlling serum IGF binding protein levels of mice

A segregating F(2) pedigree based on two mouse lines (DU6i and DBA/2) with extremely different growth characteristics was generated to search for loci affecting serum levels of insulin-like growth factor (IGF) binding proteins (IGFBPs) and to estimate their effects on growth and body composition. DU6i is characterized by high body mass and obesity associated with hyperinsulinemia, hyperleptinemia, and elevated serum IGF-I concentrations. Furthermore, significantly elevated serum levels of IGFBP-2, IGFBP-3, and IGFBP-4 were found in DU6i vs. DBA/2 mice. Linkage analysis identified loci with major effects on the serum level of IGFBP-3 on Chromosome 5 at 58 cM (Igfbp3q1; F = 9.9) and on Chromosome 10 at 46 cM (Igfbp3q2; F = 33.8). A locus significantly influencing serum IGFBP-2 levels in males was found on Chromosome 7. Additional linkage was detected in males and females for IGFBP-2 on Chromosomes 8, 11, 14, 17, and X, and for IGFBP-4 on Chromosome 4. Additional loci affecting IGFBPs acted in a sex-specific manner. The identified loci coincide in part with chromosomal regions controlling growth and obesity. Thus, multiple genes or pleiotropic gene effects may be assumed for these chromosomal regions. The identification of quantitative trait loci for IGFBPs as subcomponents of growth regulation and differentiation will further improve the understanding of complex trait regulation.

Chromatin structure of the bovine Cyp19 promoter 1.1. DNaseI hypersensitive sites and DNA hypomethylation correlate with placental expression

Expression of the Cyp19 gene, encoding aromatase cytochrome P450, is driven by several tissue-specific promoters. The underlying mechanisms of this complex regulation have not yet been elucidated in detail. In the present report we investigate a possible link between chromatin structure and tissue-specific regulation of the bovine Cyp19 gene. We analysed the DNA methylation status and mapped DNaseI hypersensitive sites in the region encompassing the Cyp19 promoter 1.1 (P1.1) which controls Cyp19 expression in the bovine placenta. We show that P1.1 is hypomethylated in placental cotyledons (foetal layer) whereas it is methylated in placental caruncles (maternal layer), testis and corpus luteum. Furthermore, two placenta-specific DNaseI hypersensitive sites, HS1 and HS2, were observed within P1.1. Both DNA hypomethylation and the presence of DNaseI hypersensitive sites correlate with transcriptional activity of P1.1. Sequence analysis of hypersensitive sites revealed potential cis-regulatory elements, an E-box in HS1 and a trophoblast-specific element-like sequence in HS2. It could be demonstrated by electrophoretic mobility shift assays that both sequence motifs are specific targets for placenta-derived nuclear factors. In conclusion, observed tissue-specific differences of the chromatin structure which correlate with tissue-specific promoter activity suggest that chromatin might be an important regulator of aromatase expression in cattle.