Multifunctionality and provision of ecosystem services by livestock species and breeds at global level

Beyond providing food, livestock species are linked to a wide range of uses and ecosystem services (ESs). Based on information reported by 41 countries on 3 361 national breed populations to the Domestic Animal Diversity Information System of the Food and Agriculture Organization of the United Nations, we investigated how factors such as species, region, breed adaptedness, or management system associate with the recognition of provision of a set of 52 ESs. Among species, a greater number of cultural ESs were reported for horses (2.47 for horses vs 0.75 on average across all species), while the major ruminant species (cattle, goats and sheep) were on average associated with more provisioning ESs (2.99 vs 2.39), and more regulating and maintenance ESs (1.86 vs 1.32). Compared to European breeds, African livestock contribute more provisioning ES (3.95 vs 1.88). Native breeds and, to a lesser extent, locally adapted breeds, were linked to more ESs than were exotic breeds (5.97 and 4.10 vs 2.90, respectively), regardless of the ES category considered. The total number of ES reported was greater for breeds primarily kept under Back Yard/Farm Yard and extensive management systems than in other production environments. Different "bundles" of ES were identified in relation to the interdependence among themselves, or according to species or regional specificities. Overall, our results highlight that native and locally adapted breeds, which tend to be raised in less specialized production systems than exotic breeds, are reported to play multiple roles contributing to rural community livelihoods and environmental sustainability of food systems.

Fateful triad of reactive oxygen species, mitochondrial dysfunction and lipid accumulation is associated with expression outline of the AMP-activated protein kinase pathway in bovine blastocysts

Low cryotolerance is considered as the major drawback of in vitro-produced bovine embryos and is frequently associated with a triad encompassing increased cytoplasmic lipid accumulation, enhanced levels of reactive oxygen species (ROS) and mitochondrial dysfunction. The aim of the present study was to explore the role of the AMP-activated protein kinase (AMPK) pathway in the process resulting such phenotypes. Comparative analysis under different environmental conditions revealed downregulation of AMP-activated protein kinase cytalytic subunit 1alpha (AMPKA1), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1A) and carnitine palmitoyltransferase 1 (CPT1) genes and upregulation of acetyl-CoA carboxylase α (ACC). In contrast, the presence of fatty acids within the culture medium resulted in a distinct molecular profile in the embryo associated with enhanced levels of ROS, mitochondrial dysfunction and elevated lipid accumulation in bovine embryos. Because AMPKA1 regulates PGC1A, CPT1 and ACC, the results of the present study reveal that AMPK in active its form is the key enzyme promoting lipolysis. Because AMPK1 activity is, in turn, controlled by the AMP : ATP ratio, it is possible to speculate that excessive uptake of exogenous free fatty acids could increase cellular ATP levels as a result of the disturbed β-oxidation of these external fatty acids and could therefore bypass that molecular feedback mechanism. Subsequently, this condition would cause enhanced generation of ROS, which negatively affect mitochondrial activity. Both enhanced generation of ROS and low mitochondrial activity are suggested to enhance the accumulation of lipids in bovine embryos.

142 microRNA-17-92 CLUSTER REGULATES BOVINE GRANULOSA CELL FUNCTION BY TARGETING BMPR2 AND PTEN GENES

Normal follicular development, especially from the preantral stage until ovulation, is the critical to ensure the release of a developmentally competent oocyte. We have previously shown that among several clusters of microRNAs, microRNA-17-92 cluster (miR-17-5p, miR-19a, miR-20a, and miR-92a) is differentially expressed between bovine granulosa cells (bGC) derived from preovulatory dominant and subordinate follicles. Here, we aimed to investigate the regulatory role of microRNA-17-92 cluster in bGC function. Among the target genes predicted by the miRWalk database, BMPR2 and PTEN genes were experimentally validated using the pmirGLO Dual Luciferase Reporter Assay System (Promega Corporation, Madison, WI, USA). The bGC were aspirated from ovaries obtained from a local slaughterhouse. After determining cell viability and concentration using the trypan blue exclusion method, a total 2.5 × 105 bGC per well were seeded into CytoOne 24-well plate in DMEM/F12-Ham medium (Sigma Aldrich Chemie GmbH, Munich, Germany) supplemented with 10% FBS (Gibco BRL USA, Grand Isalnd, NY, USA) and 1% penicillin/streptomycin (Gibco BRL USA). Then, the bGC were cultured at 37°C with 5% CO2 and O2. To investigate the role of microRNA-17-92 cluster in bGC function, 100 nM of individual and cluster of microRNA-17-92 mimic, inhibitor, and negative controls were transfected into subconfluent-cultured bGC. The bGC were harvested 48 h post-transfection and used for RNA isolation and subsequent cDNA synthesis and expression analysis of candidate genes using real-time qPCR. Data analysis was performed using the comparative cycle threshold (Ct) method. A cell proliferation assay was performed using CCK-8 kit (Dojindo EU GmbH, Munich, Germany). Based on the cell diameter measurement done using ImageJ 1.48v software (National Institutes for Health, Bethesda, MD, USA), those bGC with diameter >14 µm were categorized as differentiated cells, whereas those with diameter = 14 µm were considered as undifferentiated cells. MicroRNA-17-92 cluster overexpression on bGC reduced both mRNA and protein expression of BMPR2 and PTEN genes, whereas inhibition of microRNA-17-92 cluster increased their expression. Bovine GC transfected with microRNA-17-92 cluster mimic showed higher proliferation activity and decreased rate of differentiation. The opposite phenotype was observed in bGC transfected with microRNA-17-92 cluster inhibitor. Similarly, miRNA-17-92 cluster mimic transfection increased the expression of markers of proliferation, CCND2 and PCNA, and resulted in down-regulation of CYP11A1 and STAR genes as markers of differentiation. The opposite expression pattern was observed after transfection of miRNA-17-92 cluster inhibitors. In conclusion, the miRNA-17-92 cluster members coordinately regulate bGC proliferation and differentiation by targeting the expression of BMPR2 and PTEN genes.

129 microRNA-183~96~182 CLUSTER PROMOTE BOVINE GRANULOSA CELL PROLIFERATION THROUGH COORDINATED REGULATION OF FOXO1

Among other microRNA clusters, we previously showed that the miR-183~96~182 cluster (miR-183, miR-96, and miR-182) is abundantly expressed in bovine granulosa cells (bGC) of preovulatory dominant follicles obtained at the follicular phase of the bovine oestrous cycle. Moreover, this miRNA cluster are validated to coordinately target the Fork head O1 (FOXO1), a subfamily of transcription factors that regulate genes involved in cell proliferation, apoptosis, cell cycle arrest, and metabolism. However, the functional involvement of miR-183~96~182 cluster in bGC function by regulation of FOXO1 is not yet determined. Here, we aimed to investigate the function of miR-183~96~182 cluster in bGC using in vitro cell culture model. For this, bGC were aspirated from ovarian follicles (Ø 3–5 mm) obtained from local abattoir. Cells were plated in 24-well plate (2.5 × 105 cells well–1) in DMEM/F-12 (Sigma, Germany) supplemented with 10% FBS (GIBCO, Grand Island, NY) and 1% penicillin/streptomycin (GIBCO) and incubated at 37°C in 5% CO2. Transfection of bGC with miRNA mimics, inhibitors, FOXO1-siRNA, and appropriate controls (Exiqon, Vedbæk, Denmark) was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA). Cell proliferation was determined using Cell Counting Kit-8 (CCK-8; Dojindo Molecular Technology, Kumamoto, Japan). Cell cycle distribution was determined with flow cytometric analysis. Total RNA was isolated using miRNeasy mini kit (Qiagen, Hilden, Germany), quantification of target gene was performed using qPCR, and data were analysed using ΔΔCT method. Differences in the mean expression values between treatments were analysed with two-tailed Student’s t-test and statistical significance was defined at P ≤ 0.05. Results showed that a sponge effect was observed upon inhibition in individual miRNA of the cluster, which could be attributed to the partial sequence similarity among cluster members. Both FOXO1 mRNA and protein expression were significantly reduced upon transfection of bGC with miR-183~96~182 cluster mimics, while miR-183~96~182 cluster inhibition increased both FOXO1 mRNA and protein expression. Transfection of bGC with miR-183~96~182 mimics promoted cell proliferation, while inhibition tends to slow down proliferation. Furthermore, the proportion of bGC under G0/G1 arrest markedly declined (P < 0.05), while the S and G2/M phases increased in response to miR-183~96~182 mimicking. Selective knockdown of FOXO1 with FOXO1-siRNA significantly reduced FOXO1 mRNA and protein expression. Interestingly, knockdown of FOXO1 showed similar phenotypic effects such as that of miR-183~96~182 mimics transfection, which resulted in elevated bGC proliferation and reduction in the proportion of cells under G0/G1 arrest. In conclusion, overexpression of miR-183~96~182 cluster promote bGC proliferation and G0/G1 to S and G2/M cell cycle transition through coordinated regulation of genes in the FOXO1 signaling axis.

MicroRNA-regulated molecular mechanism underlying bovine subclinical endometritis

An impaired uterine environment triggered by the incidence of subclinical endometritis often compromises fertility in the bovine. The uterus is a dynamic organ with tight regulation of specific genes at the transcriptional and translational levels. Herein, we hypothesised that subclinical endometritis alters the expression of uterine microRNAs (miRNAs), which may result in the dysregulation of corresponding target genes and biological pathways. To test this hypothesis, we used a genome-wide RT(2) (Exiqon, Vedbaek, Denmark) miRNA PCR array consisting of 354 miRNA primers and analysed miRNA expression in uterine cytobrush samples taken from cows with and without subclinical endometritis. The results revealed aberrant expression of 23 miRNAs in cows with subclinical endometritis compared with healthy cows. Furthermore, we designed an in vitro endometrial cell culture model challenged by lipopolysaccharide (LPS) to validate the differential regulation of miRNAs in cytobrush samples. Interestingly, we observed similar expression miRNA patterns in cytobrush samples taken from cows with or without subclinical endometritis and in vitro cultured endometrial cells challenged by LPS. To trace signalling pathways and biological functions potentially controlled by the aberrantly expressed miRNAs, we filtered high-ranking target genes from miRBase and analysed them using ingenuity pathway analysis. The gene networks, canonical pathways and biological functions strikingly converged to signalling pathways that mediate inflammatory responses, cellular proliferation, cell movement, the cell cycle and apoptosis in the bovine endometrium. In addition, expression analysis of key genes from the gene networks confirmed their presence and the potential regulation of these genes by uterine miRNAs. Furthermore, luciferase assay data substantiated the primary information from bioinformatic prediction that generated potential target genes for the dysregulated miRNAs in subclinical endometritis. Together, these data suggest the potential regulatory role of uterine miRNAs in the development and progression of bovine subclinical endometritis.

129 EFFECT OF SERUM SUPPLEMENTATION ON AMP-ACTIVATED PROTEIN KINASE (AMPK) ACTIVITY AND LIPID METABOLISM OF IN VITRO-CULTURED BOVINE EMBRYOS

A major problem of embryos cultured in vitro with serum is cytoplasmic lipid accumulation resulting in lower cryotolerance compared with those derived from in vivo or in the absence of serum. AMPK is known as a master regulator of lipid, glucose, and protein metabolism in mammalian cells. Moreover, it has been reported as controller of acetyl-CoA carboxylase α (ACC), the gene responsible for lipid synthesis, and associated with mitochondrial biogenesis and activities in response to oxidative stress. In the present study we aimed to investigate the regulation of AMPK during serum supplementation in vitro. For this, bovine embryos were produced in vitro in SOF media supplemented with oestrous cow serum or fatty acid–free BSA as a system without serum. Triplicate pools (each 10 blastocysts) from each group were used for RNA isolation using Arcturus®PicoPure®RNA Isolation Kit (Life Technologies, USA). Reverse transcription was performed using a combination of Oligo(dT)23 and random primers. Quantification of AMPK catalytic α1 (AMPKA1), ACC, peroxisome proliferator-activated receptor gamma coactivator 1 α (PGC1A), and sterol regulatory element binding transcription factor 2 (SREBP2) transcripts were performed using ABI PRISM® 7000 SDS system (Applied Biosystems, Foster City, CA, USA) using GAPDH as internal control. Normalized log-transformed transcript amount data were statistically analysed using t-test. In addition, AMPK protein was detected by immunofluorescence, mitochondrial activity by MitoTracker® Red (Invitrogen, Carlsbad, CA, USA), and reactive oxygen species by H2DCFDA molecular probe (Life Technologies, USA), and fluorescent intensity signals were visualised under confocal laser scanning microscopy LSM 710 (Carl Zeiss, Germany). Results showed that the expression of AMPKA1, PGC1A, a mitochondrial biogenesis protein, and SREBP2, a regulator of lipid oxidation, were found to be lower (0.4-, 0.2-, and 0.7-fold, respectively; P < 0.05) in blastocysts derived from cultured with serum compared to without serum. By contrast, ACC was up-regulated in blastocysts cultured with serum by 1.8-fold (P < 0.05) compared to without serum. In comparison to blastocyst cultured without serum, a reduced fluorescent intensity was observed in AMPKA1 protein and mitochondrial activity in blastocyst cultured with serum. The presence of serum was also found to be involved in increasing reactive oxygen species accumulation in embryos cultured with serum. The reduced level of AMPK leads to increased ACC and subsequently enhanced conversion of fatty acids into lipid, which is associated with reduced mitochondrial biogenesis protein, elevated reactive oxygen species level, and reduced lipid oxidation by suppression of SREBP2. In conclusion, the presence of serum in in vitro culture environment affected the AMPK activity and thereby genes associated with lipid metabolism in early bovine embryos.

199 IN VITRO-DEVELOPED BOVINE BLASTOCYSTS ARE MARKED WITH ABERRANT HYPER- AND HYPO-METHYLATED GENOMIC REGIONS

Most often, in vitro produced embryos display poor quality and altered gene expression patterns compared to their in vivo counterparts. Aberrant DNA methylation occurring during in vitro embryo development is believed to be one of the multifaceted factors which may cause altered gene expression and poor embryo quality. Here, we investigated the genome-wide DNA methylation patterns of in vitro derived embryos using the recently developed Bovine EmbryoGENE Methylation Platform (BEGMP) array (Shojaei Saadi et al. BMC Genomics 2014 15, 451. doi: 10.1186/1471-2164-15-451) to unravel the aberrantly methylated genomic region in in vitro developed embryos. For this, in vitro and in vivo produced blastocysts were produced and used for genome-wide DNA methylation analysis. In vitro blastocysts were produced from oocytes retrieved from ovaries collected from the local abattoir and matured, fertilized, and cultured in vitro using SOF media. The in vivo blastocysts were produced by superovulation and AI of Simmental heifers followed by uterine flushing. Genomic DNA (gDNA) was then isolated from four replicates (each 10 blastocysts) of in vivo and in vitro derived blastocysts using Allprep DNA/RNA micro kit (Qiagen, Valencia, CA, USA) and the gDNA was then fragmented using the MseI enzyme. Following this, MseLig21 and MseLig were ligated to the MseI-digested genomic fragments in the presence of Ligase enzyme. Methyl-sensitive enzymes, HpaII, AciI, and Hinp1I, were used to cleave unmethlayted genomic regions within the MseI-MseI region of the fragmented DNA. The gDNA was subjected to two rounds of ligation-mediated polymerase chain reaction (LM-PCR) amplification. After removal of the adapters, the amplified gDNA samples from in vivo or in vitro groups were labelled either Cy-3 or Cy-5 dyes in dye-swap design using ULS Fluorescent gDNA labelling kit (Kreatech Biotechnology BV, Amsterdam, The Netherlands). Hybridization was performed for 40 h at 65°C. Slides were scanned using Agilent's High-Resolution C Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) and features were extracted with Agilent's Feature Extraction software (Agilent Technologies Inc.). The results have shown that from a total of 414 566 probes harboured by the BEGMP array, 248 453 and 253 147 probes were detected in in vitro and in vivo derived blastocysts, respectively. Data analysis using the linear modelling for microarray (LIMMA) package and R software (The R Project for Statistical Computing, Vienna, Austria) revealed a total of 3434 differentially methylated regions (DMRs; Fold change ≥1.5, P-value <0.05), of which 42 and 58% were hyper- and hypo-methylated, respectively, in in vitro derived blastocysts compared to their in vivo counterparts. The DMRs were found to be localised in the intronic, exonic, promoter, proximal promoter, and distal promoter, and some of the probes did not have nearby genes. In addition, 10.8% of the DMRs were found to be stretched in short, long, or intermediate CpG islands. Thus, this study demonstrated genome-wide dysregulation in the epigenome landscape of in vitro-derived embryos by the time they reach to the blastocysts stage.

Implications of genetic selection on yolk proportion on the dry matter content of eggs in a White Leghorn population

1. The responses to genetic selection on yolk proportion as a technique for increasing egg dry matter content, an important criterion for the egg-product industry, was investigated in a pedigree flock of White Leghorn hens. 2. Parents were preselected on high and low yolk proportion from a base population. The absolute estimated breeding value for yolk proportion of both groups differed by 3%. The realised selection difference in dry matter content of eggs between groups was more than 1% in the analysed offspring population. 3. Heritability estimates were moderate and dry matter had a lower heritability (h(2) = 0.39) than yolk proportion (h(2) = 0.44). 4. The genetic correlation between yolk proportion and dry matter content was highly positive (rg = 0.91). Genetic correlations with egg weight were negative and would have to be compensated for in a breeding programme (rg = -0.76 with yolk proportion and rg = -0.64 with dry matter content). The genetic correlation between the laying performance and yolk proportion was rg = 0.28 and close to zero (rg = -0.05) for dry matter content. 5. Easy recording and lower undesirable correlations make yolk proportion more suitable for commercial selection compared with egg dry matter content in layer breeding.

113 EXPRESSION PROFILING OF NONCODING microRNAs IN BOVINE GRANULOSA CELLS OF PREOVULATORY DOMINANT FOLLICLE USING DEEP SEQUENCING

In cattle, follicles grow in a wave-like pattern, with typically 2 or 3 waves per oestrous cycle. During each wave, one follicle of a cohort becomes dominant (DF), whereas the remaining subordinate follicles (SF) in the cohort undergo atresia. If the endocrine conditions are appropriate (low progesterone), the dominant follicle goes on to ovulate. In order to unravel the molecular mechanisms associated with ovulation and follicular atresia, here we aimed to investigate the expression of short regulatory microRNA (miRNA) in granulosa cells of DF and SF using deep sequencing. For this, Simmental heifers (n = 7) were synchronized according to standard protocols and slaughtered at Day 19 of the oestrous cycle. Follicles were categorized as DF (≥12 mm; n = 5) and SF (≤10 mm; n = 78). Granulosa cells from both follicle groups were used for total RNA (enriched with miRNA) isolation using miRNeasy mini kit (Qiagen GmbH, Hilden, Germany). The RNA concentration and integrity were measured using Nano Drop 8000 spectrophotometer (Nano Drop, Wilmington, DE, USA) and Agilent, 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively. Libraries were constructed by GATC BioTech AG (Konstanz, Germany) and sequenced on Illumina HISEqn 2000. Prediction of both known and novel miRNA was done using miRDeep2 software packages. Quantification of differentially expressed miRNA was done using R software and DESEqn 2 packages. The MiRNA with log2 fold change difference ≥1, P-value ≤0.05, and false discovery rate of ≤0.1 were considered to be significant. Results showed that 318 and 322 known miRNA were detected in DF and SF, respectively. It was shown that 28 miRNA including bta-miR-122, bta-miR-139, and bta-miR-375, and 35 others including bta-miR-138, bta-miR-20b, and bta-miR-33a were uniquely detected in DF and SF, respectively. In addition to the known annotated miRNA, 20 and 24 novel miRNA were detected in DF and SF, respectively. Expression analysis revealed that 65 miRNA were differentially expressed in granulosa cells of SF compared with DF. Thirty miRNA including bta-miR-409a (involved in cell death by targeting genes BCL2l11, BIRC5, and PTEN) and bta-miR-335 (involved in cell proliferation, migration, and differentiation) are up-regulated in SF, whereas 35 miRNA including the miR-183 cluster (bta-mir-183, bta-miR-182, and bta-mir-96) involved in apoptosis inhibition are down-regulated in SF. The pathway analysis of potential target genes of differentially expressed miRNA is found to be involved in pathways, namely Wnt signalling, MAPK signalling, TGF-β signaling, and other pathways related to cell proliferation and apoptosis. In conclusion, the presence of stage-specific miRNA in granulosa cells support the potential role of miRNA in posttranscriptional regulation of genes during follicular development, mainly ovulation and follicular atresia.

111 REGULATORY microRNA ENRICHMENT AND DEGRADATION IN GRANULOSA CELLS DURING BOVINE FOLLICULAR RECRUITMENT AND DOMINANCE

Follicular development is a result of complex hormonal and biochemical synergies that could be activated or deactivated in a spatiotemporal manner in oocytes and surrounding cells including theca, granulosa, and cumulus cells. The microRNA (miRNA), 19 to 22 nucleotides noncoding RNA, are one of the molecular cues that could play a role in posttranscriptional regulation of genes involved in follicular development. Here we aimed to understand the availability and abundance of miRNA in bovine granulosa cells (GC) derived from subordinate (SF) and leading or dominant (DF) follicles during bovine follicular recruitment and dominance at Day 3 and 7 of the oestrus cycle, respectively. For this, Simmental heifers (n = 15) were oestrus synchronized and slaughtered at 3 (n = 6) and 7 (n = 7) days after the onset of the oestrous. The SF and DF were retrieved from each animal to obtain the corresponding GC, which were subjected to miRNA-enriched total RNA isolation using the miRNeasy mini kit (Qiagen GmbH, Hilden, Germany). The integrity and quality of RNA was determined using Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) and Nanodrop 8000 Spectrophotometer (Thermo Fisher Scientific Inc., DE, USA), respectively. The RNA was then subjected to miRNA deep sequencing using the Illumina HISEqn 2000. Raw sequence data were further processed and analysed using miRDeep2 software package. Quantification of differentially expressed (DE) miRNA was done using R software and DESEqn 2 package. MiRNA with log2 fold change difference ≥1, P-value ≤0.05, and false discovery rate ≤1 were considered to be significant. Data analysis revealed that 291 and 311 miRNA were detected in GC of SF and 312 and 314 were detected in GC of DF at Days 3 and 7, respectively. A total of 17 miRNA were DE in GC from SF compared with the DF at Day 3, of which 15 miRNA were enriched and the remaining 2 were down-regulated in SF. Similarly, at Day 7 a total of 136 miRNA was altered with 51 miRNA showed to be enriched, whereas 85 others remained low in SF compared with the DF. Nine miRNA (bta-miR-21–3p, bta-miR-221, bta-miR-708, bta-miR-214, bta-miR-335, bta-miR-155, bta-miR-199a-5p, bta-miR-21–5p and bta-miR-222) were commonly differentially expressed both at Day 3 and 7 between SF and DF. Interestingly, all of the commonly DE miRNA, except bta-miR-335, were enriched in GC of SF at both days. Gene ontological analysis indicated that majority of the DE miRNA were found to be involved in regulation of programmed cell death, cell projection morphogenesis, regulation of cell proliferation, and macromolecule biosynthesis. Therefore, the temporal abundance of mature miRNAs in GC during bovine follicular development may suggest their potential role in regulation of follicular development in general and follicular recruitment and dominance in particular.

Investigation on association and expression of ESR2 as a candidate gene for boar sperm quality and fertility

ESR2 is involved in oestrogen-related apoptosis in cell cycle spermatogenesis but their effects have not yet confirmed in pig. Therefore, this study was aimed to investigate the association of ESR2 polymorphism with sperm quality and boar fertility traits and to analyse the ESR2 mRNA and protein expressions in boar reproductive tissues. DNA samples from 203 Pietrain (PI) and 100 Pietrain × Hampshire (PIHA) pigs with records of sperm quality [sperm concentration (SCON), motility (MOT), semen volume (VOL), plasma droplet rate (PDR) and abnormal spermatozoa rate (ASR)] and fertility [non-return rate (NRR) and number of piglet born alive (NBA)] traits were available. A SNP in coding region of ESR2 g.35547A>G in exon 5 was associated with MOT and PDR in the PI and with SCON, VOL, MOT and PDR in PIHA population. For mRNA and protein expression study, a total of six boars were divided into two groups with group I (G-I) and group II (G-II) where G-I characterized for relatively a better sperm quality according to the mean of two groups. mRNA expression was higher in brain and testis than that in all parts of epididymis. Both qRT-PCR and western blot analysis revealed that the ESR2 gene expression and protein expression were significantly higher in testis collected from G-II compared with that of G-I boars. Moreover, ESR2 protein localization in germ cell, Leydig and Sertoli cells, epithelial cells and spermatozoa was remarkable, which indicated the important role of ESR2 in spermatogenesis process. These results might shed new light on the roles of ESR2 in spermatogenesis as candidate for boar fertility, but still the lack of association across populations should be considered.

Bovine blastocysts with developmental competence to term share similar expression of developmentally important genes although derived from different culture environments

This study was conducted to investigate the gene expression profile of in vivo-derived bovine embryo biopsies based on pregnancy outcomes after transferring to recipients. For this, biopsies of 30-40% embryos were taken from grade I blastocysts (International Embryo Transfer Society Manual) and the remaining 60-70% of the intact embryos were transferred to recipients. Frozen biopsies were pooled into three distinct groups based on the pregnancy outcome after transferring the corresponding parts, namely those resulting in no pregnancy (NP), pregnancy loss (PL), and calf delivery (CD). Array analysis revealed a total of 41 and 43 genes to be differentially expressed between biopsies derived from blastocysts resulting in NP versus CD and PL versus CD respectively. Genes regulating placental development and embryo maternal interaction (PLAC8) were found to be upregulated in embryo biopsies that ended up with CD. Embryo biopsies that failed to induce pregnancy were enriched with mitochondrial transcripts (Fl405) and stress-related genes (HSPD1). Overall, gene expression profiles of blastocysts resulting in NP and CD shared similar expression profiles with respect to genes playing significant roles in preimplantation development of embryo. Finally, comparing the transcript signatures of in vivo- and in vitro-derived embryos with developmental competence to term revealed a similarity in the relative abundance of 18 genes. Therefore, we were able to present a genetic signature associated with term developmental competence independent of the environmental origin of the transferred blastocysts.

Investigation into association and expression of PLCz and COX-2 as candidate genes for boar sperm quality and fertility

Phospholipase C zeta (PLCz) and cyclooxygenase isoenzyme type 2 (COX-2) are important in spermatogenesis, but their effect has not yet confirmed in pigs. Therefore, this study was aimed to analyse their association with sperm quality and fertility and to identify the mRNA and protein expression in boars reproductive tissues. DNA samples from 231 Pietrain (PI) and 109 Pietrain × Hampshire (PIHA) pigs with records of sperm quality [sperm concentration (SCON), motility, semen volume, plasma droplet and abnormal spermatozoa rate] and fertility (non-return rate and number of piglet born alive) traits were available. A SNP in non-coding region of PLCz g.158 A > C was associated with SCON (p < 0.05) in PIHA population while the polymorphism of COX-2 g.68 G > A in 3' UTR was not associated with any traits. For mRNA and protein expression study, a total of six boars were divided into two groups with G-I and G-II, where G-I was characterized for relatively better sperm quality. Both genes expressed higher in reproductive tissues compared with non-reproductive tissues. Phospholipase C zeta mRNA expressed higher in testis (p < 0.01), all parts of epididymis and spermatozoa from G-I, while COX-2 expressed higher in testis (p < 0.05), head and body of epididymis (p < 0.01), and spermatozoa from G-II boar. Both proteins were localized in Leydig cells and spermatozoa. These results might shed light on roles of these genes in spermatogenesis as candidate for boar sperm quality and fertility, but still the lack of association across populations should be considered.

Polymorphism and expression of the porcine Tenascin C gene associated with meat and carcass quality

The research aimed to screen for polymorphism, expression of Tenascin C (TNC) and association with meat and carcass quality traits. Three single nucleotide polymorphisms were detected. In a Duroc×Pietrain F2 cross (DuPi) population, g.44488C>T was associated with meat color and ham weight; g.68794A>G was associated with pH at 24h post mortem in ham (pH24(H)) and muscle area but g.68841C>T was not statistically associated. Genotyping in a commercial Pietrain (Pi) population showed that g.44488C>T was associated with pH24(H), whereas g.68794A>G was associated with conductivity at 45 min post mortem in loin and backfat thickness. Diplotypes showed significant effects on pH24(H) in both populations. The expression was associated with pH at 45 min post mortem in loin and cooking loss. TNC was significantly higher in animals with higher muscle pH. Linkage analysis revealed four trans-regulated eQTL on four autosomes. These results suggest that TNC could be a potential candidate gene for meat quality traits in pigs.

Investigation on interferon alpha-inducible protein 6 (IFI6) gene as a candidate for meat and carcass quality in pig

The aim of this research was to screen for polymorphism and to perform an association study of IFI6 with meat and carcass quality traits. A SNP (g.370A>G) was detected which was associated (P<0.05) with meat colour, pH 24h post mortem (p.m.) in ham, conductivity 45 min p.m. in loin and conductivity 24 h p.m. in ham, drip loss and carcass length in Duroc x Pietrain and with meat colour, muscle area and ham percentage in the Pietrain population. Highest expression of IFI6 mRNA was detected in skeletal muscle (longissimus dorsi) by qRT-PCR comparing different tissues. Both qRT-PCR and western blot revealed that the IFI6 gene and protein expressions were significantly (P<0.05) higher in skeletal muscle with low drip loss compared to that of high drip loss. IFI6 protein was localized in the myocytes membrane. Results suggested that IFI6 might play roles in meat and carcass quality and is a potential positional, physiological and functional candidate gene for improving meat quality traits in pigs.

Transcriptome dynamics and molecular cross-talk between bovine oocyte and its companion cumulus cells

BACKGROUND

The bi-directional communication between the oocyte and its companion cumulus cells (CCs) is crucial for development and functions of both cell types. Transcripts that are exclusively expressed either in oocytes or CCs and molecular mechanisms affected due to removal of the communication axis between the two cell types is not investigated at a larger scale. The main objectives of this study were: 1. To identify transcripts exclusively expressed either in oocyte or CCs and 2. To identify those which are differentially expressed when the oocyte is cultured with or without its companion CCs and vice versa.

RESULTS

We analyzed transcriptome profile of different oocyte and CC samples using Affymetrix GeneChip Bovine Genome array containing 23000 transcripts. Out of 13162 genes detected in germinal vesicle (GV) oocytes and their companion CCs, 1516 and 2727 are exclusively expressed in oocytes and CCs, respectively, while 8919 are expressed in both. Similarly, of 13602 genes detected in metaphase II (MII) oocytes and CCs, 1423 and 3100 are exclusively expressed in oocytes and CCs, respectively, while 9079 are expressed in both. A total of 265 transcripts are differentially expressed between oocytes cultured with (OO+CCs) and without (OO-CCs) CCs, of which 217 and 48 are over expressed in the former and the later groups, respectively. Similarly, 566 transcripts are differentially expressed when CCs mature with (CCs+OO) or without (CCs-OO) their enclosed oocytes. Of these, 320 and 246 are over expressed in CCs+OO and CCs-OO, respectively.While oocyte specific transcripts include those involved in transcription (IRF6, POU5F1, MYF5, MED18), translation (EIF2AK1, EIF4ENIF1) and CCs specific ones include those involved in carbohydrate metabolism (HYAL1, PFKL, PYGL, MPI), protein metabolic processes (IHH, APOA1, PLOD1), steroid biosynthetic process (APOA1, CYP11A1, HSD3B1, HSD3B7). Similarly, while transcripts over expressed in OO+CCs are involved in carbohydrate metabolism (ACO1, 2), molecular transport (GAPDH, GFPT1) and nucleic acid metabolism (CBS, NOS2), those over expressed in CCs+ OO are involved in cellular growth and proliferation (FOS, GADD45A), cell cycle (HAS2, VEGFA), cellular development (AMD1, AURKA, DPP4) and gene expression (FOSB, TGFB2).

CONCLUSION

In conclusion, this study has generated large scale gene expression data from different oocyte and CCs samples that would provide insights into gene functions and interactions within and across different pathways that are involved in the maturation of bovine oocytes. Moreover, the presence or absence of oocyte and CC factors during bovine oocyte maturation can have a profound effect on transcript abundance of each cell types, thereby showing the prevailing molecular cross-talk between oocytes and their corresponding CCs.

254 REGULATORY microRNA IN THE BIDIRECTIONAL COMMUNICATION OF BOVINE OOCYTES AND THE SURROUNDING CUMULUS CELLS

MicroRNA (miRNA) are small molecules (˜22 nucleotide in length) that influence the expression of hundreds of genes for numerous biological processes including development. In this study we aimed to investigate the presence and role of miRNA in the bidirectional communication of oocyte and cumulus cells. For this, triplicate pools each containing 1600 immature and mature oocytes and their corresponding cumulus cells were used for miRNA isolation using miRNeasy® Mini Kit (Qiagen, Hilden, Germany). From each oocyte and cumulus cell group, 50 ng of small RNA was used for reverse transcription using RT2 miRNA First Strand Kit (SABiosciences, Frederick, MD, USA). The resulting small RNA cDNA was used as a template to profile 88 human miRNA related to cell development and differentiation using SYBR green-based real-time PCR system. Data analysis was preformed using the comparative Ct method after normalization using endogenous control RNA (SNORD44, SNORD47, SNORD48, and U6). In addition, miR-205 and miR-210 were used for localization in pre-implantation stages of embryo using 3′digoxigenin labeled, LNA- modified in situ oligonucleotide probes (Exiqon, Vedbaek, Denmark). The result of the PCR array revealed a total of 34 and 49 miRNA to be greatly abundant in immature and mature oocyte, respectively, compared with the corresponding cumulus cells, whereas only 5 and 4 miRNA were enriched in cumulus cells compared with immature and matured oocytes, respectively. Based on expression intensity, 6 oocyte enriched (miR-205, miR-150, miR-96, miR-122, miR-146a, and miR-146b-5p) and 2 cumulus-cell enriched (miR-452 and miR-210) were selected for expression analysis in pre-implantation-stage embryos and in oocyte and cumulus cells matured with or without cumulus and oocyte factors, respectively. All oocyte-specific miRNA were found to be greatly abundant in early stages of embryo development and drop after 4-cells until the blastocyst stage, following a typical maternal transcript profile. Similar results were obtained by localization of miR-205 in pre-implantation-stage embryos, in which signals were greater until the 4-cell stage and reduced thereafter. However, miR-210 and miR-452 showed no defined profile. miR-205, miR-150, miR-122, miR-146a, miR-146b-5p, and miR-452 were found to be abundant at a greater level (P < 0.05) in oocytes matured without cumulus cells compared with those matured in the presence of cumulus cells. The expression of miR-205, miR-150, and miR-122 in cumulus cells was greater in the presence of oocyte cytoplasm during maturation, whereas 16-fold increases in relative abundance of miR-210 were observed in oocyte- optimized cumulus cells. These results evidenced that oocyte and cumulus cells have a distinct set of miRNA, which is dependent on the bidirectional communication of the oocyte and the surrounding cumulus cells. Moreover, maternal miRNA were found to persist until the major genome activation in bovine.

A high-density linkage map of the RN region in pigs

The porcine RN locus affects muscle glycogen content and meat quality. We previously mapped the RN locus to chromosome 15. This study describes the identification of polymorphisms for four class I and four class II markers located in the RN region. Resource families were genotyped with F-SSCP markers (fluorescent single strand conformation polymorphism) and microsatellite markers. Subsequent multipoint linkage analysis revealed the order FN1-IGFBP5-S1000-S1001-IL8RB-VIL1-RN-Sw936-Sw906. The gene order is identical to the previously reported porcine RH map of the same region. The described map will facilitate positional cloning of the RN gene.

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.

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.

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.

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.

Construction of a high-resolution RH map of the human 2q35 region on TNG panel and comparison with a physical map of the porcine homologous region 15q25

This article describes the construction of a high-resolution radiation hybrid map of Hsap 2q35 by using the TNG RH panel generated by irradiation with 50,000 rads. We were able to build a framework map of 1300 cR(50,000) including 34 markers ordered with odds higher than 1000:1. The comprehensive map includes 77 loci and describes a region of 3 Mb around the SLC11A1 gene. Because of the very small size of the fragments retained and a reduced retention frequency, it was difficult to build a high-resolution multi-point map of this region by using the TNG RH panel. Nevertheless, this study confirmed the very high potential of this RH panel for constructing a human, high-resolution physical map (2.3 kb/cR(50,000)). Moreover, human ESTs from Hsap 2q35 were hybridized with porcine BAC contigs to establish a porcine transcript map of the homologous region Sscr 15q25 (greater than 2.5 Mb). We identified 17 new genes in this porcine chromosomal region. We were able to compare the location of 26 genes mapped in both species. The gene order was similar except for two possible minor discrepancies in the Desmin sub-region, suggesting the existence of a porcine micro-region between TNP1 and IL8RB with an unknown origin.

Comparative analysis of a BAC contig of the porcine RN region and the human transcript map: implications for the cloning of trait loci

The poorly developed transcript maps and the limited resources for genome analysis hamper positional cloning of trait loci in farm animals. This study demonstrates that this will now be easier by the combined use of BAC contigs and the import of the near complete human transcript map. The conclusion was obtained by a comparative analysis of a 2.4-Mb BAC contig of the RN region in pigs. The contig was constructed as part of a successful positional cloning project, which identified PRKAG3 as the causative gene for the RN phenotype. A comparative map including the corresponding regions on human chromosome 2q35 and mouse chromosome 1 (region 36-44 cM) is reported. Sixteen coding sequences were mapped on the BAC contig. The majority of these were identified by BLAST searches of BAC end sequences and BAC shotgun sequences generated during the positional cloning project. Map data for the orthologues in humans were available for 12 of the 16 coding sequences, and all 12 have been assigned to 2q35. Furthermore, no evidence for any rearrangement in gene order was obtained. The extensive linkage conservation indicates that the near complete human transcript map will be an invaluable resource for positional cloning projects in pigs and other domestic animals.

Relationships between the endangered Pustertaler-Sprinzen and three related European cattle breeds as analysed with 20 microsatellite loci

We estimated the genetic relationships between the endangered German Pustertaler-Sprinzen cattle breed and the Pinzgauer, Vosges and Simmental breeds--decided upon after consultation of the available historical literature. Within-breed diversity of the four breeds was also assessed. Twenty microsatellite markers were amplified in 27-50 unrelated individuals from populations of each breed. Within-breed variation was estimated from average heterozygosity values and mean number of alleles. Breed relationships were evaluated by genetic distance and a neighbour-joining tree was calculated from these estimates. Bootstrap resampling of loci tested the robustness of the tree topology obtained. A tree was also constructed from distance matrices using individual animals as operational taxonomic units. From both the average heterozygosity values and mean number of alleles calculated, the Pustertaler breed appears to be no more genetically impoverished than the other breeds analysed. The breed tree showed an 85% support for the Pustertaler-Pinzgauer grouping, and this result is echoed in the genetic distance values and allele-sharing individual tree.

A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle

A high proportion of purebred Hampshire pigs carries the dominant RN- mutation, which causes high glycogen content in skeletal muscle. The mutation has beneficial effects on meat content but detrimental effects on processing yield. Here, it is shown that the mutation is a nonconservative substitution (R200Q) in the PRKAG3 gene, which encodes a muscle-specific isoform of the regulatory gamma subunit of adenosine monophosphate-activated protein kinase (AMPK). Loss-of-function mutations in the homologous gene in yeast (SNF4) cause defects in glucose metabolism, including glycogen storage. Further analysis of the PRKAG3 signaling pathway may provide insights into muscle physiology as well as the pathogenesis of noninsulin-dependent diabetes mellitus in humans, a metabolic disorder associated with impaired glycogen synthesis.

Mapping of 16 ESTs expressed in the bovine mammary gland during lactation

A bovine mammary gland cDNA-library was used to characterize and map genes expressed during lactation. Fifty cDNA clones selected by differential hybridization were sequenced from both ends, and sequences were examined for similarities with database sequences. For 34 of the transcripts, the sequences showed more than 80% similarity to previously characterized genes or expressed sequence tags (ESTs). Twenty cDNAs that could be of interest as candidate genes for milk production are selected for genetic or chromosomal mapping. Twenty-three out of the 39 designed primer pairs representing 16 cDNA clones amplified the expected fragments and were used for subsequent fluorescent single-strand conformation polymorphism analysis (F-SSCP) in the International Bovine Reference Panel families (IBRP). Ten polymorphic loci could be identified and used to genotype the IBRP animals, and nine of them were subsequently genetically mapped on nine chromosomes. In addition, eight loci from the 16 cDNA clones could be mapped by somatic cell hybrids, bringing the total number of mapped genes to 16, one of which was mapped genetically as well as physically. The mapped mammary gland ESTs are potentially useful for cloning economic trait loci by a positional candidate gene cloning approach.

[Study of mapping QTLs for milk traits on the German dairy cattle]

A total of 1,130 bulls belonging to 20 half-sib families of German dairy cattle were genotyped for 229 microsatellite markers on 30 chromosomes. The data were used in an attempt to map quantitative trait loci applying regression as multiple-marker regression. For association analysis with a granddaughter design, the estimated breeding values for 3 milk traits were used: milk production, fat production and protein production. The empirical values of significance thresholds were determined by using a permutation test on the experimental data. Several significant QTLs were found on some chromosomes, especially on the chromosome 14. The results give a strong support for the experiments of Coppieters et al. and Ron et al.

A QTL for the degree of spotting in cattle shows synteny with the KIT locus on chromosome 6

The proportion of unpigmented coat on the trunk was determined from photographs of 38 German Simmental and 627 German Holstein bulls distributed over three generations. All 665 animals were members of 18 Holstein and 3 Simmental half-sib families. A Bayesian estimation of heritability yielded a posterior mean of 0.88 and a standard error of 0.08. A quantitative trait loci (QTL) scan over all chromosomes covered by 229 microsatellite marker loci (2926 cM) was performed by fitting a multiple marker regression model to 625 observations from the youngest generation in 18 families. On chromosome 6 a QTL for the proportion of white coat with large effects (experiment-wise error probability < .0001) was found and a less important one on chromosome 3 (chromosome-wise error probability < .009). Chromosome 6 is known to harbor the KIT locus (receptor tyrosinase kinase), which is associated with various depigmentation phenotypes in mice, humans, and pigs. Similarity of phenotypic KIT effects in other species and synteny with the reported QTL suggest that KIT is a serious candidate gene for the degree of spotting in cattle. The results are also discussed with respect to resistance to solar radiation, heat stress, and photosensitization.

The Kiel RN experiment: final porcine chromosome 15 mapping results

SUMMARY

A marker experiment with pigs from commercially selected lines is described. One important goal of the experiment was to map the porcine RN locus, a major gene responsible for lowered terminal pH and increased glycogen level in muscle tissue. Experimental families comprised 15 Piétrain × Hampshire boars, of which 14 were heterozygous at the RN locus, 61 homozygous rn(+) /rn(+) sows (five Landrace, 12 Large White, and 44 Landrace × Large White crossbreds), and 509 progenies, 496 of them from heterozygous boars, in total 585 animals. Genotyping was done for seven chromosome 15 microsatellite loci: Sw919, Sw964, S0088, Sw120, Sw906, Sw936, and Sw312. Genotype assignment for the RN locus was based on musculus longissimus dorsi glycogen content. The heterozygosity of markers ranged from 0.47 to 1 in boars and from 0.71 to 0.88 in sows. RN was mapped to the centre of an interval, flanked by Sw120 and the marker pair Sw906/Sw936. Male multipoint distances between RN and Sw120, Sw906, and Sw936 were estimated as 5 cM, 5 cM, and 6.9 cM, respectively. Two-point recombination rates between these markers and RN were 0.05 in all cases, with corresponding lod scores of 52.09, 29.30, and 42.53. Concordances and disconcordances of mapping results in the RN region from different studies are discussed. The male map length of the chromosome region covered was 68.8 cM, in contrast to the female map length of 124.7 cM. Significant differences in recombination rates between sexes were found in intervals Sw919-Sw964, Sw964-S0088, and Sw936-Sw312, but not in the neighbourhood of the RN gene. ZUSAMMENFASSUNG: Es wird ein Kartierungsexperiment mit Schweinen aus kommerziell genutzten Linien beschrieben. Vordringliches Ziel dieses Experimentes war es, das RN-Gen zu kartieren, das für einen erniedrigten End-pH-Wert und einen erhöhten Glykogengehalt im Musklegewebe verantwortlich ist. Die Daten stammen von 15 Hampshire × Piétrain Ebern, von denen 14 am RN Locus heterozygot waren, 61 homozygoten rn(+) /rn(+) Sauen (5 Landrasse-, 12 Large White und 44 Landrasse × Large White Kreuzungssauen) sowie 509 Nachkommen, 496 davon von heterozygoten Ebern, insgesamt also 585 Tiere. Für sieben Mikrosatellitenmarker auf Chromosom 15 wurden die Tiere typisiert: Sw919, Sw964, S0088, Sw120, Sw906 und Sw312. Die Bestimmung der Genotypen am RN-locus erfolgte anhand des Glykogenghalts im Musculus longissimus dorsi. Der Heterozygotiegrad der Marker lag zwischen 0, 47 und 1 bei Ebern und zwischen 0, 71 und 0, 88 bei den Sauen. Als Position des RN-Gens wurde die Mitte eines Intervalles bestimmt, der von dem Marker Sw120 sowie dem Markerpaar Sw906/Sw936 begrenzt wird. Für das männliche Geschlect wurden die Kartenabstände zwischen RN und Sw120, Sw906 und Sw936 in einer Mehrpunktanalyse auf 5 cM, 5 cM und 6, 9 cM geschätzt. Paarweise Schätzungen der Rekombinationsraten zwischen diesen Markern und RN betrugen in allen Fällen 0, 5, mit zugehörigen lod scores vol 52, 09, 29, 30 und 42, 53. übereinstimmungen und Diskrepanzen zwischen Kartierungsergebnissen verschiedener Arbeitsgruppen werden diskutiert. Die Kartenlänge des mit Markern abgedeckten Teils von Chromsom 15 betrug beim männlichen Geschlecht 68, 8 cM, im Gegensatz zu einer Länge von 124, 7 cM beim weiblichen Geschlecht. Signifikante Unterschiede in den Rekombinationsraten beider Geschlechter wurden in den Intervallen Sw919-Sw964, Sw964-S0088 und Sw936-Sw312 gefunden, nicht jedoch in der Umgebung des RN-Genes.