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

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

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

Need for sharp phenotypes in QTL detection for calving traits in dairy cattle

The aim of the study was to investigate whether parity-specific phenotypes provide a clearer picture of quantitative trait loci (QTL) affecting calving traits in German Holsteins than breeding values estimated across parities. In experiment I, approximate daughter yield deviations were calculated by applying a univariate sire model assuming unrelated sires used as phenotypes in a QTL mapping study. These results were compared with those obtained using deregressed estimated breeding values obtained from the routine German sire evaluation (experiment II). In experiment I, 17 chromosome-wise significant QTL were found for the first parity, but only 12 for the second parity. Only three QTL for maternal stillbirth, located on BTA7, 15 and 23, showed an experiment-wise significance. Experiment II revealed 15 chromosome-wise significant QTL. The results differed markedly between first and second parity within experiment I, as well as between experiment I and II. The present study showed that parity-specific daughter yield deviations are beneficial for mapping QTL for calving traits. Furthermore, it is expected that the use of sharper phenotypes will also be advantageous for QTL fine mapping and the identification of candidate genes.

A genome-wide scan for signatures of recent selection in Holstein cattle

The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.

Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle

The Toll-like receptor (TLR) and peptidoglycan recognition protein 1 (PGLYRP1) genes play key roles in the innate immune systems of mammals. While the TLRs recognize a variety of invading pathogens and induce innate immune responses, PGLYRP1 is directly microbicidal. We used custom allele-specific assays to genotype and validate 220 diallelic variants, including 54 nonsynonymous SNPs in 11 bovine innate immune genes (TLR1-TLR10, PGLYRP1) for 37 cattle breeds. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and we were unable to differentiate between the specialized B. t. taurus beef and dairy breeds, despite an average polymorphism density of one locus per 219 bp. Ninety-nine tagSNPs and one tag insertion-deletion polymorphism were sufficient to predict 100% of the variation at all 11 innate immune loci in both subspecies and their hybrids, whereas 58 tagSNPs captured 100% of the variation at 172 loci in B. t. taurus. PolyPhen and SIFT analyses of nonsynonymous SNPs encoding amino acid replacements indicated that the majority of these substitutions were benign, but up to 31% were expected to potentially impact protein function. Several diversity-based tests provided support for strong purifying selection acting on TLR10 in B. t. taurus cattle. These results will broadly impact efforts related to bovine translational genomics.

Genome-wide association study of growth in crossbred beef cattle

Chromosomal regions harboring variation affecting cattle birth weight and BW gain to 1 yr of age were identified by marker association using the highly parallel BovineSNP50 BeadChip (50K) assay composed of 54,001 individual SNP. Genotypes were obtained from progeny (F(1); 590 steers) and 2-, 3-, and 4-breed cross grandprogeny (F(1)(2) = F(1) x F(1); 1,306 steers and 707 females) of 150 AI sires representing 7 breeds (22 sires per breed; Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental). Genotypes and birth, weaning, and yearling BW records were used in whole-genome association analyses to estimate effects of individual SNP on growth. Traits analyzed included growth component traits: birth weight (BWT), 205-d adjusted birth to weaning BW gain (WG), 160-d adjusted postweaning BW gain (PWG); cumulative traits: 205-d adjusted weaning weight (WW = BWT + WG) and 365-d adjusted yearling weight (YW = BWT + WG + PWG); and indexes of relative differences between postnatal growth and birth weight. Modeled fixed effects included additive effects of calf and dam SNP genotype, year-sex-management contemporary groups, and covariates for calf and dam breed composition and heterosis. Direct and maternal additive polygenic effects and maternal permanent environment effects were random. Missing genotypes, including 50K genotypes of most dams, were approximated with a single-locus BLUP procedure from pedigree relationships and known 50K genotypes. Various association criteria were applied: stringent tests to account for multiple testing but with limited power to detect associations with small effects, and relaxed nominal P that may detect SNP associated with small effects but include excessive false positive associations. Genomic locations of the 231 SNP meeting stringent criteria generally coincided with described previously QTL affecting growth traits. The 12,425 SNP satisfying relaxed tests were located throughout the genome. Most SNP associated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatal growth relative to BWT.

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

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

A genome wide association study for QTL affecting direct and maternal effects of stillbirth and dystocia in cattle

Dystocia and stillbirth are significant causes of female and neonatal death in many species and there is evidence for a genetic component to both traits. Identifying causal mutations affecting these traits through genome wide association studies could reveal the genetic pathways involved and will be a step towards targeted interventions. Norwegian Red cattle are an ideal model breed for such studies as very large numbers of records are available. We conducted a genome wide association study for direct and maternal effects of dystocia and stillbirth using almost 1 million records of these traits. Genotyping costs were minimized by genotyping the sires of the recorded cows, and using daughter averages as phenotypes. A dense marker map containing 17,343 single nucleotide polymorphisms covering all autosomal chromosomes was utilized. The genotyped sires were assigned to one of two groups in an attempt to ensure independence between the groups. Associations were only considered validated if they occurred in both groups. Strong associations were found and validated on chromosomes 4, 5, 6, 9, 12, 20, 22 and 28. The QTL region on chromosome 6 was refined using LDLA analysis. The results showed that this chromosome most probably contains two QTL for direct effect on dystocia and one for direct effect on stillbirth. Several candidate genes may be identified close to these QTL. Of these, a cluster of genes expected to affect bone and cartilage formation (i.e. SPP1, IBSP and MEPE) are of particular interest and we suggest that these genes are screened in candidate gene studies for dystocia and stillbirth in cattle as well as other species.

Refined positioning of a quantitative trait locus affecting somatic cell score on chromosome 18 in the German Holstein using linkage disequilibrium

Combined linkage and linkage disequilibrium analysis (LALD) was conducted to more accurately map a previously reported quantitative trait locus (QTL) affecting somatic cell score on bovine chromosome 18. A grand-daughter design consisting of 6 German Holstein grandsire families with 1,054 progeny-tested genotyped sons was used in this study. Twenty microsatellite markers, 5 single nucleotide polymorphisms, and an erythrocyte antigen marker with an average marker spacing of 1.95 cM were analyzed along a chromosomal segment of 50.80 cM. Variance components were estimated and restricted maximum likelihood test statistics were calculated at the midpoint of each marker interval. The test statistics calculated in single-QTL linkage analysis exceeded the genome-wide significance threshold at several putative QTL positions. Using LALD, we were successful in assigning a genome-wide significant QTL to a confidence interval of 10.8 cM between the markers ILSTS002 and BMS833. The QTL in this marker interval was estimated to be responsible for between 5.89 and 13.86% of the genetic variation in somatic cell score. In contrast to the single-QTL linkage analysis model, LALD analyses with a 2-QTL model confirmed the position of one QTL, but gave no conclusive evidence for the existence or position of a second QTL. Ultimately, the QTL position was narrowed down considerably compared with previous results with a refined confidence interval of less than 11 cM.

Characterization of maternal antigen that embryos require (MATER/NLRP5) gene and protein in pig somatic tissues and germ cells

Maternal effect genes produce mRNA or proteins that accumulate in the egg during oogenesis and control the developmental program until embryonic genome activation takes place. NLRP5 (NLR family, Pyrin domain containing 5), also called MATER (Maternal Antigen That Embryos Require) is one of the genes required for normal early embryonic development, although its precise function remains to be elucidated. The aim of the present study was to analyze the NLRP5 gene expression pattern and protein distribution in somatic tissues and germ cells in the pig. Reverse transcription was performed on mRNA from germinal vescicle (GV) oocytes and total RNA from spermatozoa and tissues from different organs. The transcript for NLRP5 gene was identified only in ovaries and oocytes. The presence of NLRP5 protein was detected only in ovaries by western blot analysis and immunohistochemistry.

Identification of a two-marker-haplotype on Bos taurus autosome 18 associated with somatic cell score in German Holstein cattle

Background

The somatic cell score (SCS) is implemented in routine sire evaluations in many countries as an indicator trait for udder health. Somatic cell score is highly correlated with clinical mastitis, and in the German Holstein population quantitative trait loci (QTL) for SCS have been repeatedly mapped on Bos taurus autosome 18 (BTA18). In the present study, we report a refined analysis of previously detected QTL regions on BTA18 with the aim of identifying marker and marker haplotypes in linkage disequilibrium with SCS. A combined linkage and linkage disequilibrium approach was implemented, and association analyses of marker genotypes and maternally inherited two-marker-haplotypes were conducted to identify marker and haplotypes in linkage disequilibrium with a locus affecting SCS in the German Holstein population.

Results

We detected a genome-wide significant QTL within marker interval 9 (HAMP_c.366+109G>A - BMS833) in the middle to telomeric region on BTA18 and a second putative QTL in marker interval 12-13 (BB710 - PVRL2_c.392G>A). Association analyses with genotypes of markers flanking the most likely QTL positions revealed the microsatellite marker BMS833 (interval 9) to be associated with a locus affecting SCS within the families investigated. A further analysis of maternally inherited two-marker haplotypes and effects of maternally inherited two-marker-interval gametes indicated haplotype 249-G in marker interval 12-13 (BB710 - PVRL2_c.392G>A) to be associated with SCS in the German Holstein population.

Conclusion

Our results confirmed previous QTL mapping results for SCS and support the hypothesis that more than one locus presumably affects udder health in the middle to telomeric region of BTA18. However, a subsequent investigation of the reported QTL regions is necessary to verify the two-QTL hypothesis and confirm the association of two-marker-haplotype 249-G in marker interval 12-13 (BB710 - PVRL2_c.392G>A) with SCS. For this purpose, higher marker density and multiple-trait and multiple-QTL models are required to narrow down the position of the causal mutation or mutations affecting SCS in German Holstein cattle.

Dissection of genetic factors modulating fetal growth in cattle indicates a substantial role of the non-SMC condensin I complex, subunit G (NCAPG) gene

The increasing evidence of fetal developmental effects on postnatal life, the still unknown fetal growth mechanisms impairing offspring generated by somatic nuclear transfer techniques, and the impact on stillbirth and dystocia in conventional reproduction have generated increasing attention toward mammalian fetal growth. We identified a highly significant quantitative trait locus (QTL) affecting fetal growth on bovine chromosome 6 in a specific resource population, which was set up by consistent use of embryo transfer and foster mothers and, thus, enabled dissection of fetal-specific genetic components of fetal growth. Merging our data with results from other cattle populations differing in historical and geographical origin and with comparative data from human whole-genome association mapping suggests that a nonsynonymous polymorphism in the non-SMC condensin I complex, subunit G (NCAPG) gene, NCAPG c.1326T>G, is the potential cause of the identified QTL resulting in divergent bovine fetal growth. NCAPG gene expression data in fetal placentomes with different NCAPG c.1326T>G genotypes, which are in line with recent results about differential NCAPG expression in placentomes from studies on assisted reproduction techniques, indicate that the NCAPG locus may give valuable information on the specific mechanisms regulating fetal growth in mammals.

Distribution and location of genetic effects for dairy traits

Genetic effects for many dairy traits and for total economic merit are evenly distributed across all chromosomes. A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects. Markers on BTA18 had the largest effects on calving ease, several conformation traits, longevity, and total merit. Prediction accuracy was highest using a heavy-tailed prior assuming that each marker had an effect on each trait, rather than assuming a normal distribution of effects as in a linear model, or that only some loci have nonzero effects. A prior model combining heavy tails with finite alleles produced results that were intermediate compared with the individual models. Differences between models were small (1 to 2%) for traits with no major genes and larger for heavy tails with traits having known quantitative trait loci (QTL; 6 to 8%). Analysis of bull recessive codes suggested that marker effects from genomic selection may be used to identify regions of chromosomes to search in detail for candidate genes, but individual single nucleotide polymorphisms were not tracking causative mutations with the exception of diacylglycerol O-acyltransferase 1. Additive genetic merits were constructed for each chromosome, and the distribution of BTA14-specific estimated breeding value (EBV) showed that selection primarily for milk yield has not changed the distribution of EBV for fat percentage even in the presence of a known QTL. Such chromosomal EBV also may be useful for identifying complementary mates in breeding programs. The QTL affecting dystocia, conformation, and economic merit on BTA18 appear to be related to calf size or birth weight and may be the result of longer gestation lengths. Results validate quantitative genetic assumptions that most traits are due to the contributions of a large number of genes of small additive effect, rather than support the finite locus model.

Genome scan detects quantitative trait loci affecting female fertility traits in Danish and Swedish Holstein cattle

Data from the joint Nordic breeding value prediction for Danish and Swedish Holstein grandsire families were used to locate quantitative trait loci (QTL) for female fertility traits in Danish and Swedish Holstein cattle. Up to 36 Holstein grandsires with over 2,000 sons were genotyped for 416 microsatellite markers. Single trait breeding values were used for 12 traits relating to female fertility and female reproductive disorders. Data were analyzed by least squares regression analysis within and across families. Twenty-six QTL were detected on 17 different chromosomes. The best evidence was found for QTL segregating on Bos taurus chromosome (BTA)1, BTA7, BTA10, and BTA26. On each of these chromosomes, several QTL were detected affecting more than one of the fertility traits investigated in this study. Evidence for segregation of additional QTL on BTA2, BTA9, and BTA24 was found.

Genomic scan for quantitative trait loci of chemical and physical body composition and deposition on pig chromosome X including the pseudoautosomal region of males

A QTL analysis of pig chromosome X (SSCX) was carried out using an approach that accurately takes into account the specific features of sex chromosomes i.e. their heterogeneity, the presence of a pseudoautosomal region and the dosage compensation phenomenon. A three-generation full-sib population of 386 animals was created by crossing Pietrain sires with a crossbred dam line. Phenotypic data on 72 traits were recorded for at least 292 and up to 315 F2 animals including chemical body composition measured on live animals at five target weights ranging from 30 to 140 kg, daily gain and feed intake measured throughout growth, and carcass characteristics obtained at slaughter weight (140 kg). Several significant and suggestive QTL were detected on pig chromosome X: (1) in the pseudoautosomal region of SSCX, a QTL for entire loin weight, which showed paternal imprinting, (2) closely linked to marker SW2456, a suggestive QTL for feed intake at which Pietrain alleles were found to be associated with higher feed intake, which is unexpected for a breed known for its low feed intake capacity, (3) at the telomeric end of the q arm of SSCX, QTL for jowl weight and lipid accretion and (4) suggestive QTL for chemical body composition at 30 kg. These results indicate that SSCX is important for physical and chemical body composition and accretion as well as feed intake regulation.

Fine mapping of quantitative trait Loci on bovine chromosome 6 affecting calving difficulty

Calving difficulty is an economically and ethically important trait for dairy cattle breeding. The aim of the present paper was to refine the position of a previously detected quantitative trait locus (QTL) affecting calving difficulty (direct effect) in Norwegian Red dairy cows. A granddaughter design consisting of 18 elite sire families and a total of 713 sons was genotyped for 154 markers spanning the QTL region, and the trait data were analyzed by using a combined linkage and linkage disequilibrium approach. A highly significant QTL was detected in a 150-kb interval between the markers LAP3_281 and BTA-114677. Additionally, there were some indications of a second QTL between the markers BTA-75776 and BTA-75780 located less than 500 kb apart. Several candidate genes may be identified close to these QTL. Of these, a cluster of genes expected to affect bone and cartilage formation may be of particular interest for follow-up studies.

A genome scan to detect quantitative trait loci for economically important traits in Holstein cattle using two methods and a dense single nucleotide polymorphism map

Genome scans for detection of bovine quantitative trait loci (QTL) were performed via variance component linkage analysis and linkage disequilibrium single-locus regression (LDRM). Four hundred eighty-four Holstein sires, of which 427 were from 10 grandsire families, were genotyped for 9,919 single nucleotide polymorphisms (SNP) using the Affymetrix MegAllele GeneChip Bovine Mapping 10K SNP array. A hybrid of the grand-daughter and selective genotyping designs was applied. Four thousand eight hundred fifty-six of the 9,919 SNP were located to chromosomes in base-pairs and formed the basis for the analyses. The mean polymorphism information content of the SNP was 0.25. The SNP centimorgan position was interpolated from their base-pair position using a microsatellite framework map. Estimated breeding values were used as observations, and the following traits were analyzed: 305-d lactation milk, fat, and protein yield; somatic cell score; herd life; interval of calving to first service; and age at first service. The variance component linkage analysis detected 102 potential QTL, whereas LDRM analysis found 144 significant SNP associations after accounting for a 5% false discovery rate. Twenty potential QTL and 49 significant SNP associations were in close proximity to QTL cited in the literature. Both methods found significant regions on Bos taurus autosome (BTA) 3, 5, and 16 for milk yield; BTA 14 and 19 for fat yield; BTA 1, 3, 16, and 28 for protein yield; BTA 2 and 13 for calving to first service; and BTA 14 for age at first service. Both approaches were effective in detecting potential QTL with a dense SNP map. The LDRM was well suited for a first genome scan due to its approximately 8 times lower computational demands. Further fine mapping should be applied on the chromosomal regions of interest found in this study.

Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle

A genome scan to detect QTL influencing growth and carcass-related traits was conducted in a Charolais x Holstein crossbred cattle population. Phenotypic measurements related to growth and carcass traits were made on the 235 second-generation crossbred males of this herd (F2 and reciprocal backcrosses), which were born in 4 consecutive annual cohorts. Traits measured in vivo were related to birth dimensions, growth rates, and ultrasound measurements of fat and muscle depth. The animals were slaughtered near a target BW of 550 kg, and a wide range of postmortem traits were measured: visual assessment of carcass conformation and carcass fatness, estimated subcutaneous fat percentage, weights of kidney knob and channel fat, and weights of carcass components after commercial and full-tissue dissections. The whole population, including grandparents, parents, and the crossbred bulls, was genotyped initially for 139 genome-wide microsatellite markers. Twenty-six additional markers were subsequently analyzed to increase marker density on some of the chromosomes where QTL had been initially identified. The linear regression analyses based on the 165 markers revealed a total of 51 significant QTL at the suggestive level, 21 of which were highly significant (F-value >or=9; based on the genome-wide thresholds obtained in the initial scan). A large proportion of the highly significant associations were found on chromosomes 5 and 6. The most highly significant QTL was localized between markers DIK1054 and DIK082 on chromosome 6 and explained about 20% of the phenotypic variance for the total bone proportion estimated after the commercial dissection. In the adjacent marker interval on this chromosome, 2 other highly significant QTL were found that explain about 30% of the phenotypic variance for birth dimension traits (BW and body length at birth). On chromosome 5, the most significant association influenced the lean:bone ratio at the forerib joint and was flanked by markers DIK4782 and BR2936. Other highly significant associations were detected on chromosomes 10 (estimated subcutaneous fat percentage), 11 (total saleable meat proportion), 16 (prehousing growth rate), and 22 (bone proportion at the leg joint). These results provide a useful starting point for the identification of the genes associated with traits of direct interest to the beef industry, using fine mapping or positional candidate gene approaches.

A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls

Genetic improvement of livestock populations can be achieved through detection and mapping of genetic markers linked to quantitative trait loci (QTL). With the completion of the bovine genome sequence assembly, single nucleotide polymorphism (SNP) assays spanning the whole bovine genome and research work on large-scale identification, validation, and analysis of genotypic variation in cattle has become possible. A total of 462 Canadian Holstein Bulls were used to test the association between SNP and QTL. Single locus linkage disequilibrium regression model was implemented to perform a whole genome scan to identify and map QTL affecting conformation and functional traits. One thousand five hundred thirty-six SNP markers from introns and exons of potential QTL regions for economically important traits across the bovine genome were selected for association analysis. A total of 45 and 151 SNP were found to be associated with 17 conformation and functional traits at a genome- and chromosome-wise significance level, respectively. Among the 196 significant SNP, 169 of them are newly detected in this study, whereas 27 of them have been reported in previous literature and 161 of these were located in genes and are worth further investigating to potentially identify the causative mutations underlying the QTL. The single locus linkage disequilibrium regression method using SNP marker genotypes has proven to be a successful methodology for detecting and mapping QTL in dairy cattle populations.

Breeding for resistance to mastitis in United Kingdom sheep, a review and economic appraisal

Mastitis is a problem in the sheep industry, and its incidence varies widely with how it is recorded, the breed of sheep and the farm. Virtually all the published information about the genetics of mastitis refers to dairy breeds of cattle and sheep, and there is little information for meat sheep breeds. Many dairy breeding programmes worldwide use the somatic cell count (scc) in milk as an indicator of resistance to clinical and subclinical mastitis, but it is difficult to measure in meat sheep breeds. Molecular genetic technologies may therefore be a more practical way to assess susceptibility to mastitis. This paper reviews the genetics of mastitis and considers the opportunities for breeding for resistance to mastitis, with particular reference to sheep. In addition, to investigate the potential economic effects of mastitis in a purebred sheep population, a computer model of flock dynamics was developed. By making a modest set of assumptions about the key farm parameters that influence lowland sheep production, the model showed that breeding for resistance (or other control methods), if it could reduce the risk of contracting mastitis by 10 per cent, would be worth pounds 8.40 per ewe, equivalent annually to pounds 2.7 million for the purebred sector of the Texel breed alone.

Detection and analysis of quantitative trait loci affecting production and secondary traits on chromosome 7 in Israeli Holsteins

A total of 5,459 Israeli Holstein cows, daughters of 11 sires, were genotyped for 29 microsatellites spanning chromosome 7 and analyzed by the daughter design for 9 economic traits: milk, fat, and protein yield, fat and protein percentage, somatic cell score, female fertility, herd life, and milk persistency. Quantitative trait loci at chromosome-wise 0.05 significance were obtained for fat and protein yield, fat percentage, somatic cell score, and female fertility. Peak F-values were obtained at 29 cM for fat and protein yield and fat percentage, at 60 cM for somatic cell score, at 74 cM for herd life, and at 11 cM for female fertility. The 0.95 confidence intervals for quantitative trait loci locations were 20 cM for kilograms of fat, 27 cM for fertility, and 51 cM for somatic cell score. Two loci affecting fertility at opposite ends of the chromosome are apparently segregating in the population. A quantitative trait locus for fertility near the centromere was confirmed by application of the modified granddaughter design to a single family. Estimated frequency of the economically favorable allele in the Israeli Holstein cattle was less than 0.5. Significant genetic gain for fertility seems possible by marker-assisted selection.

Identification of single nucleotide polymorphisms in bovine CARD15 and their associations with health and production traits in Canadian Holsteins

Background

Toll-like receptor-2 (TLR2) and Caspase Recruitment Domain 15 (CARD15) are important pattern recognition receptors that play a role in the initiation of the inflammatory and subsequent immune response. They have been previously identified as susceptibility loci for inflammatory bowel diseases in humans and are, therefore, suitable candidate genes for inflammatory disease resistance in cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the bovine TLR2 and CARD15 and evaluate the association of these SNPs with health and production traits in a population of Canadian Holstein bulls.

Results

A selective DNA pool was constructed based on the estimated breeding values (EBVs) for SCS. Gene segments were amplified from this pool in PCR reactions and the amplicons sequenced to reveal polymorphisms. A total of four SNPs, including one in intron 10 (c.2886-14A>G) and three in the exon 12 (c.3020A>T, c.4500A>C and c.4950C>T) were identified in CARD15; none were identified in TLR2. Canadian Holstein bulls (n = 338) were genotyped and haplotypes were reconstructed. Two SNPs, c.3020A>T and c.4500A>C, were associated with EBVs for health and production traits. The SNP, c.3020A>T, for example, was associated with SCS EBVs (p = 0.0097) with an allele substitution effect of 0.07 score. When compared to the most frequent haplotype Hap12(AC), Hap22(TC) was associated with increased milk (p < 0.0001) and protein (p = 0.0007) yield EBVs, and hap21(TA) was significantly associated with increased SCS EBV(p = 0.0120). All significant comparison-wise associations retained significance at 8% experimental-wise level by permutation test.

Conclusion

This study indicates that SNP c.3020A>T might play a role in the host response against mastitis and further detailed studies are needed to understand its functional mechanisms.

Fine mapping of a quantitative trait locus on chromosome 9 affecting non-return rate in Swedish dairy cattle

We previously mapped a quantitative trait locus (QTL) affecting the trait non-return rate at 56 days in heifers to bovine chromosome 9. The purpose of this study was to confirm and refine the position of the QTL by using a denser marker map and fine mapping methods. Five families that previously showed segregation for the QTL were included in the study. The mapping population consisted of 139 bulls in a granddaughter design. All bulls were genotyped for 25 microsatellite markers surrounding the QTL on chromosome 9. We also analysed the correlated trait number of inseminations per service period in heifers. Both traits describe the heifer's ability to become pregnant after insemination. Linkage analysis, linkage disequilibrium and combined linkage and linkage disequilibrium analysis were used to analyse the data. Analysis of the families jointly by linkage analysis resulted in a significant but broad QTL peak for non-return rate. Results from the combined analysis gave a sharp QTL peak with a well-defined maximum in between markers BMS1724 and BM7209, at the same position as where the highest peak from the linkage disequilibrium analysis was found. One of the sire families segregated clearly at this position and the difference in effects between the two sire haplotypes was 2.9 percentage units in non-return rate. No significant results were found for the number of inseminations in the combined analysis.

Genetic variation and responses to vaccines

Disease is a major source of economic loss to the livestock industry. Understanding the role of genetic factors in immune responsiveness and disease resistance should provide new approaches to the control of disease through development of safe synthetic subunit vaccines and breeding for disease resistance. The major histocompatibility complex (MHC) has been an important candidate locus for immune responsiveness studies. However, it is clear that other loci play an important role. Identifying these and quantifying the relative importance of MHC and non-MHC genes should result in new insights into host–pathogen interactions, and information that can be exploited by vaccine designers. The rapidly increasing information available about the bovine genome and the identification of polymorphisms in immune-related genes will offer potential candidates that control immune responses to vaccines. The bovine MHC,BoLA, encodes two distinct isotypes of class II molecules, DR and DQ, and in about half the common haplotypes theDQgenes are duplicated and expressed. DQ molecules are composed of two polymorphic chains whereas DR consists of one polymorphic and one non-polymorphic chain. Although, it is clear that MHC polymorphism is related to immune responsiveness, it is less clear how different allelic and locus products influence the outcome of an immune response in terms of generating protective immunity in outbred animals. A peptide derived from foot-and-mouth disease virus (FMDV) was used as a probe for BoLA class II function. Both DR and DQ are involved in antigen presentation. In an analysis of T-cell clones specific for the peptide, distinct biases to particular restriction elements were observed. In addition inter-haplotype pairings of DQA and DQB molecules produced functional molecules, which greatly increases the numbers of possible restriction elements, compared with the number of genes, particularly in cattle with duplicatedDQgenes. In a vaccine trial with several peptides derived from FMDV,BoLAclass IIDRB3polymorphisms were correlated with both protection and non-protection. Although variation in immune responsiveness to the FMDV peptide between different individuals is partly explainable byBoLAclass II alleles, other genetic factors play an important role. In a quantitative trait locus project, employing a second-generation cross between Charolais and Holstein cattle, significant sire and breed effects were also observed in T-cell, cytokine and antibody responses to the FMDV peptide. These results suggest that both MHC and non-MHC genes play a role in regulating bovine immune traits of relevance to vaccine design. Identifying these genes and quantifying their relative contributions is the subject of further studies.

An investigation into the genetic background of coat colour dilution in a Charolais x German Holstein F2 resource population

The molecular background of many loci affecting coat colour inheritance in cattle is still incompletely characterized, although it is known that coat colour results from the joint effects of several loci, e.g. agouti, extension and dilution. Dilution alleles are responsible for a dilution effect on the original coat colour of an individual, which is determined by the agouti and extension loci. Different loci affecting dilution of pigment are suggested in Charolais (Dc) and Simmental (Ds). To enable chromosomal mapping of the Dc mutation, 133 animals from an F2 full-sib resource population generated from a cross of Charolais and German Holstein were scored for the coat colour dilution phenotype. Linkage analysis covering all autosomes revealed a significant linkage of the dilution phenotype with microsatellite markers on bovine chromosome 5. No recombination was observed between marker ETH10 and the Dc locus. Positional and functional information identified the bovine silver homolog (SILV) gene as a candidate for the Dc mutation. Results from comparative sequencing of the SILV gene in individuals with different dilution coat colour phenotypes confirmed the presence of a c.64G>A non-synonymous mutation, which had previously been identified in the Charolais breed. The alleles at this locus were associated with coat colour dilution in this study. However, further investigation of colour inheritance within the F2 resource population indicated that a single diallelic mutation in the SILV gene cannot explain the total observed variation of coat colour dilution.

Joint analysis of the influence of CYP11B1 and DGAT1 genetic variation on milk production, somatic cell score, conformation, reproduction, and productive lifespan in German Holstein cattle1

Recent publications indicate genetic variation in milk production traits on proximal BTA14, which cannot be explained solely with genetic variation in the DGAT1 gene. To elucidate these QTL effects, animals from a German Holstein granddaughter design (18 families, 1,291 sons) were genotyped for CYP11B1 (V30A) and DGAT1 (K232A) polymorphisms. Frequencies of alleles of maternal descent were estimated for CYP11B1(V) (0.776) and DGAT1(K) (0.549). Allele substitution effects (alpha/2) were first calculated for both alleles in separate models and then in a joint model. From the joint analysis, CYP11B1(V) effects on fat content (+0.04%) and protein content (+0.01%) were positive. Effects on milk yield (-82 kg), fat yield (-0.5 kg), and protein yield (-1.9 kg) were negative. Compared with the individual analysis, DGAT1(K) effects on fat content (+0.28%), protein content (+0.06%), and milk yield (-258 kg) were reduced; fat yield (+10.8 kg) was enhanced; and protein yield (-3.8 kg) was reduced. In the joint analysis, allele substitution effects of CYP11B1(V) and DGAT1(K) together explained more of the variation in milk production traits than DGAT1(K) alone. Further significant effects were found for CYP11B1(V) and DGAT1(K) among 6 reproduction traits and 14 conformational traits. These observations indicate a possible negative influence of DGAT1(K) on maternal nonreturn rate, and thus, on length of productive life.

Detection of Quantitative Trait Loci Affecting Lameness and Leg Conformation Traits in Danish Holstein Cattle

Lameness is an important factor for culling animals. Strong legs and feet improve herd life of dairy cows. Therefore, many countries include leg and feet conformation traits in their breeding programs, often as early predictors of longevity. However, few countries directly measure lameness related traits to include these in a breeding program. Lameness indices in 3 different lactations and 5 leg conformation traits (rear legs side view, rear legs rear view, hock quality, bone quality, and foot angle) were measured on granddaughters of 19 Danish Holstein grandsires with 33 to 105 sons. A genome scan was performed to detect quantitative trait loci (QTL) based on the 29 autosomes using microsatellite markers. Data were analyzed across and within families for QTL affecting lameness and leg conformation traits. A regression method and a variance component method were used for QTL detection. Two QTL each for lameness in the first [Bos taurus autosome (BTA); BTA5, BTA26] and second (BTA19, BTA22) lactations were detected. For the 5 different leg conformation traits, 7 chromosome-wise significant QTL were detected across families for rear legs side view, 5 for rear legs rear view, 4 for hock quality, 4 for bone quality, and 1 for foot angle. For those chromosomes where a QTL associated with 2 different traits was detected (BTA1, BTA11, BTA15, BTA26, and BTA27), a multitrait-1-QTL model and a multitrait-2-QTL model were performed to characterize these QTL as single QTL with pleiotropic effects or distinct QTL.

Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate

Continued validation of genetic markers for economically important traits is crucial to establishing marker-assisted selection as a tool in the cattle industry. The objective of the current study was to evaluate the association of a SNP (T(9)/T(10)) in the osteopontin gene (SPP1) with growth rate in a large cattle population spanning multiple generations and representing alleles from 12 founding breeds. This population has been maintained at the US Meat Animal Research Center since 1981 and subjected to selection for twinning rate. Phenotypic records for this population included twinning rate and ovulation rate, providing an opportunity to examine the potential effects of SPP1 genotype on reproductive traits. A set of 2,701 animals was geno-typed for the T(9)/T(10) polymorphism at SPP1. The geno-typic data, including previously genotyped markers on chromosome 6 (BTA6), were used in conjunction with pedigree information to estimate genotypic probabilities for all 14,714 animals with phenotypic records. The genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a mixed model analysis, in which each trait was analyzed in a 2-trait model where single births were treated as a separate trait from twin births. The association of the SPP1 marker with birth weight (P < 0.006), weaning weight (P < 0.007), and yearling weight (P < 0.003) was consistent with the previously reported effects of SPP1 genotype on yearling weight. Our data supports the conclusion that the SNP successfully tracks functional alleles affecting growth in cattle. The previously undetected effect of the SNP on birth and weaning weight suggests this particular SPP1 marker may explain a portion of the phenotypic variance explained by QTL for birth and HCW on BTA6.

Quantitative Trait Loci Affecting Fertility and Calving Traits in Swedish Dairy Cattle

Impaired fertility is the main reason for involuntary culling of dairy cows in Sweden. The objective of this study was to map quantitative trait loci (QTL) influencing fertility and calving traits in the Swedish dairy cattle population. The traits analyzed were number of inseminations, 56-d nonreturn rate, interval from calving to first insemination, fertility treatments, heat intensity score, stillbirth, and calving performance. A genome scan covering 20 bovine chromosomes was performed using 145 microsatellite markers. The mapping population consisted of 10 sires and their 417 sons in a granddaughter design. Nine of the sires were of the Swedish Red Breed, and one was a Swedish Holstein. Least squares regression was used to map loci affecting the analyzed traits, and permutation tests were used to set significance thresholds. Cofactors were used in the analyses of individual chromosomes to adjust for QTL found on other chromosomes. The use of cofactors increased both the number of QTL found and the significance level. In the initial analysis, we found 13 suggestive QTL that were mapped to chromosomes 6, 7, 9, 11, 13, 15, 20, and 29. When cofactors were included, 30 QTL were detected on chromosomes 1, 3, 4, 18, 19, 22, and 25, in addition to the 8 previously mentioned chromosomes. Some of the results from the cofactor analysis may be false positives and require further validation. In conclusion, we were able to map several QTL affecting fertility and calving traits in Swedish dairy cattle.

Refinement of quantitative trait loci on bovine chromosome 18 affecting health and reproduction in US Holsteins

Selection for increased milk yield is associated with decreased fertility in US Holsteins. Previously, a putative quantitative trait locus (QTL) on chromosome 18 affecting daughter pregnancy rate (DPR) was identified in one family. Our aim was to determine the validity of the QTL using additional markers and an extended pedigree. Twelve markers were genotyped in 940 descendants of the original sire in which the QTL was identified. Analysis of the extended pedigree detected significant and suggestive QTL for DPR, productive life and somatic cell score. Further analysis is underway to refine the QTL region so that positional candidate genes can be identified.

Linkage disequilibrium on the bovine X chromosome: characterization and use in quantitative trait locus mapping

We herein demonstrate that in the Holstein-Friesian dairy cattle population, microsatellites are as polymorphic on the X chromosome as on the autosomes but that the level of linkage disequilibrium between these markers is higher on the X chromosome than on the autosomes. The latter observation is not compatible with the small male-to-female ratio that prevails in this population and results in a higher gonosomal than autosomal effective population size. It suggests that the X chromosome undergoes distinct selective or mutational forces. We describe and characterize a novel Markovian approach to exploit this linkage disequilibrium to compute the probability that two chromosomes are identical-by-descent conditional on flanking marker data. We use the ensuing probabilities in a restricted maximum-likelihood approach to search for quantitative trait loci (QTL) affecting 48 traits of importance to the dairy industry and provide evidence for the presence of QTL affecting 5 of these traits on the bovine X chromosome.

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

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

Bovine NALP5, NALP8, and NALP9 Genes: Assignment to a QTL Region and the Expression in Adult Tissues, Oocytes, and Preimplantation Embryos

A 3204-bp full-length cDNA of bovine NALP9 was cloned and its genomic organization was analyzed. The 2988-bp open reading frame covers 9 exons and encodes a deduced protein of 996 amino acids containing Pyrin, Nacht and leucine-rich repeat domains like the human NALP gene family members. Mapping with the WGRH5000 panel and fluorescence in situ hybridization assigned NALP9 in close vicinity to BM2078 (LOD score 25.71; distance 0.0 cR5000) on bovine chromosome 18, BTA18q25-q26, within a previously identified QTL region for reproductive traits flanked by the bovine marker BM2078 and TGLA227. BAC contig analysis revealed that NALP9, NALP8, and NALP5 map in this QTL region. Temporospatial expression of these members of the NALP gene family was monitored. Among the adult tissues examined, transcripts of NALP8 and NALP9 were detected exclusively in testis and ovary, whereas transcripts of the NALP5 gene are limited to the ovary. The transcripts of NALP9, NALP8, and NALP5 were detected in oocytes before and after in vitro maturation and with a gradual decline from 2-cell to 8-cell stage, suggesting no reactivation at the time of bovine maternal to embryonic transition. Assignment to a QTL region for reproductive traits and preferential expression of NALP9, NALP8, and NALP5 in oocyte, germinal lineage, and gonad cells may suggest their functional relevance to reproduction and possible contribution to phenotypic variation.

Sequencing, chromosomal mapping, and functional characterization of bovine FLICE-like inhibitory protein (FLIP)

FLICE-like inhibitory protein (FLIP) has been shown in both humans and mice to inhibit apoptosis and NF-kappaB activation induced by pro-inflammatory mediators. The activation of NF-kappaB and the induction of apoptosis are critical events in the pathogenesis of a variety of disease states in cattle, including mastitis. Since FLIP is known to moderate these events in other species, we mapped the bovine FLIP gene, sequenced bovine FLIP cDNA, and characterized its expression in cultured primary bovine endothelial cells. Sequencing of bovine FLIP revealed approximately 83, 74, and 68% amino acid sequence identity to its porcine, human, and murine orthologs, respectively. Bovine FLIP was mapped to chromosome 2 by radiation hybrid mapping. Interestingly the region to which bovine FLIP maps contains a putative quantitative trait locus for functional herd life which is an indicator of a cow's ability to survive involuntary culling due primarily to mastitis and infertility. In addition to sequencing and mapping, the function of bovine FLIP was studied. Over-expression of bovine FLIP protected against bacterial lipopolysaccharide (LPS)- and TNF-alpha-induced apoptosis in bovine endothelial cells consistent with previous studies of human FLIP. In addition, elevated expression of bovine FLIP blocked LPS- and TNF-alpha-induced upregulation of NF-kappaB-dependent gene products as assayed by E-selectin expression. Only the full-length bovine FLIP protein could inhibit NF-kappaB activation induced by LPS, whereas the death effector domain region alone was able to inhibit TNF-alpha-induced NF-kappaB activation. Together, these data demonstrate the conservation of FLIP's ability to inhibit apoptosis and to downregulate NF-kappaB activation across species.

Whole-genome scan to detect QTL for milk production, conformation, fertility and functional traits in two US Holstein families

A genome scan was conducted in two US Holstein half-sib families to identify quantitative trait loci (QTL) affecting milk production and conformation traits using the granddaughter design. The sires of the two studied families were related as sire and son and had 96 and 212 sons respectively. A total of 221 microsatellite loci were scored in both families. Statistical analysis was performed using two different analytical methods; half-sib least squares regression and Bayesian Monte Carlo Markov Chain. Traits analysed included five traditional milk production traits, somatic cell count, daughter pregnancy rate, male fertility and 20 conformation traits. A total of 47 tests achieved at least genome-wise significance. However, results from the two methods of analysis were only concordant for QTL location and level of significance in eight instances.

A refined radiation hybrid map of the telomeric region of bovine chromosome 18q25-q26 compared with human chromosome 19q13

Genome-wide scans have mapped economically important quantitative trait loci (QTL) for mastitis susceptibility in dairy cattle at the telomeric end of bovine chromosome 18 (BTA18). In order to increase the density of markers in this chromosomal region and to improve breakpoint resolution in the human-bovine comparative map, this study describes the chromosomal assignment of seven newly developed gene-associated markers and five microsatellites and eight previously mapped sequence tagged site markers near these QTL. The orientation of KCNJ14, BAX, CD37, NKG7, LIM2, PRKCG, TNNT1, MGC2705, RPL28, EPN1, ZNF582, ZIM2, STK13, ZNF132 and SLC27A5 on the 3000-rad radiation hybrid (RH) map of BTA18 is homologous to the organization found on the corresponding 10 Mbp of human chromosome 19q (HSA19q). The resulting bovine RH map with a length of 20.9 cR spans over about 11 cM on the bovine linkage map. The location of KCNJ14 and SLC27A5 flanking the RH map on BTA18q25-26 has been confirmed by fluorescence in situ hybridization. The data of this refined human-bovine comparative map should improve selection of candidate genes for mastitis susceptibility in dairy cattle.

Evidence for multiple alleles at the DGAT1 locus better explains a quantitative trait locus with major effect on milk fat content in cattle

A quantitative trait locus (QTL) for milk fat percentage has been mapped consistently to the centromeric region of bovine chromosome 14 (BTA14). Two independent studies have identified the nonconservative mutation K232A in the acylCoA-diacylglycerol-acyltransferase 1 (DGAT1) gene as likely to be causal for the observed variation. Here we provide evidence for additional genetic variability at the same QTL that is associated with milk fat percentage variation within the German Holstein population. Namely, we show that alleles of the DGAT1 promoter derived from the variable number of tandem repeat (VNTR) polymorphism are associated with milk fat content in animals homozygous for the allele 232A at DGAT1. Our results present another example for more than two trait-associated alleles being involved in a major gene effect on a quantitative trait. The segregation of multiple alleles affecting milk production traits at the QTL on BTA14 has to be considered whenever marker-assisted selection programs are implemented in dairy cattle. Due to the presence of a potential transcription factor binding site in the 18mer element of the VNTR, the variation in the number of tandem repeats of the 18mer element might be causal for the variability in the transcription level of the DGAT1 gene.

High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle

To get more information about the order of genes located in Bos taurus (BTA) chromosome 27 segments, supposed to harbor loci influencing clinical mastitis and somatic cell count, and to identify genes that serve as positional candidates for the mentioned traits, we constructed a high-resolution, comparative, and comprehensive gene map for BTA27. The map includes 57 loci in a 5000-rad cattle-hamster whole genome radiation hybrid panel supported by 50 syntenic assignments in a cattle-murine somatic hybrid cell panel. Thirty-eight new loci (36 genes, 2 microsatellites) together with repeated mappings of 5 genes and 7 microsatellites and integration of existing data from 7 microsatellites were used to generate a comprehensive RH5000 map. The RH map, constructed at lod score criterion 8 using the software RHMAP v.3.0, consisted of three linkage groups 23, 22, and 590 cR5000 in length. Gene assignments on BTA27 and the localization of 8 more genes on BTA8 and BTA14 previously predicted on BTA8/BTA27 and BTA14/BTA27 narrowed down significantly the chromosome break points between the three cattle chromosomes and segments on Homo sapiens chromosomes HSA4 and HSA8. Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27.