Summer mortality is a phenomenon severely affecting the aquaculture production of the Pacific oyster (Crassostrea gigas). Although its causal factors are complex, resistance to mortality has been ...described as a highly heritable trait, and several pathogens including the virus Ostreid Herpes virus type 1 (OsHV-1) have been associated with this phenomenon. A QTL analysis for survival of summer mortality and OsHV-1 load, estimated using real-time PCR, was performed using five F₂ full-sib families resulting from a divergent selection experiment for resistance to summer mortality. A consensus linkage map was built using 29 SNPs and 51 microsatellite markers. Five significant QTL were identified and assigned to linkage groups V, VI, VII and IX. Analysis of single full-sib families revealed differential QTL segregation between families. QTL for the two-recorded traits presented very similar locations, highlighting the interest of further study of their respective genetic controls. These QTL show substantial genetic variation in resistance to summer mortality, and present new opportunities for selection for resistance to OsHV-1.
The rennet-induced coagulation ability of milk is important in cheese production. For Swedish Red Dairy Cattle (RDC), this ability is reduced because of a high prevalence of noncoagulating (NC) milk. ...In this study, we simultaneously combined genetic parameters for NC milk, milk coagulation properties, milk composition, physical traits, and milk protein composition. Our aim was to estimate heritability and genetic and phenotypic correlations for NC milk and 24 traits (milk coagulation properties, milk composition, physical traits, and milk protein composition). Phenotypes and ∼7,000 SNP genotypes were available for all 600 Swedish RDC. The genotypes were imputed from ∼7,000 SNP to 50,000 SNP. Variance components and genetic parameters were estimated with an animal model. In Swedish RDC, a moderate heritability estimate of 0.28 was found for NC milk. For the other 24 traits, heritability estimates ranged from 0.12 to 0.77 (standard errors from 0.08 to 0.18). A total of 300 phenotypic and genetic correlations were estimated. For phenotypic and genetic correlations, 172 and 95 were significant, respectively. In general, most traits showing significant genetic correlations also showed significant phenotypic correlations. In this study, phenotypic and genetic correlations with NC milk suggest that many correlations between traits exist, making it difficult to predict the real consequences on the composition of milk, if selective breeding is applied on NC milk. We speculate that some of these consequences may lead to changes in the composition of milk, most likely affecting its physical and organoleptic properties. However, our results suggest that κ-casein could be used as an indicator trait to predict the occurrence of NC milk at the herd level.
Genomic selection has been widely implemented in national and international genetic evaluation in the dairy cattle industry, because of its potential advantages over traditional selection methods and ...the availability of commercial high-density (HD) single nucleotide polymorphism (SNP) panels. However, this method may not be cost-effective for cow selection and for other livestock species, because the cost of HD SNP panels is still relatively high. One possible solution that can enable other species to benefit from this promising method is genomic selection with low-density (LD) SNP panels. In this simulation study, LD SNP panels designed with different strategies and different SNP densities were compared. The effects of number of quantitative trait loci, heritability, and effective population size were evaluated in the framework of genomic selection with LD SNP panels. Methodologies of Bayesian variable selection; BLUP with a trait-specific, marker-derived relationship matrix; and BLUP with a realized relationship matrix were employed to predict genomic estimated breeding values with both HD and LD SNP panels. Up to 95% of accuracy obtained by using an HD panel can be obtained by using only a small proportion of markers. The LD panel with markers selected on the basis of their effects always performs better than the LD panel with evenly spaced markers. Both the genetic architecture of the trait and the effective population size have a significant effect on the performance of the LD panels. We concluded that, to implement genomic selection with LD panels, a training population of sufficient size and genotyped with an HD panel is necessary. The trade-off between the LD panels with evenly spaced markers and selected markers must be considered, which depends on the number of target traits in a breeding program and the genetic architecture of these traits. Genomic selection with LD panels could be feasible and cost-effective, though before implementation, a further detailed genetic and economic analysis is recommended.
The intestinal influx oligopeptide transporter peptide transporter 1 (PEPT1) (SLC15A1) is best known for nutrient-derived di- and tripeptide transport. Its role in drug absorption is increasingly ...recognized. To better understand the disposition of PEPT1 substrate drugs in young infants, we studied intestinal PEPT1 mRNA expression and tissue localization across the pediatric age range. PEPT1 mRNA expression was determined using real-time reverse-transcription polymerase chain reaction in small intestinal tissues collected from surgical procedures (neonates and infants) or biopsies (older children and adolescents). PEPT1 mRNA relative to villin mRNA expression was compared between neonates/infants and older children/adolescents. PEPT1 was visualized in infant tissue using immunohistochemical staining. Other transporters multidrug resistance protein 1 (MDR1), multidrug resistance-like protein 2 (MRP2), and organic anion transporter polypeptide 2B1 (OATP2B1) were also stained to describe the localization in relation to PEPT1. Twenty-six intestinal samples (n = 20 neonates/infants, n = 2 pediatric, n = 4 adolescents) were analyzed. The young infant samples were collected at a median (range) gestational age at birth of 29.2 weeks (24.7-40) and postnatal age of 2.4 weeks (0-16.6). The PEPT1 mRNA expression of the neonates/infants was only marginally lower (0.8-fold) than the older children (P < 0.05). Similar and clear apical PEPT1 and MRP2 staining, apical and lateral MDR1 staining, and intraepithelial OATP2B1 staining at the basolateral membrane of the enterocyte were detected in 12 infant and 2 adolescent samples. Although small intestinal PEPT1 expression tended to be lower in neonates than in older children, this difference is small and tissue distribution is similar. This finding suggests similar oral absorption of PEPT1 substrates across the pediatric age range.
In across-country genomic predictions for dairy cattle, 2 kinds of bull information can be used as dependent variables. The first is estimated breeding value (EBV) from the national genetic ...evaluations, assuming genetic correlations between countries are less than 1. The second is EBV from multitrait across-countries evaluation (MACE), assuming genetic correlations between countries equal 1. In the present study, the level of bias and reliability of a cross-countries genomic prediction using national EBV or MACE EBV as the dependent variable were investigated. Data from Brown Swiss Organizations joining the InterGenomics Service by Interbull Centre (Uppsala, Sweden) were used. National and MACE EBV of 3 traits (protein yield, cow conception rate, and calving interval) from 7, 5, and 4 countries, respectively, were used, resulting in 16 trait-country combinations. Genotypes for 45,473 SNP markers and deregressed (national or MACE) EBV of 7,490; 5,833; and 5,177 bulls were used in analysis of protein yield, cow conception rate, and calving interval, respectively. For most of trait-country combinations, the use of MACE EBV via single-trait approach resulted in less biased and more reliable across-countries genomic predictions. In case some of the MACE EBV might have been inflated, the resulting single-trait genomic predictions were inflated as well. For these specific cases, the use of national EBV via multitrait approach provided less bias and more reliable across-countries genomic predictions.
Endocrine fertility traits, which are defined from progesterone concentration levels in milk, are interesting indicators of dairy cow fertility because they more directly reflect the cows own ...reproductive physiology than classical fertility traits, which are more biased by farm management decisions. The aim of this study was to detect quantitative trait loci (QTL) for 7 endocrine fertility traits in dairy cows by performing a genome-wide association study with 85k single nucleotide polymorphisms (SNP), and then fine-map targeted QTL regions, using imputed sequence variants. Two classical fertility traits were also analyzed for QTL with 85k SNP. The association between a SNP and a phenotype was assessed by single-locus regression for each SNP, using a linear mixed model that included a random polygenic effect. A total of 2,447 Holstein Friesian cows with 5,339 lactations with both phenotypes and genotypes were used for association analysis. Heritability estimates ranged from 0.09 to 0.15 for endocrine fertility traits and 0.03 to 0.10 for classical fertility traits. The genome-wide association study identified 17 QTL regions for endocrine fertility traits on Bos taurus autosomes (BTA) 2, 3, 8, 12, 15, 17, 23, and 25. The highest number (5) of QTL regions from the genome-wide association study was identified for the endocrine trait “proportion of samples with luteal activity.” Overlapping QTL regions were found between endocrine traits on BTA 2, 3, and 17. For the classical trait calving to first service, 3 QTL regions were identified on BTA 3, 15, and 23, and an overlapping region was identified on BTA 23 with endocrine traits. Fine-mapping target regions for the endocrine traits on BTA 2 and 3 using imputed sequence variants confirmed the QTL from the genome-wide association study, and identified several associated variants that can contribute to an index of markers for genetic improvement of fertility. Several potential candidate genes underlying endocrine fertility traits were also identified in the target regions and are discussed. However, due to high linkage disequilibrium, it was not possible to specify genes or polymorphisms as causal factors for any of the regions.
Summary
In pig breeding, as the final product is a cross bred (CB) animal, the goal is to increase the CB performance. This goal requires different strategies for the implementation of genomic ...selection from what is currently implemented in, for example dairy cattle breeding. A good strategy is to estimate marker effects on the basis of CB performance and subsequently use them to select pure bred (PB) breeding animals. The objective of our study was to assess empirically the predictive ability (accuracy) of direct genomic values of PB for CB performance across two traits using CB and PB genomic and phenotypic data. We studied three scenarios in which genetic merit was predicted within each population, and four scenarios where PB genetic merit for CB performance was predicted based on either CB or a PB training data. Accuracy of prediction of PB genetic merit for CB performance based on CB training data ranged from 0.23 to 0.27 for gestation length (GLE), whereas it ranged from 0.11 to 0.22 for total number of piglets born (TNB). When based on PB training data, it ranged from 0.35 to 0.55 for GLE and from 0.30 to 0.40 for TNB. Our results showed that it is possible to predict PB genetic merit for CB performance using CB training data, but predictive ability was lower than training using PB training data. This result is mainly due to the structure of our data, which had small‐to‐moderate size of the CB training data set, low relationship between the CB training and the PB validation populations, and a high genetic correlation (0.94 for GLE and 0.90 for TNB) between the studied traits in PB and CB individuals, thus favouring selection on the basis of PB data.
OBJECTIVE—The presence of kinase-insert domain-containing receptor (KDR) on circulating CD34 cells is assumed to be indicative for the potential of these cells to support vascular maintenance and ...repair. However, in bone marrow and in granulocyte colony-stimulating factor (G-CSF)-mobilized peripheral blood, less than 0.5% of CD34 cells co-express KDR. Therefore, we studied whether CD34/KDR cells are generated in the peripheral circulation.
METHODS AND RESULTS—Using an ex vivo flow model, we show that activated platelets enable CD34 cells to home to sites of vascular injury and that upon immobilization, KDR is translocated from an endosomal compartment to the cell-surface within 15 minutes. In patients with diabetes mellitus type 2, the percentage of circulating CD34 co-expressing KDR was significantly elevated compared to age-matched controls. When treated with aspirin, the patients showed a 49% reduction in the generation of CD34/KDR cells, indicating that the level of circulating CD34/KDR cells also relates to in vivo platelet activation.
CONCLUSION—Circulating CD34/KDR are not mobilized from bone marrow as a predestined endothelial progenitor cell population but are mostly generated from circulating multipotent CD34 cells at sites of vascular injury. Therefore, the number of circulating CD34/KDR cells may serve as a marker for vascular injury.
Bull fertility is an important trait in breeding as the semen of one bull can, potentially, be used to perform thousands of inseminations. The high number of inseminations needed to obtain reliable ...measures from Non-Return Rates to oestrus creates difficulties in assessing fertility accurately. Improving molecular knowledge of seminal properties may provide ways to facilitate selection of bulls with good semen quality. In this study, liquid chromatography mass spectrometry (LC-MS/MS) was used to analyze the protein content from the seminal plasma of 20 bulls with Non-Return Rates between 35 and 60%, sampled across three seasons. Overall, 1343 proteins were identified and proteins with consistent correlation to fertility across multiple seasons found. From these, nine protein groups had a significant Pearson correlation (p < 0.1) with fertility in all three seasons and 34 protein groups had a similar correlation in at least two seasons. Among notable proteins showing a high and consistent correlation across seasons were Osteopontin, a lipase (LIPA) and N-acetylglucosamine-1phosphotransferase subunit gamma. Three proteins were combined in a multiple linear regression to predict fertility (r = 0.81). These sets of proteins represent potential markers, which could be used by the breeding industry to phenotype bull fertility.
The ability of bull spermatozoa to fertilize oocytes is crucial for breeding efficiency. However, the reliability of this trait from field measures is relatively low and the prediction of fertility given by conventional methods to evaluate sperm quality is currently not very accurate. In this work, we identify sets of proteins in bull seminal plasma from repeated samples collected at different times of the year that correlate to fertility in a consistent way. We combined these individual proteins to build a molecular signature predictive of fertility. This study provides an overview of proteins linked to fertility in seminal plasma, thereby increasing knowledge of the bull seminal plasma proteome. Protein signatures from the latter, potentially related to fertility, may be of use to predict fertility for individual bulls.
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•Deep proteomic profiling was done on bull seminal plasma samples.•Proteins with consistent correlation with fertility across seasons were found.•Top candidates were A5D7U1, A6H713 and M5FJT7.•A molecular signature predictive of fertility was established.
Milk that does not coagulate after rennet addition, also called noncoagulating (NC) milk, is unwanted in cheese production due to prolonged processing time. Amounts of whey and casein proteins, ...genetic variants, as well as posttranslational modifications (PTM) of proteins are all contributing factors in rennet-induced coagulation of milk. In this study, we conducted a wide-ranging investigation of milk proteins in milk samples from 616 Swedish Red dairy cattle using liquid chromatography-high resolution mass spectrometry. Relative concentration of proteins, genetic variants, and PTM were compared between NC milk and coagulating milk. The PTM investigated were phosphorylation of caseins and glycosylation of κ-casein. Several genetic variants and PTM were found, including rare phosphorylation variants of the αS-caseins. Genetic variants were found to effect the expressed amount of different proteins. Further, the effect of protein amounts and PTM on a binary NC milk trait was modeled using a generalized linear model. The model showed that NC milk significantly correlated with higher relative concentrations of α-lactalbumin and β-casein and lower relative concentrations of β-lactoglobulin and κ-casein. Regarding PTM of caseins, an effect on NC milk from a lower relative concentration of αS1-casein with 8 phosphate groups were found, even though an effect from total relative concentration of αS1-casein was not found. This study has provided insights into protein variants and PTM important for NC milk to improve this undesirable property.
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