Autism spectrum disorders and autistic traits share genetics and biology.

Autism spectrum disorders (ASDs) and autistic traits in the general population may share genetic susceptibility factors. In this study, we investigated such potential overlap based on common genetic variants. We developed and validated a self-report questionnaire of autistic traits in adults. We then conducted genome-wide association studies (GWASs) of six trait scores derived from the questionnaire through exploratory factor analysis in 1981 adults from the general population. Using the results from the Psychiatric Genomics Consortium GWAS of ASDs, we observed genetic sharing between ASDs and the autistic traits 'childhood behavior', 'rigidity' and 'attention to detail'. Gene-set analysis subsequently identified 'rigidity' to be significantly associated with a network of ASD gene-encoded proteins that regulates neurite outgrowth. Gene-wide association with the well-established ASD gene MET reached significance. Taken together, our findings provide evidence for an overlapping genetic and biological etiology underlying ASDs and autistic population traits, which suggests that genetic studies in the general population may yield novel ASD genes.

Autism spectrum disorders and autistic traits share genetics and biology.

This corrects the article DOI: 10.1038/mp.2017.98.

The effect of genetic selection for Johne's disease resistance in dairy cattle: Results of a genetic-epidemiological model.

The objective of this study was to model genetic selection for Johne's disease resistance and to study the effect of different selection strategies on the prevalence in the dairy cattle population. In the Netherlands, a certification-and-surveillance program is in use to reduce prevalence and presence of sources of infection in milk by culling ELISA-positive dairy cows in infected herds. To investigate the additional genetic effect of this program, a genetic-epidemiological model was developed to assess the effect of selection of cows that test negative for Johne's disease (dam selection). The genetic effect of selection at the sire level was also considered (sire selection), assuming selection of 80% of sires producing the most resistant offspring based on their breeding values, as well as the combined effect. Parameters assumed to be affected by genetic selection were the length of the latent period, susceptibility (i.e., the number of infectious doses needed to become infected), or the length of susceptible period as a calf. The effect of selection was measured by the time in years required to eliminate infection. Sensitivity analysis was performed for heritability, accuracy of selection, and intensity of selection. For dam selection, responses to selection were small, requiring 379 to 702 yr for elimination. For sire selection, responses were much larger, although elimination still required 147 to 223 yr. The response to selection was largest if genetic selection affected the length of the susceptible period, followed by the susceptibility, and finally the length of the latent period. Genetic selection for Johne's disease resistance by certification and surveillance is too slow for practical purpose, but that selection on the sire level is able to contribute to the control of Johne's disease in the long run.

Genetic and nongenetic variation in plasma and milk ß-hydroxybutyrate and milk acetone concentrations of early-lactation dairy cows.

This study assessed genetic variation, heritability estimates, and genetic correlations for concentrations of plasma ß-hydroxybutyrate (BHBA), milk BHBA, and milk acetone in early lactation to investigate differences between cows in susceptibility to hyperketonemia and possibilities to use test-day milk ketone bodies for genetic improvement. Blood and test-day milk samples were collected on randomly selected dairy farms in the Netherlands from cows of various parities between 5 and 60 d in milk. Plasma samples were analyzed for BHBA (reference test for hyperketonemia) and test-day milk samples were analyzed for BHBA and acetone using Fourier-transform infrared spectroscopy. The final data set consisted of plasma BHBA concentrations of 1,615 cows from 122 herds. Milk BHBA and milk acetone concentrations were determined for 1,565 cows. Genetic variation, heritability, and proportion of phenotypic variation attributable to the herd were estimated using an animal model with fixed effects for parity and season, a covariate for days in milk, and random effects for herd, animal, and error. Genetic correlations for plasma BHBA, milk BHBA, and milk acetone were estimated using bivariate analyses. The heritability estimate for plasma BHBA concentrations in early lactation was 0.17, whereas heritability estimates for milk BHBA and milk acetone were 0.16 and 0.10, respectively. This indicates that selective breeding may contribute to a lower incidence of hyperketonemia in early lactation. For the 3 traits, the proportion of variance attributable to herd was larger than the additive genetic variance, underlining the importance of on-farm feeding and management in the etiology of hyperketonemia in fresh cows. Prevention strategies for hyperketonemia can, therefore, include both feeding and management strategies at dairy farms (short-term) and genetic improvement through breeding programs (long-term). Genetic correlations between concentrations of plasma BHBA and milk BHBA (0.52) or milk acetone (0.52) were moderate. As milk ketone bodies can be routinely analyzed at test days, this may provide a practical alternative for breeding programs aimed at reducing hyperketonemia in early lactation.

Genetic variation for infection status as determined by a specific antibody response against Mycobacterium avium subspecies paratuberculosis in milk of Dutch dairy goats.

Classical control strategies based on management restrictions to reduce transmission, culling of infected goats, and vaccination have not been able to eradicate Johne's disease from infected herds. Selective breeding for less susceptibility to disease may be a useful additional tool to contribute to control of the disease. The aim of this study was to estimate genetic variation and heritability for infection status as determined by a specific antibody response against Mycobacterium avium subspecies paratuberculosis in milk of Dutch dairy goats. Milk samples from 950 goats were tested for antibodies specific to Johne's disease by ELISA on 5 consecutive test days, with a time interval of around 3 mo. Test results were coded as infected or not infected according to the instructions of the manufacturer. Heritability of infection status was estimated for 3 data sets to determine the effect of repeated sampling: only test results obtained on the first test day (first-test); the maximum test result of each animal obtained on 1 of the 5 test days (max-test); and all test results per animal, with a maximum of 5 consecutive samplings (all-test). Data sets first-test and max-test were analyzed with a sire model with fixed effects for year of birth and stage of lactation, and random effects for sire and error. For data set all-test, an additional permanent environment effect was included in the model. The estimated heritability on the underlying scale ranged from 0.12 in data set first-test, to 0.09 in data set max-test, to 0.07 in data set all-test.

Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians.

Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.

Effect of herd prevalence on heritability estimates of antibody response to Mycobacterium avium subspecies paratuberculosis.

Worldwide, classical control strategies based on hygiene and culling of infected animals have been implemented to eradicate Johne's disease. Breeding for disease resistance may be a useful additional tool to control the disease. The aim of this study was to estimate genetic parameters for the presence of a Mycobacterium avium ssp. paratuberculosis specific antibody response in milk of Dutch Holstein-Friesian cows using subsets of data based on within-herd test prevalence. The analyzed data set consisted of milk samples of 684,364 animals from 12,077 herds collected during the routine milk production scheme. Milk samples were tested for antibodies specific for Johne's disease by an ELISA test. Heritability estimates were calculated for 4 different subsets of data to determine the sensitivity of heritability for within-herd test prevalence. Results expressed as percentage of the sample to positive ratio were analyzed with a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield at test day; and random effects for sire, maternal grandsire, and error. The estimated heritability ranged from 0.031 for the complete data set to 0.097 for herds with a test prevalence of at least 10%. Cross-validation was applied to determine which of the subsets of data produced the most accurate estimated breeding values. Results showed that for genetic selection to contribute to disease control, breeding values were estimated most accurately from herds with at least 2 animals that tested positive. In this subset the heritability was 0.041.

Different Mycobacterium avium subsp. paratuberculosis MIRU-VNTR patterns coexist within cattle herds.

A better understanding of the biodiversity of Mycobacterium avium subsp. paratuberculosis (MAP) offers more insight in the epidemiology of paratuberculosis and therefore may contribute to the control of the disease. The aim of this study was to investigate the genetic diversity in bovine MAP isolates using PCR-based methods detecting genetic elements called Variable-Number Tandem Repeats (VNTRs) and Mycobacterial Interspersed Repetitive Units (MIRUs) to determine if multiple MAP strains can coexist on farms with endemic MAP infection. For 52 temporal isolates originating from infected cattle from 32 commercial dairy herds with known trading history, MIRU-VNTR analysis was applied at 10 loci of which six showed variation. Within the group of 52 isolates, 17 different MIRU-VNTR patterns were detected. One MIRU-VNTR pattern was found in 29 isolates, one pattern in four isolates, one pattern in three isolates, two times one MIRU-VNTR pattern was found occurring in two isolates, and 12 patterns were found only once. Eleven herds provided multiple isolates. In five herds a single MIRU-VNTR pattern was detected among multiple isolates whereas in six herds more than one pattern was found. This study confirms that between dairy farms as well as within dairy farms, infected animals shed MAP with different MIRU-VNTR patterns. Analysis of trading history and age within herds indicated that cows born within the same birth cohort can be infected with MAP strains exhibiting variations in the number of MIRU-VNTR repeats. These data indicate that such multiple genotypes of MAP can coexist within one herd.

Genetic and nongenetic variation in concentration of selenium, calcium, potassium, zinc, magnesium, and phosphorus in milk of Dutch Holstein-Friesian cows.

Minerals found in milk, such as Se, Ca, K, Zn, Mg, and P, contribute to several vital physiological processes. The aim of this study was to quantify the genetic variation in levels of Se, Ca, K, Zn, Mg, and P in milk and to quantify the between-herd variation in the levels of these minerals in milk. One morning milk sample from each of 1,860 Dutch Holstein-Friesian cows from 388 commercial herds in the Netherlands was used. Concentration of minerals was determined by inductively coupled plasma-atomic emission spectrometry. Variance components were estimated using an animal model with covariates for days in milk and age at first calving; fixed effects for season of calving and effect of test or proven bull; and random effects for animal, herd, and error. Heritability and proportion of phenotypic variation that can be explained by herd were estimated using univariate analysis. The intraherd heritability for Se was low (0.20) whereas herd explained 65% of the total variation in Se. Variation between herds most likely results from variation in Se content in the feed, which partly reflects variation in Se levels in the soil. Intraherd heritabilities for Ca, K, Zn, Mg, and P were moderate to high and were 0.57, 0.46, 0.41, 0.60, and 0.62, respectively. For Ca, K, Zn, Mg, and P, the proportions of phenotypic variation that could be explained by herd were low (0.13-0.24). This study shows that there are possibilities for altering the mineral composition of milk. For Ca, K, Zn, Mg, and P, there are good prospects for selective breeding whereas, for Se, measures at farm level may be more effective.