Invited review: Bioinformatic methods to discover the likely causal variant of a new autosomal recessive genetic condition using genome-wide data

In animals, new autosomal recessive genetic diseases (ARGD) arise all the time due to the regular, random mutations that occur during meiosis. In order to reduce the effect of any damaging new variant, it is necessary to find its cause. To evaluate the best way of doing this, 34 papers which found the exact location of a new genetic disease in livestock were reviewed and found to require at least two stages. In the initial stage the commonly used χ2 method, applied in a case-control association analysis with single nucleotide polymorphism (SNP)-chip data, was found to have limitations and was almost always used in conjunction with a second method to locate the target region on the genome containing the variant. The commonly used methods had their drawbacks; so a new method was devised based on long runs of homozygosity, a common feature of new ARGD. This ‘autozygosity by difference’ method was found to be as good as, or better than, all the reviewed methods tested based on its ability to unambiguously find the shortest known target region in an already analysed data set. Mean target region length was found to be 4.6 megabases in the published reports. Success did not depend on the size of commercial SNP-chip used, and studies with as few as three cases and four controls were large enough to find the target region. The final stage relied on either sequencing the candidate genes found in the target region or using whole genome sequencing (WGS) on a small number of cases. Sometimes this latter method was used in conjunction with WGS on a number of control animals or resources such as the 1000 bull genomes data. Calculations showed that, in cattle, less than 15 animals would be needed in order to locate the new variant when using WGS data. This could be any combination of cases plus parents or other unrelated animals in the breed. Using WGS data, it would be necessary to search the three billion bases of the cattle genome for base positions which were homozygous for the same allele in all cases and heterozygous for that allele in parents, or not containing that homozygote in unrelated controls. This site could be confirmed on other healthy animals using much cheaper methods, and then a genetic test could be devised for that variant in order to screen the whole population and to devise a breeding programme to eliminate the disorder from the population

A noninvasive method for measuring mammary apoptosis and epithelial cell activation in dairy animals using microparticles extracted from milk

AbstractMilk production from dairy animals has been described in terms of 3 processes: the increase in secretory cell numbers in late pregnancy and early lactation, secretion rate of milk per cell, and the decline in cell numbers as lactation progresses. This latter process is thought to be determined by the level of programmed cell death (apoptosis) found in the animal. Until now, apoptosis has been measured by taking udder biopsies, using magnetic resonance imaging scans, or using animals postmortem. This paper describes an alternative, noninvasive method for estimating apoptosis by measuring microparticles in milk samples. Microparticles are the product of several processes in dairy animals, including apoptosis. Milk samples from 12 Holstein cows, at or past peak lactation, were collected at 5 monthly samplings. The samples (n=57) were used to measure the number of microparticles and calculate microparticle density for 4 metrics: annexin V positive and merocyanine 540 dye positive, for both and total particles, in both whole milk (WM) and spun milk. Various measures of milk production were also recorded for the 12 cows, including daily milk yield, fat and protein percentage in the milk, somatic cell count, and the days in milk when the samples were taken. A high correlation was found between the 4 WM microparticle densities and days in milk (0.46 to 0.64), and a moderate correlation between WM microparticle densities and daily milk yield (−0.33 to −0.44). No significant relationships were found involving spun milk samples, somatic cell count, or fat and protein percentage. General linear model analyses revealed differences between cows for both level of microparticle density and its rate of change in late lactation. Persistency of lactation was also found to be correlated with the WM microparticle traits (−0.65 to −0.32). As apoptosis is likely to be the major contributor to microparticle numbers in late lactation, this work found a noninvasive method for estimating apoptosis that gave promising results. Further investigation is required to find out the factors affecting microparticle production and how it changes throughout lactation

Age at First Viral Infection Determines the Pattern of T Cell–mediated Disease during Reinfection in Adulthood

Infants experiencing severe respiratory syncytial virus (RSV) bronchiolitis have an increased frequency of wheeze and asthma in later childhood. Since most severe RSV infections occur between the 8th and 24th postnatal week, we examined whether age at first infection determines the balance of cytokine production and lung pathology during subsequent rechallenge. Primary RSV infection in newborn mice followed the same viral kinetics as in adults but was associated with reduced and delayed IFN-γ responses. To study rechallenge, mice were infected at 1 day or 1, 4, or 8 weeks of age and reinfected at 12 weeks. Neonatal priming produced more severe weight loss and increased inflammatory cell recruitment (including T helper 2 cells and eosinophils) during reinfection, whereas delayed priming led to enhanced interferon γ production and less severe disease during reinfection. These results show the crucial importance of age at first infection in determining the outcome of reinfection and suggest that the environment of the neonatal lung is a major determinant of cytokine production and disease patterns in later life. Thus, simply delaying RSV infection beyond infancy might reduce subsequent respiratory morbidity in later childhood

Association between Single Nucleotide Polymorphism in RelA with Somatic Cell Count and Longevity Supports Importance of NF-¦ÊB Signalling in Cattle Health

Mastitis reduces milk production and causes culling. The NF-κB transcription factor RelA plays a central regulatory role in innate immunity. This study used a candidate gene approach to investigate associations between the synonymous C/G SNP rs48035703 in RELA with somatic cell count (SCC) and survival time. Blood samples were collected from 337 Holstein-Friesian heifers on 19 farms and genotyped by PCR-restriction fragment length polymorphism. Animals were monitored from 6 months until 2340 d of age. Pedigree, milk production and disease records were obtained. Genotype frequencies were CC 0.63, CG 0.30 and GG 0.06. The C allele had a favourable additive effect on survival: average longevities from birth were CC, 1872 d; CG, 1745 d and GG 1596 d (P < 0.003). Log transformed first lactation somatic cell count (SCC)data showed a significant association with this SNP using an allele substitution model (mean residuals ± SD: GG 0.30 ± 1.263; CG 0.22 ± 0.994, CC −0.04 ± 0.803, P < 0.05). More CC cows than expected were classified as intermediate and fewer as mastitic (30.4% v 45.9%) with respect to SCC class when categorised as 0 (unaffected), 1 (intermediate) and 2 (mastitic), whereas for CG heterozygotes fewer were intermediate and more were mastitic (12.1% v 60.3%) (p = 0.05). RELA rs48035703 CC genotype cows were therefore less likely to experience a high SCC and survived longer. These results support a role for RelA in combating mammary gland infection and warrant further studies in additional populations

A Nonsynonymous Change in Adhesion G Protein–Coupled Receptor L3 Associated With Risk for Equine Degenerative Myeloencephalopathy in the Caspian Horse

Equine degenerative myeloencephalopathy (EDM), a neurological disease of young horses, causes progressive development of symmetric ataxia predominantly in the pelvic limbs. Equine degenerative myeloencephalopathy is likely inherited and with no known treatment affected horses frequently need euthanasia. Alpha-tocopherol deficiency during early life appears to contribute to the phenotype. This study sought to identify any genetic variants correlated with EDM in Caspian foals. Two half-sibling EDM-diagnosed cases were genotyped at 52,063 loci and evaluated by the Autozygosity by Difference statistic. Additional horses not affected by EDM were used for genetic comparison to identify regions unique to the case phenotype. The associated region on chromosome 3 contains only one gene encoding adhesion G protein–coupled receptor L3 (ADGRL3). Adhesion G protein–coupled receptor L3 is a member of the latrophilin subfamily of G protein–coupled receptors and may contribute to attention deficit/hyperactivity disorder in humans and hyperactive motor function in mice and zebrafish. Analysis of the predicted coding regions for Equine ADGRL3 in affected horses revealed a nonsynonymous single nucleotide polymorphism at Chr3:71,917,591 bp. Caspian and Caspian cross-relatives (n = 81) of the two initial cases and unrelated horses from similar breeds (n = 130, including Arabians, American Miniatures, and Shetlands) possessed this allele at 5% frequency, with no homozygotes observed within the non-Caspian breeds. This study suggests that a polymorphism in ADGRL3 could contribute to a genetic predisposition to Caspian horse EDM

Locating a novel autosomal recessive genetic condition using only WGS data from three cases and six controls; a case study of a new variant in the cattle glucokinase gene

New Mendelian genetic conditions, which adversely affect livestock, arise all the time. To manage them effectively, some methods need to be devised that are quick and accurate. Until recently, finding the causal genomic site of a new autosomal recessive genetic disease has required a two-stage approach using single-nucleotide polymorphism (SNP) chip genotyping to locate the region containing the new variant. This region is then explored using fine-mapping methods to locate the actual site of the new variant. This study explores bioinformatic methods that can be used to identify the causative variants of recessive genetic disorders with full penetrance with just nine whole genome-sequenced animals to simplify and expedite the process to a one-step procedure. Using whole genome sequencing of only three cases and six carriers, the site of a novel variant causing perinatal mortality in Irish moiled calves was located. Four methods were used to interrogate the variant call format (VCF) data file of these nine animals, they are genotype criteria (GCR), autozygosity-by-difference (ABD), variant prediction scoring, and registered SNP information. From more than nine million variants in the VCF file, only one site was identified by all four methods (Chr4: g.77173487A>T (ARS-UCD1.2 (GCF_002263795.1)). This site was a splice acceptor variant located in the glucokinase gene (GCK). It was verified on an independent sample of animals from the breed using genotyping by polymerase chain reaction at the candidate site and autozygosity-by-difference using SNP-chips. Both methods confirmed the candidate site. Investigation of the GCR method found that sites meeting the GCR were not evenly spread across the genome but concentrated in regions of long runs of homozygosity. Locating GCR sites was best performed using two carriers to every case, and the carriers should be distantly related to the cases, within the breed concerned. Fewer than 20 animals need to be sequenced when using the GCR and ABD methods together. The genomic site of novel autosomal recessive Mendelian genetic diseases can be located using fewer than 20 animals combined with two bioinformatic methods, autozygosity-by-difference, and genotype criteria. In many instances it may also be confirmed with variant prediction scoring. This should speed-up and simplify the management of new genetic diseases to a single-step process

Environmental factors affecting lactation curve parameters in the United Kingdom’s commercial dairy herds

Environmental factors affecting lactation curve parameters in the United Kingdom&apos;s commercial dairy herds Factores ambientales que determinan los parámetros de la curva de lactación usando un modelo biológico en rebaños lecheros comerciales en el Reino Unido RESUMEN El objetivo del trabajo fue determinar los factores ambientales que determinan los parámetros de la curva de lactación utilizando un modelo biológico de ajuste de curva. El modelo propuesto ajusta dos curvas logísticas que simulan el incremento inicial en el número de células secretoras de leche en la lactación temprana, y la progresión de la apoptosis en la lactación tardía. Se analizaron lactaciones de 182.987 vacas Holstein-Friesian. Los factores vaca, rebaño y número de lactación explican el 74% de la suma total de cuadrados (P &lt; 0,001). La edad promedio a primer parto fue de 28 meses, teniendo un efecto significativo sobre la mayoría de los parámetros de la curva. Incrementos en la edad a primer de parto (20-40 meses) fueron asociados con incrementos lineales en los rendimientos totales de leche. Los parámetros tasa máxima de secreción y máximo de lactación estuvieron altamente correlacionados entre sí, indicando que son virtualmente los mismos. Adicionalmente, altos valores de estos dos parámetros indican altos rendimientos totales de leche. El día del máximo de lactación se correlacionó negativamente (0,64) con persistencia de la lactación. Los factores vaca, rebaño número de lactación y edad a primer parto fueron los factores más determinantes sobre los parámetros de la curva de lactación de vacas de primera lactancia así como de lactaciones múltiples

Blunted cardiomyocyte remodeling response in exercise-resistant rats

Increasing a subject’s aerobic exercise capacity with training decreases cardiovascular morbidity and mortality. Of major concern is the key observation that up to 20% of subjects demonstrate little or no change in maximal oxygen consumption (VO2max) with exercise training (1) and can be considered exercise resistant. Our goal with the current research was to test the hypothesis that variation in training response is associated with cardiomyocyte functional response to training