Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle

Background

We have used a linear mixed model (LMM) approach to examine the joint contribution of genetic markers associated with a biological pathway. However, with these markers being scattered throughout the genome, we are faced with the challenge of modelling the contribution from several, sometimes even all, chromosomes at once. Due to linkage disequilibrium (LD), all markers may be assumed to account for some genomic variance; but the question is whether random sets of markers account for the same genomic variance as markers associated with a biological pathway?

Results

We applied the LMM approach to identify biological pathways associated with udder health and milk production traits in dairy cattle. A random gene sampling procedure was applied to assess the biological pathways in a dataset that has an inherently complex genetic correlation pattern due to the population structure of dairy cattle, and to linkage disequilibrium within the bovine genome and within the genes associated to the biological pathway.

Conclusions

Several biological pathways that were significantly associated with health and production traits were identified in dairy cattle; i.e. the markers linked to these pathways explained more of the genomic variance and provided a better model fit than 95 % of the randomly sampled gene groups. Our results show that immune related pathways are associated with production traits, and that pathways that include a causal marker for production traits are identified with our procedure.We are confident that the LMM approach provides a general framework to exploit and integrate prior biological information and could potentially lead to improved understanding of the genetic architecture of complex traits and diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0132-6) contains supplementary material, which is available to authorized users.     

Identification of genomic regions associated with inbreeding depression in Holstein and Jersey dairy cattle

Background

Inbreeding reduces the fitness of individuals by increasing the frequency of homozygous deleterious recessive alleles. Some insight into the genetic architecture of fitness, and other complex traits, can be gained by using single nucleotide polymorphism (SNP) data to identify regions of the genome which lead to reduction in performance when identical by descent (IBD). Here, we compared the effect of genome-wide and location-specific homozygosity on fertility and milk production traits in dairy cattle.

Methods

Genotype data from more than 43 000 SNPs were available for 8853 Holstein and 4138 Jersey dairy cows that were part of a much larger dataset that had pedigree records (338 696 Holstein and 64 049 Jersey animals). Measures of inbreeding were based on: (1) pedigree data; (2) genotypes to determine the realised proportion of the genome that is IBD; (3) the proportion of the total genome that is homozygous and (4) runs of homozygosity (ROH) which are stretches of the genome that are homozygous.

Results

A 1% increase in inbreeding based either on pedigree or genomic data was associated with a decrease in milk, fat and protein yields of around 0.4 to 0.6% of the phenotypic mean, and an increase in calving interval (i.e. a deterioration in fertility) of 0.02 to 0.05% of the phenotypic mean. A genome-wide association study using ROH of more than 50 SNPs revealed genomic regions that resulted in depression of up to 12.5 d and 260 L for calving interval and milk yield, respectively, when completely homozygous.

Conclusions

Genomic measures can be used instead of pedigree-based inbreeding to estimate inbreeding depression. Both the diagonal elements of the genomic relationship matrix and the proportion of homozygous SNPs can be used to measure inbreeding. Longer ROH (>3 Mb) were found to be associated with a reduction in milk yield and captured recent inbreeding independently and in addition to overall homozygosity. Inbreeding depression can be reduced by minimizing overall inbreeding but maybe also by avoiding the production of offspring that are homozygous for deleterious alleles at specific genomic regions that are associated with inbreeding depression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0071-7) contains supplementary material, which is available to authorized users.     

Partitioning additive genetic variance into genomic and remaining polygenic components for complex traits in dairy cattle

ABSTRACT: BACKGROUND: Low cost genotyping of individuals using high density genomic markers were recently introduced as genomic selection in genetic improvement programs in dairy cattle. Most implementations of genomic selection only use marker information, in the models used for prediction of genetic merit. However, in other species it has been shown that only a fraction of the total genetic variance can be explained by markers. Using 5217 bulls in the Nordic Holstein population that were genotyped and had genetic evaluations based on progeny, we partitioned the total additive genetic variance into a genomic component explained by markers and a remaining component explained by familial relationships. The traits analyzed were production and fitness related traits in dairy cattle. Furthermore, we estimated the genomic variance that can be attributed to individual chromosomes and we illustrate methods that can predict the amount of additive genetic variance that can be explained by sets of markers with different density. RESULTS: The amount of additive genetic variance that can be explained by markers was estimated by an analysis of the matrix of genomic relationships. For the traits in the analysis, most of the additive genetic variance can be explained by 44 K informative SNP markers. The same amount of variance can be attributed to individual chromosomes but surprisingly the relation between chromosomal variance and chromosome length was weak. In models including both genomic (marker) and familial (pedigree) effects most (on average 77.2%) of total additive genetic variance was explained by genomic effects while the remaining was explained by familial relationships. CONCLUSIONS: Most of the additive genetic variance for the traits in the Nordic Holstein population can be explained using 44 K informative SNP markers. By analyzing the genomic relationship matrix it is possible to predict the amount of additive genetic variance that can be explained by a reduced (or increased) set of markers. For the population analyzed the improvement of genomic prediction by increasing marker density beyond 44 K is limited.     

ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies

ChromoScan is an implementation of a genome-based scan statistic that detects genomic regions, which are statistically significant for targeted measurements, such as genetic associations with disease, gene expression profiles, DNA copy number variations, as well as other genome-based measurements. A Java graphic user interface (GUI) is provided to allow users to select appropriate data transformations and thresholds for defining the significant events. AVAILABILITY: ChromoScan is freely available from http://www.epidkardia.sph.umich.edu/software/chromoscan/     

Accuracy of genomic predictions in Bos indicus (Nellore) cattle

Background

Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and fertility in this breed. We present the first results of the implementation of genomic prediction in a Bos indicus (Nellore) population.

Methods

Influential bulls were genotyped with the Illumina Bovine HD chip in order to assess genomic predictive ability for weight and carcass traits, gestation length, scrotal circumference and two selection indices. 685 samples and 320 238 single nucleotide polymorphisms (SNPs) were used in the analyses. A forward-prediction scheme was adopted to predict the genomic breeding values (DGV). In the training step, the estimated breeding values (EBV) of bulls were deregressed (dEBV) and used as pseudo-phenotypes to estimate marker effects using four methods: genomic BLUP with or without a residual polygenic effect (GBLUP20 and GBLUP0, respectively), a mixture model (Bayes C) and Bayesian LASSO (BLASSO). Empirical accuracies of the resulting genomic predictions were assessed based on the correlation between DGV and dEBV for the testing group.

Results

Accuracies of genomic predictions ranged from 0.17 (navel at weaning) to 0.74 (finishing precocity). Across traits, Bayesian regression models (Bayes C and BLASSO) were more accurate than GBLUP. The average empirical accuracies were 0.39 (GBLUP0), 0.40 (GBLUP20) and 0.44 (Bayes C and BLASSO). Bayes C and BLASSO tended to produce deflated predictions (i.e. slope of the regression of dEBV on DGV greater than 1). Further analyses suggested that higher-than-expected accuracies were observed for traits for which EBV means differed significantly between two breeding subgroups that were identified in a principal component analysis based on genomic relationships.

Conclusions

Bayesian regression models are of interest for future applications of genomic selection in this population, but further improvements are needed to reduce deflation of their predictions. Recurrent updates of the training population would be required to enable accurate prediction of the genetic merit of young animals. The technical feasibility of applying genomic prediction in a Bos indicus (Nellore) population was demonstrated. Further research is needed to permit cost-effective selection decisions using genomic information.     

Identifying genomic regions for fine-mapping using genome scan meta-analysis (GSMA) to identify the minimum regions of maximum significance (MRMS) across populations

In order to detect linkage of the simulated complex disease Kofendrerd Personality Disorder across studies from multiple populations, we performed a genome scan meta-analysis (GSMA). Using the 7-cM microsatellite map, nonparametric multipoint linkage analyses were performed separately on each of the four simulated populations independently to determine p-values. The genome of each population was divided into 20-cM bin regions, and each bin was rank-ordered based on the most significant linkage p-value for that population in that region. The bin ranks were then averaged across all four studies to determine the most significant 20-cM regions over all studies. Statistical significance of the averaged bin ranks was determined from a normal distribution of randomly assigned rank averages. To narrow the region of interest for fine-mapping, the meta-analysis was repeated two additional times, with each of the 20-cM bins offset by 7 cM and 13 cM, respectively, creating regions of overlap with the original method. The 6-7 cM shared regions, where the highest averaged 20-cM bins from each of the three offsets overlap, designated the minimum region of maximum significance (MRMS). Application of the GSMA-MRMS method revealed genome wide significance (p-values refer to the average rank assigned to the bin) at regions including or adjacent to all of the simulated disease loci: chromosome 1 (p < 0.0001 for 160-167 cM, including D1), chromosome 3 (p-value < 0.0000001 for 287-294 cM, including D2), chromosome 5 (p-value < 0.001 for 0-7 cM, including D3), and chromosome 9 (p-value < 0.05 for 7-14 cM, the region adjacent to D4). This GSMA analysis approach demonstrates the power of linkage meta-analysis to detect multiple genes simultaneously for a complex disorder. The MRMS method enhances this powerful tool to focus on more localized regions of linkage.     

Associations of the bovine major histocompatibility complex DRB3 (BoLA-DRB3) with production traits in Canadian dairy cattle

Associations of two alleles of the bovine major histocompatibility complex DRB3 gene (BoLA-DRB3) with lowered somatic cell score (SCS) and occurrence of disease (BoLA-DRB3.2* 16 and *23, respectively) have previously been documented. The objective of this study was to evaluate potential relationships between BoLA-DRB3 alleles with production traits, namely 305-day milk, milk fat and milk protein yield, in a population of Canadian dairy cattle (Holstein, n = 835 and Jersey, n = 66) over the course of two lactations. No significant associations were detected between BoLA alleles and production traits in Jerseys. In Holsteins, alleles *16 and *23 also did not show associations with production traits but allele *8 was significantly associated with increased 305-day milk, fat and protein yields in the previous lactation (the lactation prior to immunization with a gram negative core antigen vaccine), and with increased protein production in the subsequent (with reference to the time of immunization) lactation. Allele *22 was associated with decreased milk and protein yield in both previous and subsequent lactations. Therefore, it can be concluded that increasing or decreasing the frequency of BoLA alleles *16 and *23 to reduce SCS or increase resistance to mastitis in this population would not have adverse effects on production in this population, and that certain BoLA alleles (*8 and *22) are associated with altered production traits in Canadian Holsteins.     

Indirect effects of FRIGIDA: floral trait (co)variances are altered by seasonally variable abiotic factors associated with flowering time

Reproductive timing is a critical life‐history event that could influence the (co)variation of traits developing later in ontogeny by regulating exposure to seasonally variable factors. In a field experiment with Arabidopsis thaliana, we explore whether allelic variation at a flowering‐time gene of major effect (FRIGIDA) affects (co)variation of floral traits by regulating exposure to photoperiod, temperature, and moisture levels. We detect a positive latitudinal cline in floral organ size among plants with putatively functional FRI alleles. Statistically controlling for bolting day removes the cline, suggesting that seasonal abiotic variation affects floral morphology. Both photoperiod and precipitation at bolting correlate positively with the length of petals, stamens, and pistils. Additionally, floral (co)variances differ significantly across FRI backgrounds, such that the sign of some floral‐trait correlations reverses. Subsequent experimental manipulations of photoperiod and water availability demonstrate direct effects of these abiotic factors on floral traits. In sum, these results highlight how the timing of life‐history events can affect the expression of traits developing later in ontogeny, and provide some of the first empirical evidence for the effects of major genes on evolutionary potential.     

Advances in the design of probiotic products for the prevention of major diseases in dairy cattle

Probiotics are frequently used for multiple objectives and the majority of applications are performed both in human beings and in different animals. The specificity of species showed by the members of the indigenous microbiotia led us to isolate lactic acid bacteria (LAB) from their natural bovine ecosystems and to select those with probiotic potentiality. The beneficial probiotic LAB were isolated from the vaginal tract and mammary gland of adult heifers, faeces and oral cavity of newborn calves. Bacterial strains and their numbers varied in each tract under study. Their surface properties, evaluated using the MATH test, revealed that the higher number of low hydrophobic strains were isolated from vaginal tract, mammary gland or faeces. The capability of autoaggregation also differed with higher degree in those isolated from vagina, whereas those that originated in the mammary gland or faeces showed low autoaggregation characteristics. The production of antagonistic substances showed that the production of hydrogen peroxide was higher in the strains isolated from the vaginal tract, while those able to produce organic acid were isolated from all the environments. A few strains were able to produce bacteriocins and were isolated only from the mammary gland and faeces, but not from the vaginal tract. Further studies are being performed to complete the functional characterization of the strains in order to evaluate their survival in the environmental conditions of each tract. Finally, the selected strains could be combined for the design of probiotic products to be used both in adult cows and in neonates, based on the host-specificity, due to their autochthonous origin and their potential use in the tract where they were isolated.     

Population genomics in Sardinia: a novel approach to hunt for genomic combinations underlying complex traits and diseases.

The availability of highly polymorphic markers permits testing whether complex traits and diseases result from genomic interactions between nonallelic normal variants at separate loci. Such variants may be identified by deviations from the expected distributions of alleles at a high number of polymorphic loci, when individuals with the phenotype of interest are compared to normal controls of the same breeding unit, provided that both groups share the same remote ancestry and had no ancestors in common for the last three to four generations. The circumstances needed for such studies are ideally met on the island of Sardinia. The recurrent finding of the same type of association in separate breeding units between the phenotype of interest and a given genotype should allow a distinction between true genetic identity by descent and randomly occurring identities, as these will be obviously different in separate breeding units. The availability of several breeding units located in sharply different ecological environments will permit assessment of the role of nature/nurture factors in the degree of manifestation of each newly discovered genotype/phenotype association. A pilot study to evaluate the proposed strategy has been carried out in the Sardinian village of Carloforte, a community of about 8,000 individuals who have remained genetically homogeneous. Fifty-five control samples have been genotyped with six tetranucleotide microsatellites and with a subset of the 400 markers contained in the ABI PRISM linkage mapping panel, version 2. The allele frequencies for these microsatellite markers have been determined for these 55 individuals and compared to those from a random sampling of subsets of these 55 persons. For the six tetranucleotide microsatellites, a subset of as few as 20 people displayed the same allele frequency distributions as observed with the original 55 unrelated individuals. In conclusion, when samples are chosen from the same breeding unit, the number of individuals sufficient to draw the genomic profile of an isolated population can be relatively small. Likewise, the number of probands with the phenotype of interest can be even smaller when they are ascertained with the same genealogical criteria as the normal controls. By comparing the genomic profile of the probands to a fraction of the control samples within each of several separate breeding units of common remote ancestry, the search for genotype/phenotype association for mono- and multifactorial traits and diseases should be simplified and yield unequivocal results.     

Superovulatory response of dairy cattle (Bos taurus ) in a tropical environment

Dairy (Bos taurus) heifers and cows (n = 40) in a tropical environment were treated during mid-luteal phase using either SUPER-OV(R) or OVAGEN to induce superovulatory response after synchronization of the superovulatory estrus with a synthetic progestagen and cloprostenol (PG). Estrous cattle were inseminated twice using frozen-thawed semen, and embryos were recovered nonsurgically, on-farm, 7 d later. Between initiation of gonadotrophin treatment and recovery of embryos, 4 blood samples per animal were collected from 26 animals for determination of plasma progesterone (P4) concentration. Two (5%), 28 (70%) and 10 (22%) of the animals were observed in estrus 1.5, 2 and 2.5 to 3 d after PG, respectively. There was no difference (P = 0.7) in the number of palpable CL between animals treated with SUPER-OV (7.6 +/- 1.0; n = 18) and those treated with OVAGEN (7.9 +/- 1.1; n = 22). There was also no significant difference (P > 0.05) between Jersey vs Ayrshire breeds or heifers vs cows in the ovarian response as estimated by the number of palpable CL. However, a higher proportion of Ayrshire cattle and donors treated with OVAGEN yielded a higher total number and viable/transferable embryos than Jersey and SUPER-OV-treated cattle. There was a significant (P < 0.05) correlation between the number of CL and total number of embryos (r = 0.65); the number of transferable embryos was also significantly related to the total number of embryos per recovery (r = 0.85; P < 0.05). For 15 animals with normal P4 profiles, the mean (+/-SEM) plasma P4 concentration was 14.4 +/- 0.8, 0.5 +/- 0.2, 5.4 +/- 1.1 and 39.4 +/- 3.0 nmol L at initiation of gonadotrophin treatment, superovulatory estrus and Days 3 and 7, respectively. The mean (+/-SEM) interval between a PG injection given after embryo recovery and the induced estrus was 7.1 +/- 0.7 d (range 3 to 14 d) and the length of the superovulatory cycle was 24.1 +/- 3.2 d (range 12 to 35 d).     

Binomial sampling for pest management of stable flies (Diptera: Muscidae) that attack dairy cattle.

A binomial sampling plan for pest management of the stable fly, Stomoxys calcitrans (L.), was developed. Counts of stable flies on front legs of the same animal were independent and each leg from the same animal was considered a sample unit. The relationship between the mean number of flies per leg and the variance was determined and did not vary among farms. The relationship between the mean number of flies per leg and the proportion of legs with zero, one or less, and two or less flies (P0, P1, and P2) was determined and used as the basis of the binomial sampling plan. Predicted values of the mean number of flies per leg from P0, P1, and P2 were close to observed values of the mean number of flies per leg. Equations are presented for calculating the variance of a predicted value of the mean number of flies per leg using values of P0, P1 and P2 determined by sampling. Operating characteristic (OC) curves are also presented for determining the probability of making a treatment decision error at an economic threshold of one fly per leg (P0 = 0.47) using binomial sampling or direct counting. OC curves for binomial sampling with n = 50 legs were close to those for direct counting with n = 10 legs. Recommendations concerning the use of binomial sampling for stable flies are presented.     

JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation

SUMMARY: The characterization of deleterious genomic mutation (DGM) is of central significance for evolutionary biology and genetic studies. Fitness moment method has been developed to efficiently characterize DGM from natural population directly. In order to enable researchers to employ this method for theoretical and empirical research on characterizing DGM, we here present a distributed Java Application for DGM Estimation (JADE). AVAILABILITY: http://orclinux.creighton.edu/DGM/index.htm.     

Long-size isoelectricfocusing (IEF) in flexible silicone tubes: an application to semi-preparative fractionation of proteins

Soluble proteins extracted from porcine brains were subjected to a series of optional fractionation steps on various chromatographic media including a novel device for semi-preparative isoelectrofocusing (IEF) carried in a flexible silicone tube. The dimensions of the IEF granulated gel beds can be varied from 40 to 75 cm (length) and 0.4-1.6 cm (diameter) which are dependent on the protein's concentration. An average optimal focalisation time of proteins is dependent of the tube length, its diameter and complexity of proteins' mixtures but it is usually reached during 15,000-30,000 Vh. A series of sequential protein's fractionation techniques including semi-preparative IEF carried in the flexible silicone tube with the following dimensions: 75 cm in length and 1.6 cm in diameter permitted for observation and partial characterisation of several proteins whose expression levels are specifically high in the brain.     

Citicoline (CDP-choline): What role in the treatment of complications of infectious diseases

A dysregulated host immune response, as opposed to the intrinsic virulence of a microbial pathogen induces a large part of the pathology seen in infectious diseases. However, current therapies are designed to target the pathogen rather than the underlying pathogenic mechanisms responsible for the manifestation of the pathology. Recent studies have highlighted the role of endothelial cell alteration in the pathology induced in sepsis and cerebral malaria. The endothelial onslaught described, is similar to that seen during ischemia reperfusion in stroke. Protecting endothelial cell membranes during sepsis and cerebral malaria, using citicoline in the same way as in stroke, has thus emerged as a new strategy that needs to be evaluated urgently. Citicoline is a natural compound that is registered for use in ischemic stroke, head trauma and neurological disorders. It enters the phosphatidylcholine synthesis pathway as a rate-limiting step and is involved in the modulation of a large number of metabolic pathways and neurotransmitter levels, and also in the biosynthesis of phospholipids in neuronal membranes. This short review highlights the potential role of citicoline as part of adjunct therapy in the treatment of infectious diseases.     

Mixture model for inferring susceptibility to mastitis in dairy cattle: a procedure for likelihood-based inference

A Gaussian mixture model with a finite number of components and correlated random effects is described. The ultimate objective is to model somatic cell count information in dairy cattle and to develop criteria for genetic selection against mastitis, an important udder disease. Parameter estimation is by maximum likelihood or by an extension of restricted maximum likelihood. A Monte Carlo expectation-maximization algorithm is used for this purpose. The expectation step is carried out using Gibbs sampling, whereas the maximization step is deterministic. Ranking rules based on the conditional probability of membership in a putative group of uninfected animals, given the somatic cell information, are discussed. Several extensions of the model are suggested.     

Adsorption of molecular oxygen by polymer covalently bonded co(II) porhyrin complex in toluene

Reaction betwenn molecular oxygen and polystyrene covalently bonded Co(II) protoporphyrin IX complex, which was prepaired by the incorporation of a cobaltous ion into the metal-free porphyrin polymer, was studied in the presence of N-ethylimidazole by measuring visible absorption and electron spin resonance spectra. It was found that the complex forms a monomeric oxygen adduct reversibly at low temperature dependent on oxygen pressure. In the presence of molecular oxygen, a new electron spin resonance signal due to the oxygen complex at g_iso=2.02 shows no superhyperfine splitting structure in fluid toluene solution even at ?80 °C, but it was observed in frozen toulene glass solution at ?120°C, The oxygen adducts of the complexes between C0(II) protoporphyrin IX dimethyl ester and N-ethylimidazole and copoly(styrene-N-vinylimidazole) showed eight resolved superhyperfine splitting at ?40 and ?60°C, respectively. The polymer covalently bonded Co(II) complex with N-ethylimidazole was oxidized at room temperature under oxygen atmosphere. It was suggested that a Co(II) porphyrin–oxygen adduct with an axial ligand may be oxidised monomolecularly at high temperature.