The effect of dietary rumen-protected trans-10,cis-12 conjugated linoleic acid or a milk fat-depressing diet on energy metabolism, inflammation, and oxidative stress of dairy cows in early lactation.

The objective of this study was to determine the effects of milk fat depression induced by supplementing conjugated linoleic acid (CLA; trans-10,cis-12 and cis-9,trans-11 CLA) or feeding a higher starch and oil-containing diet (HSO) on metabolic changes in dairy cows after calving. The main hypothesis was that the 2 strategies to decrease milk fat yield could have different effects on performance, energy balance (EB), and inflammatory status in early lactation. Thirty-three Nordic Red dairy cows were used in a randomized block design from 1 to 112 d of lactation and fed one of the following treatments: control (CON), CLA-supplemented diet, or HSO diet. Dry matter intake and milk yield were measured daily whereas milk composition was measured weekly throughout the experiment. Nutrient digestibility, EB, and plasma hormones and metabolites were measured at 3, 7, 11, and 15 wk of lactation in respiration chambers. The HSO diet led to lower intakes of dry matter, neutral detergent fiber, and gross energy compared with CON and CLA diets. The CLA diet and especially the HSO diet resulted in lower energy-corrected milk yield during the first 7 wk of lactation than those fed CON. The EB was numerically higher for HSO and CLA diets compared with CON at wk 3 and 7. Plasma glucose concentration was higher by the CLA diet at wk 3 and by the HSO diet from wk 3 to 15 compared with CON. Plasma nonesterified fatty acids were higher at wk 3 in the CON group (indicating more lipid mobilization) but decreased thereafter to similar levels with the other groups. The HSO-fed cows had higher plasma ceruloplasmin, paraoxonase, and total bilirubin concentrations in the entire experiment and showed the highest levels of reactive oxygen metabolites. These results suggest an increased inflammatory and oxidative stress state in the HSO cows and probably different regulation of the innate immune system. This study provides evidence that milk fat depression induced by feeding HSO (as well as CLA) decreased milk fat secretion and improved EB compared with CON in early lactation. The increase in plasma glucose and paraoxonase levels with the HSO diet may imply a better ability of the liver to cope with the metabolic demand after parturition. However, the negative effect of HSO on feed intake, and the indication of increased inflammatory and oxidative stress warrant further studies before the HSO feeding strategy could be supported as an alternative to improve EB in early lactation.

Evaluating the effects of high-oil rapeseed cake or natural additives on methane emissions and performance of dairy cows.

We evaluated the potential of feeding high-oil rapeseed cake or natural additives as rumen modifiers on enteric methane (CH4) emissions, nutrient utilization, performance, and milk fatty acid (FA) profile of dairy cows. Eight Nordic Red dairy cows averaging (mean ± SD) 81 ± 21 d in milk and 41.0 ± 1.9 kg of milk yield at the beginning of the study were randomly assigned to a replicated 4 × 4 Latin square design with 21-d periods. Treatments comprised grass silage-based diets (45:55 forage to concentrate ratio on dry matter basis) including (1) control containing 19.3% rapeseed meal (CON), (2) CON with full replacement of rapeseed meal with rapeseed cake (RSC), (3) supplementation of CON with 50 g/d of yeast hydrolysate product plus coniferous resin acid-based compound (YHR), and (4) supplementation of CON with 20 g/d of combination of garlic-citrus extract and essential oils in a pellet (GCE). Apparent total-tract digestibility was measured using total collection of feces, and CH4 emissions were measured in respiratory chambers on 4 consecutive days. Data collected during d 17 and 21 in each period were used for ANOVA analysis using a mixed model. Treatments did not affect dry matter intake (DMI), whereas feeding RSC increased crude protein and ether extract digestibility compared with the other diets. Emissions of CH4 per day, per kilogram of DMI, and per kilogram of energy-corrected milk, and gross energy intake were lower for RSC compared with other diets. We found no effect of YHR on daily CH4 emissions, whereas CH4 yield (g of CH4/kg of DMI or as percentage of gross energy intake) decreased with GCE compared with CON. Treatments did not influence energy balance. Further, RSC reduced the proportion of N intake excreted in feces, and YHR improved N balance compared with CON diet. Feeding RSC resulted in greatest yields of milk and energy-corrected milk, and feed efficiency. Relative to the CON diet, RSC decreased saturated FA by 10% in milk fat by increasing cis-monounsaturated FA but also increased the proportion of trans FA. Proportion of odd- and branched-chain FA increased with GCE and YHR compared with CON. We conclude that replacing rapeseed meal by rapeseed cake decreased CH4 emissions, whereas YHR or GCE had no effect on CH4 emissions in this study.

Temporal changes in milk fatty acid composition during diet-induced milk fat depression in lactating cows.

Diet-induced milk fat depression (MFD) in lactating cows has been attributed to alterations in ruminal lipid metabolism leading to the formation of specific fatty acid (FA) biohydrogenation intermediates that directly inhibit milk fat synthesis. However, the mechanisms responsible for decreased lipid synthesis in the mammary gland over time are not well defined. The aim of this study was to evaluate the effect of diet on milk FA composition and milk fat production over time, especially during MFD, and explore the associations between MFD and FA biohydrogenation intermediates in omasal digesta and milk. Four lactating Finnish Ayrshire cows used in a 4 × 4 Latin square with a 2 × 2 factorial arrangement of treatments and 35-d experimental periods were fed diets formulated to cause differences in ruminal and mammary lipid metabolism. Treatments consisted of an iso-nitrogenous total mixed ration based on grass silage with a forage to concentrate ratio of 65:35 or 35:65 without added oil, or with sunflower oil at 50 g/kg of diet dry matter. The high-concentrate diet with sunflower oil (HSO) induced a 2-stage drop in milk fat synthesis that was accompanied by specific temporal changes in the milk FA composition. The MFD on HSO was associated especially with trans-10 18:1 and also with trans-9,cis-11 conjugated linoleic acid (CLA) in milk and omasal digesta across all diets and was accompanied by the appearance of trans-10,cis-15 18:2. Trans-10,cis-12 CLA was increased in HSO, but milk fat secretion was not associated with omasal or milk trans-10,cis-12 CLA. The temporal changes in milk fat content and yield and milk FA composition reflect the shift from the predominant ruminal biohydrogenation pathway to an alternative pathway. The ambiguous role of trans-10,cis-12 CLA suggests that trans-10 18:1, trans-9,cis-11 CLA and trans-10,cis-15 18:2 or additional mechanisms contributed to the diet-induced MFD in lactating cows.

Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens.

Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker-assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F2 population to include 1599 F2 females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n = 692 females) and a Hy-Line White Plymouth Rock line (n = 290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4-13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F2 population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker-assisted selection for improved eggshell quality.

Plant oil supplements reduce methane emissions and improve milk fatty acid composition in dairy cows fed grass silage-based diets without affecting milk yield.

Four lipid supplements varying in chain length or degree of unsaturation were examined for their effects on milk yield and composition, ruminal CH4 emissions, rumen fermentation, nutrient utilization, and microbial ecology in lactating dairy cows. Five Nordic Red cows fitted with rumen cannulas were used in a 5 × 5 Latin square with five 28-d periods. Treatments comprised total mixed rations based on grass silage with a forage-to-concentrate ratio of 60:40 supplemented with no lipid (CO) or 50 g/kg of diet dry matter (DM) of myristic acid (MA), rapeseed oil (RO), safflower oil (SO), or linseed oil (LO). Feeding MA resulted in the lowest DM intake, and feeding RO reduced DM intake compared with CO. Feeding MA reduced the yields of milk, milk constituents, and energy-corrected milk. Plant oils did not influence yields of milk and milk constituents, but reduced milk protein content compared with CO. Treatments had no effect on rumen fermentation characteristics, other than an increase in ammonia-N concentration due to feeding MA, RO, and SO compared with CO. Lipid supplements reduced daily ruminal CH4 emission; however, the response was to some extent a result of lower feed intake. Lipids modified microbial community structure without affecting total counts of bacteria, archaea, and ciliate protozoa. Dietary treatments had no effect on the apparent total tract digestibility of organic matter, fiber, and gross energy. Treatments did not affect either energy secreted in milk as a proportion of energy intake or efficiency of dietary N utilization. All lipids lowered de novo fatty acid synthesis in the mammary gland. Plant oils increased proportions of milk fat 18:0, cis 18:1, trans and monounsaturated fatty acids, and decreased saturated fatty acids compared with CO and MA. Both SO and LO increased the proportion of total polyunsaturated fatty acids, total conjugated linolenic acid, and cis-9,trans-11 conjugated linoleic acid. Feeding MA clearly increased the Δ9 desaturation of fatty acids. Our results provide compelling evidence that plant oils supplemented to a grass silage-based diet reduce ruminal CH4 emission and milk saturated fatty acids, and increase the proportion of unsaturated fatty acids and total conjugated linoleic acid while not interfering with digestibility, rumen fermentation, rumen microbial quantities, or milk production.

Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants.

BACKGROUND: The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. RESULTS: Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were associated with fat yield. Regions on chromosomes 5, 14, 16, 19, 20 and 25 were associated with milk yield and chromosomes 5, 14 and 25 had regions associated with protein yield. Significantly associated variations were found in 227 genes for fat yield, 72 genes for milk yield and 30 genes for protein yield. Ingenuity Pathway Analysis was used to identify networks connecting these genes displaying significant hits. When compared to previously mapped genomic regions associated with fertility, significantly associated variations were found in 5 genes common for fat yield and fertility, thus linking these two traits via biological networks. CONCLUSION: This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot unambiguously reveal which of the associated variations is causative. Linkage disequilibrium creates difficulties to pinpoint the causative genes and variations. One solution to overcome these difficulties is the identification of the functional gene networks and pathways to reveal important interacting genes as candidates for the observed effects. This information on target genomic regions may be exploited to improve genomic prediction.

Temporal variation in coat colour (genotypes) supports major changes in the Nordic cattle population after Iron Age.

Variation in coat colour genotypes of archaeological cattle samples from Finland was studied by sequencing 69 base pairs of the extension locus (melanocortin 1-receptor, MC1R) targeting both a transition and a deletion defining the three main alleles, such as dominant black (E(D) ), wild type (E(+) ) and recessive red (e). The 69-bp MC1R sequence was successfully analysed from 23 ancient (1000-1800 AD) samples. All three main alleles and genotype combinations were detected with allele frequencies of 0.26, 0.17 and 0.57 for E(D) , E(+) and e respectively. Recessive red and dominant black alleles were detected in both sexes. According to the best of our knowledge, this is the first ancient DNA study defining all three main MC1R alleles. Observed MC1R alleles are in agreement with calculated phenotype frequencies from historical sources. The division of ancient Finnish cattle population into modern Finnish breeds with settled colours was dated to the 20th century. From the existing genotyped populations in Europe (43 breeds, n = 2360), the closest match to ancient MC1R genotype frequencies was with the Norwegian native multicoloured breeds. In combined published genotype data of ancient (n = 147) and genotypes and phenotypes of modern Nordic cattle (n = 738), MC1R allele frequencies showed temporal changes similar to neutral mitochondrial DNA and Y-chromosomal haplotypes analysed earlier. All three markers indicate major change in genotypes in Nordic cattle from the Late Iron Age to the Medieval period followed by slower change through the historical periods until the present.

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia, eastern and northern Europe.

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P-value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.

A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs.

The immotile short tail sperm (ISTS) defect was recognized in the Finnish Yorkshire population at the end of the 1990s when several affected boars were identified. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene. In 2001, the insertion frequency was already 0.23. Even though all homozygous boars are eliminated from the population due to infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established. Previously we identified an association between the L1 insertion and litter size in the first parity. In this study, we analyzed the expression of the genomic region adjacent to the L1 insertion on porcine chromosome 16. Based on the RNA-seq data analysis, prolactin receptor (PRLR) was identified as down-regulated in the oviduct of ISTS homozygous sows. Quantitative PCR (qPCR) analysis confirmed the significant down-regulation of PRLR in the ovary, oviduct, and uterus of ISTS homozygous and carrier sows compared with controls. In addition, three unannotated loci between PRLR and SPEF2 showed some transcription activity in the analyzed samples. We further investigated the possible mechanisms of the L1 influence on the decrease in the identified gene expression. The methylation pattern of the PRLR gene region appeared unaffected. However, reads mapping to the L1 sequence indicated an increase in L1 antisense promoter expression in the ISTS homozygous animals. The current data suggest that the presence of the L1 affects by some mechanism the expression patterns upstream of the insertion site.

Effects of Bos taurus autosome 9-located quantitative trait loci haplotypes on the disease phenotypes of dairy cows with experimentally induced Escherichia coli mastitis.

Several quantitative trait loci (QTL) affecting mastitis incidence and mastitis-related traits such as somatic cell score exist in dairy cows. Previously, QTL haplotypes associated with susceptibility to Escherichia coli mastitis in Nordic Holstein-Friesian (HF) cows were identified on Bos taurus autosome 9. In the present study, we induced experimental E. coli mastitis in Danish HF cows to investigate the effect of 2 E. coli mastitis-associated QTL haplotypes on the cows' disease phenotypes and recovery in early lactation. Thirty-two cows were divided in 2 groups bearing haplotypes with either low (HL) or high (HH) susceptibility to E. coli. In addition, biopsies (liver and udder) were collected from half of the cows (n=16), resulting in a 2 × 2 factorial design, with haplotype being one factor (HL vs. HH) and biopsy being the other factor (biopsies vs. no biopsies). Each cow was inoculated with a low E. coli dose (20 to 40 cfu) in one front quarter at time 0 h. Liver biopsies were collected at -144, 12, 24, and 192 h; udder biopsies were collected at 24h and 192 h post-E. coli inoculation. The clinical parameters: feed intake, milk yield, body temperature, heart rate, respiration rate, rumen motility; and the paraclinical parameters: bacterial counts, somatic cell count (SCC), and milk amyloid A levels in milk; and white blood cell count, polymorphonuclear neutrophilic leukocyte (PMNL) count, and serum amyloid A levels in blood were recorded at different time points post-E. coli inoculation. Escherichia coli inoculation changed the clinical and paraclinical parameters in all cows except one that was not infected. Clinically, the HH group tended to have higher body temperature and heart rate than the HL group did. Paraclinically, the HL group had faster PMNL recruitment and SCC recovery than the HH group did. However, we also found interactions between the effects of haplotype and biopsy for body temperature, heart rate, and PMNL. In conclusion, when challenged with E. coli mastitis, HF cows with the specific Bos taurus autosome 9-located QTL haplotypes were associated with differences in leukocyte kinetics, with low-susceptibility cows having faster blood PMNL recruitment and SCC recovery and a tendency for a milder clinical response than the high-susceptibility cows did.

L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population.

Immotile, short-tail sperm defect (ISTS) expanded in the Finnish Yorkshire population in the end of 1990s. The causal mutation for this defect is a recent L1 insertion within the SPEF2 gene in chromosome 16. Even though all homozygous boars are eliminated from the population because of infertility, the amount of affected boars increased rapidly until marker-assisted selection against the defect was established. To elucidate the associated effects of the ISTS defect on production traits, we have investigated the association of the L1 insertion and PRLR haplotype with reproduction traits in the Finnish Yorkshire population. Two data sets including 357 sows and 491 AI-boars were genotyped for the presence of the L1 insertion and analysed for association with reproduction traits. A Proc Mixed procedure (SAS Inc) and a software package for analysing multivariate mixed models (DMU) were used to study the effect of polymorphisms on reproduction traits. The L1-insertion within SPEF2 gene was associated with litter size in the first parity. The SPEF2 gene is located adjacent to a candidate gene for litter size in the pig, PRLR. Haplotypes within PRLR exon 10 were analysed in data set of 93 AI-boars for the association with reproduction traits. However, no associations were detected within the analysed data set indicating that PRLR sequence variants are not the causal cause for the identified effect on litter size.

First-generation linkage map for the common frog Rana temporaria reveals sex-linkage group.

The common frog (Rana temporaria) has become a model species in the fields of ecology and evolutionary biology. However, lack of genomic resources has been limiting utility of this species for detailed evolutionary genetic studies. Using a set of 107 informative microsatellite markers genotyped in a large full-sib family (800 F1 offspring), we created the first linkage map for this species. This partial map-distributed over 15 linkage groups-has a total length of 1698.8 cM. In line with the fact that males are the heterogametic sex in this species and a reduction of recombination is expected, we observed a lower recombination rate in the males (map length: 1371.5 cM) as compared with females (2089.8 cM). Furthermore, three loci previously documented to be sex-linked (that is, carrying male-specific alleles) in adults from the wild mapped to the same linkage group. The linkage map described in this study is one of the densest ones available for amphibians. The discovery of a sex linkage group in Rana temporaria, as well as other regions with strongly reduced male recombination rates, should help to uncover the genetic underpinnings of the sex-determination system in this species. As the number of linkage groups found (n=15) is quite close to the actual number of chromosomes (n=13), the map should provide a useful resource for further evolutionary, ecological and conservation genetic work in this and other closely related species.

Quantitative trait loci affecting eggshell traits in an F(2) population.

Good eggshell quality is important for both table egg quality and chicken reproductive performance. Weak eggshells cause economic losses in all production steps. Poor eggshell quality also poses increased risk for Salmonella infections. Eggshell quality has been a difficult trait to improve by traditional breeding, as it can be measured only for females and it is difficult and expensive to measure. Breeding for improved shell quality may therefore benefit from the use of marker-assisted selection. In an effort to find markers linked to eggshell quality, we have used an F(2) population of 668 females to map quantitative trait loci (QTL) affecting eggshell traits (eggshell deformation, breaking force, weight). By using 160 microsatellite markers on 27 chromosomes, we found 11 genome-wide and 15 suggestive QTL for shell traits measured at different times during production. Loci affecting the deformation were found on chromosomes 1, 2, 6, 10, 14 and Z. Loci affecting the breaking force were detected on chromosomes 2, 3, 10, 12 and Z. Loci affecting the shell weight were detected on chromosomes 6, 12, 24 and Z. Each QTL explains between 1.5% and 4.6% of the phenotypic variance, adding up to 10-15% of total phenotypic variance explained for the different traits. No epistatic effects were observed between loci affecting eggshell traits. Because the effects for quality are mainly additive, these results provide a basis for further characterization of the loci to identify closely linked markers to be used in marker-assisted selection.

Mapping of fertility traits in Finnish Ayrshire by genome-wide association analysis.

A whole-genome scan using single marker association was used to detect chromosome regions associated with seven female fertility traits in Finnish Ayrshire dairy cattle. The phenotypic data consisted of de-regressed estimated breeding values for 340 bulls which were estimated using a single trait model. Genotypes were obtained with the Illumina BovineSNP50 panel and a total of 35 630 informative, high-quality single nucleotide polymorphism (SNP) markers were used. The association analysis was performed using a mixed-model approach which fitted a fixed effect for each SNP and a random polygenic effect. We detected eleven genome-wide significant associations on eight different chromosomes. With at least chromosome-wise significance after Bonferroni correction, sixteen SNPs on nine chromosomes showed significant associations with one or more fertility traits. The results confirmed quantitative trait loci on three chromosomes (1, 2 and 20) for fertility traits previously reported for the same breed and one on chromosome four previously detected in Holstein cattle.

Marker-assisted breeding value estimation for mastitis resistance in Finnish Ayrshire cattle.

Marker-assisted breeding value estimation is expected to increase the accuracy of estimated breeding values, especially for traits with low heritability. Several quantitative trait loci (QTL) have been found for somatic cell score and clinical mastitis. The objective of this study was to demonstrate marker-assisted breeding value estimation, combining data of genotyped and ungenotyped animals in a large pedigree population using either identical-by-descent (IBD) or identical-by-state (IBS) haplotypes for some previously identified QTL regions for somatic cell score and clinical mastitis in Finnish Ayrshire cattle. For both methods, QTL variances were estimated based on daughter yield deviations of genotyped bulls. The QTL explained only a small proportion of genetic variance, especially with IBS haplotypes. Using IBD haplotypes gave more reranking of bulls and cows than using IBS haplotypes. Cross-validation showed no increase in predictive ability when using IBS haplotypes compared with conventional breeding value estimation, whereas a decrease in predictive ability was observed with IBD haplotypes. Furthermore, computing time was lower and convergence was better with IBS haplotypes than with IBD haplotypes. In this study on mastitis resistance in Finnish Ayrshire, conventional breeding value estimation would be advocated because of the lack in improvement of accuracy and predictive ability when using marker-assisted breeding value estimation. However, in situations where IBS haplotypes would explain 10 to 20% or more of the genetic variance, marker-assisted breeding value estimation with IBS haplotypes may yield greater accuracy and predictive ability than conventional breeding value estimation.

Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus).

Maternally inherited mitochondrial DNA (mtDNA) has been used extensively to determine origin and diversity of taurine cattle (Bos taurus) but global surveys of paternally inherited Y-chromosome diversity are lacking. Here, we provide mtDNA information on previously uncharacterised Eurasian breeds and present the most comprehensive Y-chromosomal microsatellite data on domestic cattle to date. The mitochondrial haplogroup T3 was the most frequent, whereas T4 was detected only in the Yakutian cattle from Siberia. The mtDNA data indicates that the Ukrainian and Central Asian regions are zones where hybrids between taurine and zebu (B. indicus) cattle have existed. This zebu influence appears to have subsequently spread into southern and southeastern European breeds. The most common Y-chromosomal microsatellite haplotype, termed here as H11, showed an elevated frequency in the Eurasian sample set compared with that detected in Near Eastern and Anatolian breeds. The taurine Y-chromosomal microsatellite haplotypes were found to be structured in a network according to the Y-haplogroups Y1 and Y2. These data do not support the recent hypothesis on the origin of Y1 from the local European hybridization of cattle with male aurochsen. Compared with mtDNA, the intensive culling of breeding males and male-mediated crossbreeding of locally raised native breeds has accelerated loss of Y-chromosomal variation in domestic cattle, and affected the contribution of genetic drift to diversity. In conclusion, to maintain diversity, breeds showing rare Y-haplotypes should be prioritised in the conservation of cattle genetic resources.

Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11.

Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red. The families had previously been shown to segregate for udder health QTL. A total of 524 progeny tested bulls were included in the analysis. A linkage map including 33 microsatellite and five SNP markers was constructed. We performed combined linkage disequilibrium and linkage analysis (LDLA) using the whole data set. Further analyses were performed for FA and SRB separately to study the origin of the identified QTL/haplotype and to examine if it was common in both populations. Finally, different two-trait models were fitted. These postulated either a pleiotropic QTL affecting both traits; two linked QTL, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis because of lack of linkage disequilibrium between the markers used and the QTL in the region.

Molecular anatomy of the cytoplasmic domain of bovine growth hormone receptor, a quantitative trait locus.

Quantitative trait loci (QTL) studies have indicated growth hormone receptor (GHR) as a candidate gene affecting cattle milk yield and composition. In order to characterize genetic variation at GHR in cattle, we studied European and East African breeds with different histories of selection, and Bos grunniens, Ovis aries, Sus scrofa, Bison bison and Rangifer tarandus as references. We sequenced most of the cytoplasmic domain (900 bp of exon 10), 89 bp of exon 8, including the putative causative mutation for the QTL effect, and 390 bp of intron 8 for comparison. In the cytoplasmic domain, seven synonymous and seven non-synonymous single nucleotide polymorphisms (SNP) were identified in cattle. Three non-synonymous SNPs were found in sheep and one synonymous SNP in yak, while other studied species were monomorphic. Three major haplotypes were observed, one unique to African breeds, one unique to European breeds and one shared. Bison and yak haplotypes are derivatives of the European haplotype lineage. Most of the exon 10 non-synonymous cattle SNPs appear at phylogenetically highly conserved sites. The polymorphisms in exon 10 cluster around a ruminant-specific tyrosine residue, suggesting that this site may act as an additional signalling domain of GHR in ruminants. Alternative explanations for the persistent polymorphism include balancing selection, hitch-hiking, pleiotropic or sexually antagonistic fitness effects or relaxed functional constraints.

Fine-mapping QTL for mastitis resistance on BTA9 in three Nordic red cattle breeds.

A QTL affecting clinical mastitis and/or somatic cell score (SCS) has been reported previously on chromosome 9 from studies in 16 families from the Swedish Red and White (SRB), Finnish Ayrshire (FA) and Danish Red (DR) breeds. In order to refine the QTL location, 67 markers were genotyped over the whole chromosome in the 16 original families and 18 additional half-sib families. This enabled linkage disequilibrium information to be used in the analysis. Data were analysed by an approach that combines information from linkage and linkage disequilibrium, which allowed the QTL affecting clinical mastitis to be mapped to a small interval (<1 cM) between the markers BM4208 and INRA084. This QTL showed a pleiotropic effect on SCS in the DR and SRB breeds. Haplotypes associated with variations in mastitis resistance were identified. The haplotypes were predictive in the general population and can be used in marker-assisted selection. Pleiotropic effects of the mastitis QTL were studied for three milk production traits and eight udder conformation traits. This QTL was also associated with yield traits in DR but not in FA or SRB. No QTL were found for udder conformation traits on chromosome 9.

Infertile boars with knobbed and immotile short-tail sperm defects in the Finnish Yorkshire breed.

In the period 1996-2006 two specific sperm defects, the knobbed acrosome (KA) defect and the immotile short-tail sperm (ISTS) defect, showed a strong negative association with fertility in Finnish breeding boars. In this study, we examined the incidence of these two sperm defects in two pig breeds, their effects on fertility and their associations with sperm morphology and testicular histology. Semen samples from 2048 (1097 Yorkshire, 951 Landrace) boars were collected. None of the Landrace boars revealed either the KA defect or the ISTS defect. Of the Yorkshire boars, 0.8% were afflicted with the KA defect and 7.6% with the ISTS defect. Boars diagnosed with the ISTS defect produced no litters. Fertility data were available from two artificially inseminated (AI) boars and six farm breeding boars affected with the KA defect. Breeding boars with 45-81% knobbed spermatozoa (n = 6) did not produce any litters out of 71 sows bred. AI boars with 25-30% knobbed spermatozoa had a poor non-return rate (on average 47% compared with 85% for normal control boars) and produced small litters, on average 2.5 piglets less than other boars of the same breed. Morphometry of testicular tissue and distribution of different cells in the seminiferous tubules were examined in nine boars. Boars with the KA defect had a smaller diameter of the seminiferous tubules (p < 0.05) and a lower number of Sertoli cells (p < 0.05) than controls. ISTS boars, in turn, had a significantly lower number of elongated spermatids (p < 0.05), and they also produced on average only 12% of the spermatozoa of normal boars. The ISTS defect is a manifestation of an autosomal recessive disease caused by an insertion in the KPL2 gene in porcine chromosome 16. Although we tried to map the KA defect, its aetiology remains unclear.