Identification of a doublet missense substitution in the bovine LRP4 gene as a candidate causal mutation for syndactyly in Holstein cattle

Frequency of genotypic markers for genetic disorders, colour, polledness, and major genes in Blanco Orejinegro cattle

The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.

Genotypes and allele frequencies of buried SNPs in a bovine single-nucleotide polymorphism array in Japanese Black cattle

Single nucleotide polymorphism (SNP) arrays are widely used for genetic and genomic analyses in cattle breeding; thus, data derived from SNP arrays have accumulated on a large scale nationwide. Commercial SNP arrays contain a considerable number of unassigned SNPs on the chromosome/position on the genome; these SNPs are excluded in subsequent analyses. Notably, the position-unassigned SNPs, or "buried SNPs" include some of the markers associated with genetic disease. In this study, we identified the position of buried SNPs using the Basic Local Alignment Search Tool against the surrounding sequences and characterized the relationship between SNPs and genetic diseases in Online Mendelian Inheritance in Animals based on the genomic position. We determined the position of 285 buried SNPs on the genome and surveyed the genotype and allele frequencies of these SNPs in 5,955 individual Japanese Black cattle. Eleven SNPs associated with genetic disease, which contained five buried SNPs, were found in the population with the risk allele frequency ranging from 0.00008396 to 0.46. These results indicate that buried SNPs in the bovine SNP array can be utilized to identify associations with genetic disorders from large scale accumulated SNP genotype data in Japanese Black cattle.

Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle

The effects of 2 deleterious recessive haplotypes on reproduction performance of Ayrshire cattle, Ayrshire Haplotype 1 (AH1) and Ayrshire Haplotype 2 (AH2), were investigated in Canadian Ayrshire cattle. We calculated their phenotypic effects on stillbirth (SB) rate and 56-d nonreturn rate (NRR) by estimating the interaction of service sire carrier status with maternal grandsire carrier status using the official Canadian evaluation models for those 2 traits. The interaction term included 9 subclasses for the 3 possible statuses of each bull: haplotype carrier, noncarrier, or not genotyped. For AH1, 394 carriers and 1,433 noncarriers were available, whereas 313 carriers and 1,543 noncarriers were available for the AH2 haplotype. The number of matings considered for SB was 34,312 for heifers (first parity) and 115,935 for cows (later parities). For NRR, 49,479 matings for heifers and 160,528 for cows were used to estimate the haplotype effects. We observed a negative effect of AH1 on SB rates, which was 2.0% higher for matings of AH1-carrier sires to dams that had an AH1-carrier sire; this effect was found for both heifers and cows. However, AH1 had small, generally nonsignificant effects on NRR. The AH2 haplotype had a substantial negative effect on NRR, with 5.1% more heifers and 4.0% more cows returning to service, but the effects on SB rates were inconsistent and mostly small effects. Our results validate the harmful effects of AH1 and AH2 on reproduction traits in the Canadian Ayrshire population. This information will be of great interest for the dairy industry, allowing producers to make mating decisions that would reduce reproductive losses.

Implementation of Bayesian methods to identify SNP and haplotype regions with transmission ratio distortion across the whole genome: TRDscan v.1.0

Realized deviations from the expected Mendelian inheritance of alleles from heterozygous parents have been previously reported in a broad range of organisms (i.e., transmission ratio distortion; TRD). Various biological mechanisms affecting gametes, embryos, fetuses, or even postnatal offspring can produce patterns of TRD. However, knowledge about its prevalence and potential causes in livestock species is still scarce. Specific Bayesian models have been recently developed for the analyses of TRD for biallelic loci, which accommodated a wide range of population structures, enabling TRD investigation in livestock populations. The parameterization of these models is flexible and allows the study of overall (parent-unspecific) TRD and sire- and dam-specific TRD. This research aimed at deriving Bayesian models for fitting TRD on the basis of haplotypes, testing the models for both haplotype- and SNP-based methods in simulated data and actual Holstein genotypes, and developing a specific software for TRD analyses. Results obtained on simulated data sets showed that the statistical power of the analysis increased with sample size of trios (n), proportion of heterozygous parents, and the magnitude of the TRD. On the other hand, the statistical power to detect TRD decreased with the number of alleles at each loci. Bayesian analyses showed a strong Pearson correlation coefficient (≥0.97) between simulated and estimated TRD that reached the significance level of Bayes factor ≥10 for both single-marker and haplotype analyses when n ≥ 25. Moreover, the accuracy in terms of the mean absolute error decreased with the increase of the sample size and increased with the number of alleles at each loci. Using real data (55,732 genotypes of Holstein trios), SNP- and haplotype-based distortions were detected with overall TRD, sire-TRD, or dam-TRD, showing different magnitudes of TRD and statistical relevance. Additionally, the haplotype-based method showed more ability to capture TRD compared with individual SNP. To discard possible random TRD in real data, an approximate empirical null distribution of TRD was developed. The program TRDscan v.1.0 was written in Fortran 2008 language and provides a powerful statistical tool to scan for TRD regions across the whole genome. This developed program is freely available at http://www.casellas.info/files/TRDscan.zip.

Screening genetic diseases prevalence in Braunvieh cattle

Heritable abnormalities can cause a reduction in productive performance, structural defects, or death of the animal. There are reports of hereditary abnormalities in Braunvieh cattle from several countries, but no evidence was found on their existence in Mexico. In this study, 28 genes associated with hereditary diseases were screened with the GGP-LD 30K array (GeneSeek^®) in 300 Mexican registered Braunvieh animals. Allelic frequencies of the markers associated with illness were obtained for the following: citrullinaemia, spinal dysmyelination, spinal muscular atrophy, Brows Swiss fertility haplotype 2, congenital muscular dystonia, epidermolysis bullosa, Pompes, maple syrup urine, syndactyly, Weaver syndrome, crooked tail, deficiency of uridine monophosphate synthase, hypotrichosis, Marfan syndrome, and weak calf syndrome. The allelic frequency values were low for all the analysed loci (from 0.0015 to 0.0110), with exception of syndactyly (0.4145). Although homozygous animals for these genetic conditions were detected, no physical or physiological abnormalities associated with the clinical form of the diseases were observed in the sampled animals. Markers associated with a crooked tail, deficiency of uridine monophosphate synthase, hypotrichosis, Marfan syndrome, and weak calf syndrome were absent. The studied Mexican Braunvieh population does not present clinical or subclinical effects for ten diseases in homozygous animals. However, since the assessed animals are considered as breeding stock, the monitoring of carrier animals might be periodically necessary.

Fundamental Molecules and Mechanisms for Forming and Maintaining Neuromuscular Synapses

The neuromuscular synapse is a relatively large synapse with hundreds of active zones in presynaptic motor nerve terminals and more than ten million acetylcholine receptors (AChRs) in the postsynaptic membrane. The enrichment of proteins in presynaptic and postsynaptic membranes ensures a rapid, robust, and reliable synaptic transmission. Over fifty years ago, classic studies of the neuromuscular synapse led to a comprehensive understanding of how a synapse looks and works, but these landmark studies did not reveal the molecular mechanisms responsible for building and maintaining a synapse. During the past two-dozen years, the critical molecular players, responsible for assembling the specialized postsynaptic membrane and regulating nerve terminal differentiation, have begun to be identified and their mechanism of action better understood. Here, we describe and discuss five of these key molecular players, paying heed to their discovery as well as describing their currently understood mechanisms of action. In addition, we discuss the important gaps that remain to better understand how these proteins act to control synaptic differentiation and maintenance.

Role of the Wnt/β-Catenin Pathway in Renal Osteodystrophy

Vascular calcification and bone fragility are common and interrelated health problems that affect chronic kidney disease (CKD) patients. Bone fragility, which leads to higher risk of fracture and mortality, arises from the abnormal bone remodeling and mineralization that are seen in chronic kidney disease. Recently, sclerostin and Dickkopf-related protein 1 were suggested to play a significant role in CKD-related bone disease as they are known inhibitors of the Wnt pathway, thus preventing bone formation. This review focuses on new knowledge about the Wnt pathway in bone, how its function is affected by chronic kidney disease and how this affects bone structure. Expression of components and inhibitors of the Wnt pathway has been shown to be affected by the loss of kidney function, and a better understanding of the bone effects of Wnt pathway inhibitors could allow the development of new therapies to prevent bone fragility in this population.

Genetic disorders in beef cattle: a review

The main purpose of present review is to describe and organize autosomal recessive disorders (arachnomelia, syndactylism, osteopetrosis, dwarfism, crooked tail syndrome, muscular hyperplasia, glycogen storage disease, protoporphyria), which occur among beef cattle, and methods that can be applied to detect these defects. Prevalence of adverse alleles in beef breeds happens due to human activity—selections of favorable features, e.g. developed muscle tissue. Unfortunately, carriers of autosomal recessive diseases are often characterized by these attributes. Fast and effective identification of individuals, that may carry faulty genes, can prevent economical losses.

Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations

BACKGROUND

SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific mutations. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we compared - through cross-validation- five classification models (Lasso-penalized logistic regression -Lasso, Support Vector Machines with either linear or radial kernel -SVML and SVMR, k-nearest neighbors -KNN, and multi-allelic gene prediction -MAG), for the identification of carriers of the TUBD1 recessive mutation on BTA19 (Bos taurus autosome 19), known to be associated with high calf mortality. A population of 3116 Fleckvieh and 392 Brown Swiss animals genotyped with the 54K SNP-chip was available for the analysis.

RESULTS

In general, the use of SNP genotypes proved to be very effective for the identification of mutation carriers. The best predictive models were Lasso, SVML and MAG, with an average error rate, respectively, of 0.2 %, 0.4 % and 0.6 % in Fleckvieh, and 1.2 %, 0.9 % and 1.7 % in Brown Swiss. For the three models, the false positive rate was, respectively, 0.1 %, 0.1 % and 0.2 % in Fleckvieh, and 3.0 %, 2.4 % and 1.6 % in Brown Swiss; the false negative rate was 4.4 %, 7.6 %1.0 % in Fleckvieh, and 0.0 %, 0.1% and 0.8 % in Brown Swiss. MAG appeared to be more robust to sample size reduction: with 25 % of the data, the average error rate was 0.7 % and 2.2 % in Fleckvieh and Brown Swiss, compared to 2.1 % and 5.5 % with Lasso, and 2.6 % and 12.0 % with SVML.

CONCLUSIONS

The use of SNP genotypes is a very effective and efficient technique for the identification of mutation carriers in cattle populations. Very few misclassifications were observed, overall and both in the carriers and non-carriers classes. This indicates that this is a very reliable approach for potential applications in cattle breeding.

Polyhydramnios in Lrp4 knockout mice with bilateral kidney agenesis: Defects in the pathways of amniotic fluid clearance

Amniotic fluid volume during mid-to-late gestation depends mainly on the urine excretion from the foetal kidneys and partly on the fluid secretion from the foetal lungs during foetal breathing-like movements. Urine is necessary for foetal breathing-like movements, which is critical for foetal lung development. Bilateral renal agenesis and/or obstruction of the urinary tract lead to oligohydramnios, which causes infant death within a short period after birth due to pulmonary hypoplasia. Lrp4, which functions as an agrin receptor, is essential for the formation of neuromuscular junctions. Herein, we report novel phenotypes of Lrp4 knockout (Lrp4(-/-)) mice. Most Lrp4(-/-) foetuses showed unilateral or bilateral kidney agenesis, and Lrp4 knockout resulted in polyhydramnios. The loss of Lrp4 compromised foetal swallowing and breathing-like movements and downregulated the expression of aquaporin-9 in the foetal membrane and aquaporin-1 in the placenta, which possibly affected the amniotic fluid clearance. These results suggest that amniotic fluid removal was compromised in Lrp4(-/-) foetuses, resulting in polyhydramnios despite the impairment of urine production. Our findings indicate that amniotic fluid removal plays an essential role in regulating the amniotic fluid volume.

Genetic tools to improve reproduction traits in dairy cattle

Fertility is a major concern in the dairy cattle industry and has been the subject of numerous studies over the past 20 years. Surprisingly, most of these studies focused on rough female phenotypes and, despite their important role in reproductive success, male- and embryo-related traits have been poorly investigated. In recent years, the rapid and important evolution of technologies in genetic research has led to the development of genomic selection. The generalisation of this method in combination with the achievements of the AI industry have led to the constitution of large databases of genotyping and sequencing data, as well as refined phenotypes and pedigree records. These resources offer unprecedented opportunities in terms of fundamental and applied research. Here we present five such examples with a focus on reproduction-related traits: (1) detection of quantitative trait loci (QTL) for male fertility and semen quality traits; (2) detection of QTL for refined phenotypes associated with female fertility; (3) identification of recessive embryonic lethal mutations by depletion of homozygous haplotypes; (4) identification of recessive embryonic lethal mutations by mining whole-genome sequencing data; and (5) the contribution of high-density single nucleotide polymorphism chips, whole-genome sequencing and imputation to increasing the power of QTL detection methods and to the identification of causal variants.

Approach to Investigating Congenital Skeletal Abnormalities in Livestock

Congenital skeletal abnormalities may be genetic, teratogenic, or nutritional in origin; distinguishing among these different causes is essential in the management of the disease but may be challenging. In some cases, teratogenic or nutritional causes of skeletal abnormalities may appear very similar to genetic causes. For example, chondrodysplasia associated with intrauterine zinc or manganese deficiency and mild forms of hereditary chondrodysplasia have very similar clinical features and histologic lesions. Therefore, historical data are essential in any attempt to distinguish genetic and acquired causes of skeletal lesions; as many animals as possible should be examined; and samples should be collected for future analysis, such as genetic testing. Acquired causes of defects often show substantial variation in presentation and may improve with time, while genetic causes frequently have a consistent presentation. If a disease is determined to be of genetic origin, a number of approaches may be used to detect mutations, each with advantages and disadvantages. These approaches include sequencing candidate genes, single-nucleotide polymorphism array with genomewide association studies, and exome or whole genome sequencing. Despite advances in technology and increased cost-effectiveness of these techniques, a good clinical history and description of the pathology and a reliable diagnosis are still key components of any investigation.

LRP4 induces extracellular matrix productions and facilitates chondrocyte differentiation

Endochondral ossification is an essential step for skeletal development, which requires chondrocyte differentiation in growth cartilage. The low-density lipoprotein receptor-related protein 4 (LRP4), a member of LDLR family, is an inhibitor for Wnt signaling, but its roles in chondrocyte differentiation remain to be investigated. Here we found by laser capture microdissection that LRP4 expression was induced during chondrocyte differentiation in growth plate. In order to address the roles, we overexpressed recombinant human LRP4 or knocked down endogenous LRP4 by lentivirus in mouse ATDC5 chondrocyte cells. We found that LRP4 induced gene expressions of extracellular matrix proteins of type II collagen (Col2a1), aggrecan (Acan), and type X collagen (Col10a1), as well as production of total proteoglycans in ATDC5 cells, whereas LRP4 knockdown had opposite effects. Interestingly, LRP4-knockdown reduced mRNA expression of Sox9, a master regulator for chondrogenesis, as well as Dkk1, an extracellular Wnt inhibitor. Analysis of Wnt signaling revealed that LRP4 blocked the Wnt/β-catenin signaling activity in ATDC5 cells. Finally, the reduction of these extracellular matrix productions by LRP4-knockdown was rescued by a β-catenin/TCF inhibitor, suggesting that LRP4 is an important regulator for extracellular matrix productions and chondrocyte differentiation by suppressing Wnt/β-catenin signaling.

Candidate genes and biological pathways associated with carcass quality traits in beef cattle

Karisa, B. K., Thomson, J., Wang, Z., Bruce, H. L., Plastow, G. S. and Moore, S. S. 2013. Candidate genes and biological pathways associated with carcass quality traits in beef cattle. Can. J. Anim. Sci. 93: 295–306. The objective of this study was to use the candidate gene approach to identify the genes associated with carcass quality traits in beef cattle steers at the University of Alberta Ranch at Kinsella, Canada. This approach involved identifying positional candidate genes and prioritizing them according to their functions into functional candidate genes before performing statistical association analysis. The positional candidate genes and single nucleotide polymorphisms (SNP) were identified from previously reported quantitative trait loci for component traits including body weight, average daily gain, metabolic weight, feed efficiency and energy balance. Positional candidate genes were then prioritized into functional candidate genes according to the associated gene ontology terms and their functions. A total of 116 genes were considered functional candidate genes and 117 functional SNPs were genotyped and used for multiple marker association analysis using ASReml®. Seven SNPs were significantly associated with various carcass quality traits (P≤0.005). The significant genes were associated with biological processes such as fat, glucose, protein and steroid metabolism, growth, energy utilization and DNA transcription and translation as inferred from the protein knowledgebase (UniprotKB). Gene network analysis indicated significant involvement of biological processes related to fat and steroid metabolism and regulation of transcription and translation of DNA.

Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10(-4)) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.

Endocytic receptor-mediated control of morphogen signaling

Receptor-mediated endocytosis provides a mechanism by which cells take up signaling molecules from the extracellular space. Recent studies have shown that one class of endocytic receptors, the low-density lipoprotein receptor-related proteins (LRPs), is of particular relevance for embryonic development. In this Primer, we describe how LRPs constitute central pathways that modulate morphogen presentation to target tissues and cellular signal reception, and how LRP dysfunction leads to developmental disturbances in many species.

Sclerostin and Dickkopf-1 as therapeutic targets in bone diseases

The processes of bone growth, modeling, and remodeling determine the structure, mass, and biomechanical properties of the skeleton. Dysregulated bone resorption or bone formation may lead to metabolic bone diseases. The Wnt pathway plays an important role in bone formation and regeneration, and expression of two Wnt pathway inhibitors, sclerostin and Dickkopf-1 (DKK1), appears to be associated with changes in bone mass. Inactivation of sclerostin leads to substantially increased bone mass in humans and in genetically manipulated animals. Studies in various animal models of bone disease have shown that inhibition of sclerostin using a monoclonal antibody (Scl-Ab) increases bone formation, density, and strength. Additional studies show that Scl-Ab improves bone healing in models of bone repair. Inhibition of DKK1 by monoclonal antibody (DKK1-Ab) stimulates bone formation in younger animals and to a lesser extent in adult animals and enhances fracture healing. Thus, sclerostin and DKK1 are emerging as the leading new targets for anabolic therapies to treat bone diseases such as osteoporosis and for bone repair. Clinical trials are ongoing to evaluate the effects of Scl-Ab and DKK1-Ab in humans for the treatment of bone loss and for bone repair.

A sensitised mutagenesis screen in the mouse to explore the bovine genome: study of muscle characteristics

Meat yield and quality are closely related to muscle development. The muscle characteristics mainly take place during embryonic and postnatal phases. Thus, genetic control of muscle development in early stages represents a significant stake to improve product quality and production efficiency. In bovine, several programmes have been developed to detect quantitative trait loci (QTL) affecting growth, carcass composition or meat quality traits. Such strategy is incontestably very powerful yet extremely cumbersome and costly when dealing with large animals such as ruminants. Furthermore, the fine mapping of the QTL remains a real challenge. Here, we proposed an alternative approach based on chemical mutagenesis in the mouse combined with comparative genomics to identify regions or genes controlling muscle development in cattle. At present, we isolated seven independent mouse lines of high interest. Two lines exhibit a hypermuscular phenotype, and the other five show various skeletomuscular phenotypes. Detailed characterisation of these mouse mutants will give crucial input for the identification and the mapping of genes that control muscular development. Our strategy will provide the opportunity to understand the function and control of genes involved in improvement of animal physiology.

Bone overgrowth-associated mutations in the LRP4 gene impair sclerostin facilitator function

Humans lacking sclerostin display progressive bone overgrowth due to increased bone formation. Although it is well established that sclerostin is an osteocyte-secreted bone formation inhibitor, the underlying molecular mechanisms are not fully elucidated. We identified in tandem affinity purification proteomics screens LRP4 (low density lipoprotein-related protein 4) as a sclerostin interaction partner. Biochemical assays with recombinant proteins confirmed that sclerostin LRP4 interaction is direct. Interestingly, in vitro overexpression and RNAi-mediated knockdown experiments revealed that LRP4 specifically facilitates the previously described inhibitory action of sclerostin on Wnt1/β-catenin signaling. We found the extracellular β-propeller structured domain of LRP4 to be required for this sclerostin facilitator activity. Immunohistochemistry demonstrated that LRP4 protein is present in human and rodent osteoblasts and osteocytes, both presumed target cells of sclerostin action. Silencing of LRP4 by lentivirus-mediated shRNA delivery blocked sclerostin inhibitory action on in vitro bone mineralization. Notably, we identified two mutations in LRP4 (R1170W and W1186S) in patients suffering from bone overgrowth. We found that these mutations impair LRP4 interaction with sclerostin and its concomitant sclerostin facilitator effect. Together these data indicate that the interaction of sclerostin with LRP4 is required to mediate the inhibitory function of sclerostin on bone formation, thus identifying a novel role for LRP4 in bone.

Lipoprotein receptors--an evolutionarily ancient multifunctional receptor family

The evolutionarily ancient low-density lipoprotein (LDL) receptor gene family represents a class of widely expressed cell surface receptors. Since the dawn of the first primitive multicellular organisms, several structurally and functionally distinct families of lipoprotein receptors have evolved. In accordance with the now obsolete 'one-gene-one-function' hypothesis, these cell surface receptors were originally perceived as mere transporters of lipoproteins, lipids, and nutrients or as scavenger receptors, which remove other kinds of macromolecules, such as proteases and protease inhibitors from the extracellular environment and the cell surface. This picture has since undergone a fundamental change. Experimental evidence has replaced the perception that these receptors serve merely as cargo transporters. Instead it is now clear that the transport of macromolecules is inseparably intertwined with the molecular machinery by which cells communicate with each other. Lipoprotein receptors are essentially sensors of the extracellular environment that participate in a wide range of physiological processes by physically interacting and coevolving with primary signal transducers as co-regulators. Furthermore, lipoprotein receptors modulate cellular trafficking and localization of the amyloid precursor protein (APP) and the β-amyloid peptide (Aβ), suggesting a role in the pathogenesis of Alzheimer's disease. Moreover, compelling evidence shows that LDL receptor family members are involved in tumor development and progression.

A variant of the LRP4 gene affects the risk of chronic lymphocytic leukaemia transformation to Richter syndrome

Richter syndrome (RS) represents the transformation of chronic lymphocytic leukaemia (CLL) to aggressive lymphoma. Risk factors of CLL transformation to RS are only partly known. We explored the role of the host genetic background as a risk factor for RS occurrence. Forty-five single nucleotide polimorphisms (SNPs) known to be relevant for CLL prognosis were genotyped in a consecutive cohort of 331 CLL, of which 21 had transformed to RS. After correcting for multiple testing and adjusting for previously reported RS risk factors, the LRP4 rs2306029 TT variant genotype was the sole SNP independently associated with a higher risk of RS transformation (Hazard Ratio: 4·17; P = 0·001; q = 0·047). The enrichment of LRP4 TT genotype in RS was confirmed in an independent series (n = 44) used for validation purposes. The LRP4 protein was expressed in CLL (n =66). Bioinformatic analysis scored LRP4 rs2306029 as a variant with possible deleterious and damaging variant of LRP4. LRP4 genotyping may help the recognition of patients with increased risk of RS at the time of CLL diagnosis.

Mutations in VLDLR as a cause for autosomal recessive cerebellar ataxia with mental retardation (dysequilibrium syndrome)

Dysequilibrium syndrome is a genetically heterogeneous condition that combines autosomal recessive, nonprogressive cerebellar ataxia with mental retardation. Here, we report the first patient heterozygous for 2 novel mutations in VLDLR. An 18-month-old girl presented with significant hypotonia, global developmental delay, and truncal and peripheral ataxia. Magnetic resonance imaging of the brain demonstrated hypoplasia of the inferior cerebellar vermis and hemispheres, small pons, and a simplified cortical sulcation pattern. Sequence analysis of the VLDLR gene identified a nonsense and missense mutation. Six mutations in VLDLR have now been identified in 5 families with a phenotype characterized by moderate-to-profound mental retardation, delayed ambulation, truncal and peripheral ataxia, and occasional seizures. Neuroanatomically, the loss-of-function effect of the different mutations is indistinguishable. VLDLR-associated cerebellar hypoplasia is emerging as a panethnic, clinically, and molecularly well-defined genetic syndrome.

Inherited diseases of Australian Holstein-Friesian cattle

Inherited disorders are of major importance in Holstein-Friesian cattle, a breed that now dominates the global dairy industry. Recent developments in the breed reflect intensive selection programs for production traits, identifying elite sires whose genotypes are rapidly spread worldwide through the use of breeding programs involving advanced reproductive technologies. These elite sires carry mutations responsible for disease. Consequently, the mating of descendants of an elite sire (as with any sire) substantially increases the risk of producing defective progeny. The important inherited disorder citrullinaemia was disseminated globally in the 1970s and first reported in Australian Holstein-Friesians. However, a range of inherited disorders more recently recognised internationally in this breed have remained unreported in Australia, although recent genotyping studies suggest they have probably occurred. A survey of these disorders suggests a decline in surveillance for such diseases in Australia. Clinical and pathological descriptions are presented to enable practitioners and producers to recognise and report these disorders, and a proposal is advanced to establish a health program to manage this issue.

Expanding functions of lipoprotein receptors

Lipoprotein receptors are evolutionarily ancient proteins that are expressed on the surface of many cell types. Beginning with the appearance of the first primitive multicellular organisms, several structurally and functionally distinct families of lipoprotein receptors evolved. Originally, these cell surface proteins were thought to merely mediate the traffic of lipids and nutrients between cells and, in some cases, by functioning as scavenger receptors, remove other kinds of macromolecules, such as proteases and protease inhibitors from the extracellular space and the cell surface. Over the last decade, this picture has fundamentally changed. We now appreciate that many of these receptors are not mere cargo transporters; they are deeply embedded in the machinery by which cells communicate with each other. By physically interacting and coevolving with fundamental signaling pathways, lipoprotein receptors have occupied essential and surprisingly diverse functions that are indispensable for integrating the complex web of cellular signal input during development and in differentiated tissues.

Inherited abnormalities of skeletal development in sheep

Inherited diseases of the skeleton are reported less often in sheep than in most other domestic animal species but are likely to occur more frequently than the veterinary literature would suggest. Although most are lethal or semi-lethal, the gene frequency for some of these diseases has reached surprisingly high levels in defined populations, presumably due either to the founder effect or the presence of a selective advantage of heterozygous individuals. This article reviews the clinical characteristics, pathology, mode of inheritance and molecular basis of skeletal diseases known to have a genetic aetiology in sheep. Inherited skeletal diseases of sheep are potential models for studying the treatment of similar diseases in humans.

A critical analysis of disease-associated DNA polymorphisms in the genes of cattle, goat, sheep, and pig

Genetic variations through their effects on gene expression and protein function underlie disease susceptibility in farm animal species. The variations are in the form of single nucleotide polymorphisms, deletions/insertions of nucleotides or whole genes, gene or whole chromosomal rearrangements, gene duplications, and copy number polymorphisms or variants. They exert varying degrees of effects on gene action, such as substitution of an amino acid for another, shift in reading frame and premature termination of translation, and complete deletion of entire exon(s) or gene(s) in diseased individuals. These factors influence gene function by affecting mRNA splicing pattern or by altering/eliminating protein function. Elucidating the genetic bases of diseases under the control of many genes is very challenging, and it is compounded by several factors, including host x pathogen x environment interactions. In this review, the genetic variations that underlie several diseases of livestock (under monogenic and polygenic control) are analyzed. Also, factors hampering research efforts toward identification of genetic influences on animal disease identification and control are highlighted. A better understanding of the factors analyzed could be better harnessed to effectively identify and control, genetically, livestock diseases. Finally, genetic control of animal diseases can reduce the costs associated with diseases, improve animal welfare, and provide healthy animal products to consumers, and should be given more attention.

Lipoproteins and their receptors in embryonic development: more than cholesterol clearance

Previously, the relevance of lipoproteins and their receptors has mainly been discussed in terms of cholesterol clearance in the adult organism. Now, findings from nematodes to fruit flies to mammals all point towards novel and unexpected roles for lipoprotein metabolism in the control of key regulatory pathways in the developing embryo, including signaling through steroid hormones and throughout the hedgehog and Wnt signaling pathways. Here, we discuss the emerging view of how lipoproteins and their receptors regulate embryogenesis.

Genetic and haplotypic structure in 14 European and African cattle breeds

To evaluate and compare the extent of LD in cattle, 1536 SNPs, mostly localized on BTA03, were detected in silico from available sequence data using two different methods and genotyped on samples from 14 distinct breeds originating from Europe and Africa. Only 696 SNPs could be validated, confirming the importance of trace-quality information for the in silico detection. Most of the validated SNPs were informative in several breeds and were used for a detailed description of their genetic structure and relationships. Results obtained were in agreement with previous studies performed on microsatellite markers and using larger samples. In addition, the majority of the validated SNPs could be mapped precisely, reaching an average density of one marker every 311 kb. This allowed us to analyze the extent of LD in the different breeds. Decrease of LD with physical distance across breeds revealed footprints of ancestral LD at short distances (<10 kb). As suggested by the haplotype block structure, these ancestral blocks are organized, within a breed, into larger blocks of a few hundred kilobases. In practice, such a structure similar to that already reported in dogs makes it possible to develop a chip of <300,000 SNPs, which should be efficient for mapping purposes in most cattle breeds.

A role for LRP4 in neuronal cell viability is related to apoE-binding

The distribution pattern of apolipoprotein E (apoE) in cortical neurons in culture resembles that of low-density lipoprotein receptor-related protein 4 (LRP4). Both proteins are distributed in a punctate manner on the cell surface throughout neurons, including somas and dendrites. This finding prompted us to examine whether apoE is a ligand for LRP4 in the rat brain. ApoE and LRP4 from both Cos7 cells heterologous expressing LRP4 and brain homogenate were co-immunoprecipitated. We then examined the effect of antibody against the ligand-binding domain of LRP4 (anti-LB). Anti-LB applied to neuronal cells in culture down-regulated MAP2-immunoreactive neurons, reduced the viability of neurons and impaired synaptic structure. This effect was possibly due to a blockade of the binding of extraneuronal ligands, such as apoE/cholesterol, to LRP4 protein, since anti-LB suppressed binding of apoE to the LRP4 heterologously expressed in Cos7 cells. These results suggest that apoE is an endogenous ligand for LRP4 and may play a role as a receptor for extracellular signals, including those from glial cells, in the maintenance of the viability of neurons.

Congenital syndactyly in cattle: four novel mutations in the low density lipoprotein receptor-related protein 4 gene (LRP4)

Background

Isolated syndactyly in cattle, also known as mulefoot, is inherited as an autosomal recessive trait with variable penetrance in different cattle breeds. Recently, two independent mutations in the bovine LRP4 gene have been reported as the primary cause of syndactyly in the Holstein and Angus cattle breeds.

Results

We confirmed the previously described LRP4 exon 33 two nucleotide substitution in most of the affected Holstein calves and revealed additional evidence for allelic heterogeneity by the identification of four new LRP4 non-synonymous point mutations co-segregating in Holstein, German Simmental and Simmental-Charolais families.

Conclusion

We confirmed a significant role of LRP4 mutations in the pathogenesis of congenital syndactyly in cattle. The newly detected missense mutations in the LRP4 gene represent independent mutations affecting different conserved protein domains. However, the four newly described LRP4 mutations do still not explain all analyzed cases of syndactyly.

The LDL receptor-related protein (LRP) family: an old family of proteins with new physiological functions

The low-density lipoprotein (LDL) receptor is the founding member of a family of seven structurally closely related transmembrane proteins (LRP1, LRP1b, megalin/LRP2, LDL receptor, very low-density lipoprotein receptor, MEGF7/LRP4, LRP8/apolipoprotein E receptor2). These proteins participate in a wide range of physiological processes, including the regulation of lipid metabolism, protection against atherosclerosis, neurodevelopment, and transport of nutrients and vitamins. While currently available data suggest that the role of the LDL receptor is limited to the regulation of cholesterol homeostasis by receptor-mediated endocytosis of lipoprotein particles, there is growing experimental evidence that the other members of the gene family have additional physiological functions as signal transducers. In this review, we focus on the latest discovered functions of two major members of this family, LRP1 and megalin/LRP2, and on the newly elucidated physiological role of a third member of the family, MEGF7/LRP4, which can also function as a modulator of diverse signaling pathways during development.