Linkage relationship among loci determining genetic variants of serum and milk proteins in cattle

Special methods allowing usage of inadequate pedigrees were employed to examine linkage among the milk protein loci alpha s1-casein, beta-casein, chi-casein and beta-lactoglobulin, and the loci for serum amylase, ceruloplasmin and transferrin. Linkage was evident between the alpha s1-casein and beta-casein loci, the alpha s1 and chi-casein loci, the beta-casein and chi-casein loci, also amylase and transferrin loci. Recombination fractions for these corresponding combinations were 0.00; 0.00; 0.00 and 0.30. Weak linkage (recombination fraction being 0.46; 0.44 and 0.42) between the beta-lactoglobulin and beta-casein loci, the amylase and ceruloplasmin loci, ceruloplasmin and transferrin loci is supposed.     

New genetic variants identified in donkey's milk whey proteins

Novel genetic variants for donkey milk lysozyme and -lactoglobulins I and II have been identified by the combined use of peptide mass mapping and sequencing by tandem mass spectrometry in association with database searching. The novel donkey lysozyme variant designated as lysozyme B (Mr 14,631 Da) differed in three amino acid exchanges, N⁴⁹ D, Y⁵² S, and S⁶¹ N, from the previously published sequence. Three novel genetic variants for donkey -lactoglobulins were identified. One of them is a type -lactoglobulin I with three amino acid exchanges at E³⁶ S, S⁹⁷ T, and V¹⁵⁰ I (-lactoglobulin I B, Mr 18,510 Da). The two others are type -lactoglobulins II with two amino acid exchanges at C¹¹⁰ P and M¹¹⁸ T (-lactoglobulin II B, Mr 18,227 Da) and with three amino acid exchanges at D⁹⁶ E, C¹¹⁰ P, and M¹¹⁸ T (-lactoglobulin II C, Mr 18,241 Da). All these primary structures are closely related to those of homologous proteins in horse milk (percent identity >96%).     

Quantitative differences between variants of A spermatogonia in man

The area of cytoplasm, nucleus, nucleolus and mitochondria, as well as the elongation and irregular outline of the nucleus were determined, on electron micrographs by using an image analyser, for Ap (pale), Ad (dark with intranuclear vacuole), Ad-like (dark without intranuclear vacuole), Ac (cloudy) and Al (long) human spermatogonia. Ap and Ac spermatogonia had larger nucleus, larger nucleolus, and more cytoplasm than did Ad, Ad-like, and Al spermatogonia. In addition, the nuclei of Ap and Ac spermatogonia were more spherical and had a more distinct outline.     

A meta-analysis on association between CSN3 gene variants and milk yield and composition in cattle

A meta-analysis on the effects of A and B alleles, the most frequent alleles of CSN3 gene, on milk yield and composition traits was conducted by pooling a large dataset consisting of 30 471 genotyped cattle. Four genetic models, comprising dominant (AA + AB vs. BB), recessive (AA vs. AB + BB), additive (AA vs. BB) and co-dominant (AA + BB vs. AB), were employed to analyze data. Standardized mean difference (SMD) was used to measure the size of the effects of A and B alleles of CSN3 on studied traits. Effect sizes of 0.2, 0.5 and 0.8 represent small, medium and large effects, respectively. The results indicate that B allele, in the form of BB genotype, has a significant, but medium effect on lactation yield under dominant (SMD = 0.259, P-value = 0.006) and additive (SMD = 0.279, P-value = 0.035) models. Moreover, a small decrease in the fat percentage occurred in cows having A allele under dominant (SMD = −0.077, P-value = 0.006) and additive (SMD = −0.106, P-value = 0.035) models. Furthermore, CSN3 variants significantly but slightly affect protein percentage under dominant (SMD = −0.146, P-value = 0.000), recessive (SMD = −0.077, P-value = 0.000) and additive (SMD = −0.219, P-value = 0.000) models, showing the negative effect of A allele on this trait. Meta-analysis results reveal that daily milk yield is slightly affected by CSN3 variants under recessive (SMD = 0.056, P-value = 0.033) and additive (SMD = 0.061, P-value = 0.013) genetic models. There is no effect of CSN3 variants on either protein or fat yield. In addition, the effects of CSN3 variants on milk-related traits were not observed under the co-dominant model. Sensitivity and publication bias analyses were carried out to confirm the stability of meta-analyses results.     

Quantitative genetic differences between populations of Drosophila melanogaster from diverse geographic origins

Crosses were made between each seven populations of Drosophila melanogaster-three of which were laboratory populations and four were recently captured populations-and a line previously selected for low sternopleural bristle number for many generations. In each of six replicate lines from each cross, selection was practised for low sternopleural bristle number; subsequently these replicates were intercrossed and reselected. Introduction of new genetic material from four populations into the selected line was achieved, indicating the presence in these populations of particular alleles which are absent from or rare in the base populations of the selected line. Introduction of new genetic material from three populations into the selected line was not achieved. Consequently, it was possible to establish two groups of populations. In each group, the populations appear to be segregating for essentially the same alleles. Differences in gene frequency rather than the presence or absence of particular alleles are mainly responsible for the differences observed between the populations.In all, 11 populations screened for genetic differences controlling sternopleural bristle number. There are widespread genetic similarities among populations of very different geographic origin. Laboratory populations as a group are not more homogeneous than recently collected populations, although the latter are genetically more variable. Drift alone could account for the reduction of variability in the laboratory populations.     

Detection of genetic variants affecting cattle behaviour and their impact on milk production: a genome‐wide association study

Behaviour traits of cattle have been reported to affect important production traits, such as meat quality and milk performance as well as reproduction and health. Genetic predisposition is, together with environmental stimuli, undoubtedly involved in the development of behaviour phenotypes. Underlying molecular mechanisms affecting behaviour in general and behaviour and productions traits in particular still have to be studied in detail. Therefore, we performed a genome‐wide association study in an F₂ Charolais × German Holstein cross‐breed population to identify genetic variants that affect behaviour‐related traits assessed in an open‐field and novel‐object test and analysed their putative impact on milk performance. Of 37 201 tested single nucleotide polymorphism (SNPs), four showed a genome‐wide and 37 a chromosome‐wide significant association with behaviour traits assessed in both tests. Nine of the SNPs that were associated with behaviour traits likewise showed a nominal significant association with milk performance traits. On chromosomes 14 and 29, six SNPs were identified to be associated with exploratory behaviour and inactivity during the novel‐object test as well as with milk yield traits. Least squares means for behaviour and milk performance traits for these SNPs revealed that genotypes associated with higher inactivity and less exploratory behaviour promote higher milk yields. Whether these results are due to molecular mechanisms simultaneously affecting behaviour and milk performance or due to a behaviour predisposition, which causes indirect effects on milk performance by influencing individual reactivity, needs further investigation.     

Tertiary and quaternary structural differences between two genetic variants of bovine casein by small-angle X-ray scattering

The casein complexes of bovine milk consist of four major protein fractions, alpha s1, alpha s2, beta, and kappa. Colloidal particles of casein (termed micelles) contain inorganic calcium and phosphate; they are very roughly spherical with an average radius of 650 A. Removal of Ca2+ leads to the formation of smaller protein aggregates (submicelles) with an average radius of 94 A. Two genetic variants, A and B, of the predominant fraction, alpha s1-casein, result in milks with markedly different physical properties, such as solubility and heat stability. To investigate the molecular basis for these differences, small-angle X-ray scattering was performed on the respective colloidal micelles and submicelles. Scattering curves for submicelles of both variants showed multiple Gaussian character; data for the B variant were previously interpreted in terms of two concentric regions of different electron density, i.e., a "compact" core and a relatively "loose" shell. For the submicelle of A, there was a third Gaussian, reflecting a negative contribution due to interparticle interference. Molecular parameters for submicelles of both A and B are in agreement with hydrodynamic data in the literature. Data for the micelles, for which scattering yields cross-sectional information, were fitted by a sum of three Gaussians for both variants; for these, the corresponding two lower radii of gyration represent the two concentric regions of the submicelles, while the third reflects the average packing of submicelles within the micellar cross section. Most of the molecular parameters obtained showed small but consistent differences between A and B, but for submicelles within the micelle several differences were particularly notable: A has a greater molecular weight for the "compact" region of the constituent submicelle (82,000 vs 60,000) and a much greater submicellar packing number (6:1 vs 3:1). Reasons for these and other differences are to be sought in sequence differences and in differences in calcium-binding sites and charge distribution.     

Haemoglobin variants in cattle

From a comparative survey of reports on cattle Hb variants it is concluded that prior to the present communication the occurrence of at least seven different adult Hb molecules have been reported.
In addition comes the finding of a new Hb variant called HbG which is reported in this study. This was found in three animals among 101 East African Zebu cattle. It migrated more slowly than any cattle Hb variant previously reported and made up 20% of total Hb.
The gene frequencies of the East African Zebu population were: Hb^A = 0.52, Hb^B = 0.32, Hb^c = 0.14 and Hb^G = 0.01.     

Identification of allele variants of cattle milk productivity genes using PCR anti-primer method

In this work we have demonstrated two independent real-time PCR methods for detection single nucleotide polymorphism (SNP) of genes csn and acyl-CoA: diacylglycerol acyltransferase 1 (dgat) in cattle. We have analyzed 296 samples of milk production cattle of Ukrainian breeding. The genotype frequencies were AA--0.58, AB--0.34, BB--0.08 for csn gene and for dgat gene--AA--0.7, AK--0.26, KK--0.04. High efficiency of so called "anti-primer" method was shown. Duration of anti-primer PCR reaction was about 2-2.5 hours only and provided full investigation of unknown gene allele.     

Expected early genetic gain from selection for milk yield in dairy cattle

Summary A matrix program to predict short term genetic gain from single trait selection for milk yield was developed. Rate of genetic gain was calculated as the annual change in the mean breeding value of all producing females. Several parameters sets representing various selection policies were used to examine situations pertinent to dairy populations of the United States. Approach to the asymptotic rates of genetic gain within the model varied with the choice of parameters, but even with consistent selection policies, predicted total genetic gain in the first 10 years was only half of the expected from classical theory. Considerable year to year variation in the rate of gain occurred. Early gains were more dependent on female selection decisions than gains during the steady state. In a two-phase model, the approach to the linear rate of gain in the second phase was accelerated by starting with an ongoing improvement program, but considerable delays still existed. Selection for sex- limited traits such as milk yield, which require pedigree selection and a waiting time for progeny test results reached asymptotic rates more slowly than previously assumed.     

Procedure for simultaneous phenotyping of genetic variants in cow's milk by isoelectric focusing

A method is described which allows the simultaneous separation of all polymorphic protein fractions in cow's milk in one single run. The separation could be achieved by isoelectric focusing in ultrathin-layer polyacrylamide gels. The method is especially suitable for screening purposes because it combines low costs, high resolution and short separation time.     

Functional differences between TRPC4 splice variants.

Functional characterizations of heterologously expressed TRPC4 have revealed diverse regulatory mechanisms and permeation properties. We aimed to clarify whether these differences result from different species and splice variants used for heterologous expression. Like the murine beta splice variant, rat and human TRPC4beta both formed receptor-regulated cation channels when expressed in HEK293 cells. In contrast, human TRPC4alpha was poorly activated by stimulation of an H(1) histamine receptor. This was not due to reduced expression or plasma membrane targeting, because fluorescent TRPC4alpha fusion proteins were correctly inserted in the plasma membrane. Furthermore, currents through both human TRPC4alpha and TRPC4beta had similar current-voltage relationships and single channel conductances. To analyze the assembly of transient receptor potential channel subunits in functional pore complexes in living cells, a fluorescence resonance energy transfer (FRET) approach was used. TRPC4alpha and TRPC4beta homomultimers exhibited robust FRET signals. Furthermore, coexpressed TRPC4alpha and TRPC4beta subunits formed heteromultimers exhibiting comparable FRET signals. To promote variable heteromultimer assemblies, TRPC4alpha/TRPC4beta were coexpressed at different molar ratios. TRPC4beta was inhibited in the presence of TRPC4alpha with a cooperativity higher than 2, indicating a dominant negative effect of TRPC4alpha subunits in heteromultimeric TRPC4 channel complexes. Finally, C-terminal truncation of human TRPC4alpha fully restored the channel activity. Thus, TRPC4beta subunits form a receptor-dependently regulated homomultimeric channel across various species, whereas TRPC4alpha contains a C-terminal autoinhibitory domain that may require additional regulatory mechanisms.     

Procedure for simultaneous phenotyping of genetic variants in cow's milk by isoelectric focusing*

A method is described which allows the simultaneous separation of all polymorphic protein fractions in cow's milk in one single run. The separation could be achieved by isoelectric focusing in ultrathin-layer polyacrylamide gels. The method is especially suitable for screening purposes because it combines low costs, high resolution and short separation time.     

Identification of allele variants of cattle milk productivity genes using PCR and the anti-primer method

In this study, we present two independent approaches in using Real-Time PCR for the detection of single nucleotide polymorphism (SNP) in genes encoding a kappa-casein and an acyl CoA: diacylglycerol acyltransferase 1 (DGAT 1) in cattle. The samples from 296 Ukrainian-bred dairy cows were analyzed. The genotype frequencies for the kappa-casein gene were as follows: AA, 0.58; AB, 0.34; and BB, 0.08; the frequencies for the acyl-CoA: diacylglycerol acyltransferase 1 gene were as follows: AA, 0.7; AK, 0.26; and KK, 0.04. The high efficiency of the anti-primer method was shown. The anti-primer Real-Time PCR test takes only 2–2.5 h and allows for the complete identification of the unknown allelic variant of the studied genes.     

Genetic differences in milk proteins among laboratory rats (Rattus norvegicus)

Genetic differences in the electrophoretic pattern of milk proteins were observed among different inbred rat strains. The results of segregation analysis made on a limited number of females is consistent with the hypothesis of two codominant autosomal alleles system.     

Key genetic variants associated with variation of milk oligosaccharides from diverse human populations

Human milk oligosaccharides (HMO), the third most abundant component of human milk, are thought to be important contributors to infant health. Studies have provided evidence that geography, stage of lactation, and Lewis and secretor blood groups are associated with HMO profile. However, little is known about how variation across the genome may influence HMO composition among women in various populations. In this study, we performed genome-wide association analyses of 395 women from 8 countries to identify genetic regions associated with 19 different HMO. Our data support FUT2 as the most significantly associated (P < 4.23⁻⁹ to P < 4.5⁻⁷⁰) gene with seven HMO and provide evidence of balancing selection for FUT2. Although polymorphisms in FUT3 were also associated with variation in lacto-N-fucopentaose II and difucosyllacto-N-tetrose, we found little evidence of selection on FUT3. To our knowledge, this is the first report of the use of genome-wide association analyses on HMO.