Casein haplotypes and their association with milk production traits in the Finnish Ayrshire cattle

A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle

In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.

Effects of protein genetic variants on their phosphorylation levels, milk composition, milk proteome, and milk coagulation ability in Chinese Holstein bovine milk

Milk samples were collected from 3625 Chinese Holstein cows to assess the effects of κ-casein (κ-CN) and β-lactoglobulin (β-LG) genetic variants on its milk coagulation properties. The results show that Chinese Holstein cows have a higher frequency of the κ-CN AA and AB variants, and β-LG of the AB and AA variants. Of these, κ-CN B variants, the β-LG AA and BB variants were more frequent in milk showing good coagulation. The effects of the genetic variants on milk composition, milk proteome, and protein phosphorylation sites were studied. The results showed that higher concentrations of protein and dry matter were found in κ-CN BE variant. Moreover, large variations in milk proteome among different κ-CN and β-LG variants were observed. Highly phosphorylated for κ-CN, especially Ser97, was observed in cows with the κ-CN BE variant, but no effect of β-LG variants on phosphorylation site was found. Of the various factors examined, variation of κ-CN phosphorylation sites Ser97 may be the most important in affecting casein structure and milk coagulation ability. Some milk protein contents were found to be negative factors for milk coagulation. In summary, this study showed that κ-CN genetic variants contained different milk compositions and phosphorylation site Ser97 influenced milk coagulation.

Milking It for All It's Worth: The Effects of Environmental Enrichment on Maternal Nurturance, Lactation Quality, and Offspring Social Behavior

Breastfeeding confers robust benefits to offspring development in terms of growth, immunity, and neurophysiology. Similarly, improving environmental complexity, i.e., environmental enrichment (EE), contributes developmental advantages to both humans and laboratory animal models. However, the impact of environmental context on maternal care and milk quality has not been thoroughly evaluated, nor are the biological underpinnings of EE on offspring development understood. Here, Sprague Dawley rats were housed and bred in either EE or standard-housed (SD) conditions. EE dams gave birth to a larger number of pups, and litters were standardized and cross-fostered across groups on postnatal day (P)1. Maternal milk samples were then collected on P1 (transitional milk phase) and P10 (mature milk phase) for analysis. While EE dams spent less time nursing, postnatal enrichment exposure was associated with heavier offspring bodyweights. Milk from EE mothers had increased triglyceride levels, a greater microbiome diversity, and a significantly higher abundance of bacterial families related to bodyweight and energy metabolism. These differences reflected comparable transcriptomic changes at the genome-wide level. In addition to changes in lactational quality, we observed elevated levels of cannabinoid receptor 1 in the hypothalamus of EE dams, and sex-dependent and time-dependent effects of EE on offspring social behavior. Together, these results underscore the multidimensional impact of the combined neonatal and maternal environments on offspring development and maternal health. Moreover, they highlight potential deficiencies in the use of "gold standard" laboratory housing in the attempt to design translationally relevant animal models in biomedical research.

Effect of Protein Genotypes on Physicochemical Properties and Protein Functionality of Bovine Milk: A Review

Milk protein comprises caseins (CNs) and whey proteins, each of which has different genetic variants. Several studies have reported the frequencies of these genetic variants and the effects of variants on milk physicochemical properties and functionality. For example, the C variant and the BC haplotype of αS1-casein (αS1-CN), β-casein (β-CN) B and A1 variants, and κ-casein (κ-CN) B variant, are favourable for rennet coagulation, as well as the B variant of β-lactoglobulin (β-lg). κ-CN is reported to be the only protein influencing acid gel formation, with the AA variant contributing to a firmer acid curd. For heat stability, κ-CN B variant improves the heat resistance of milk at natural pH, and the order of heat stability between phenotypes is BB > AB > AA. The A2 variant of β-CN is more efficient in emulsion formation, but the emulsion stability is lower than the A1 and B variants. Foaming properties of milk with β-lg variant B are better than A, but the differences between β-CN A1 and A2 variants are controversial. Genetic variants of milk proteins also influence milk yield, composition, quality and processability; thus, study of such relationships offers guidance for the selection of targeted genetic variants.

Beta-Casein Gene Polymorphism in Serbian Holstein-Friesian Cows and Its Relationship with Milk Production Traits

The most common types of beta-casein in cow’s milk are A1 and A2, which differ in one amino acid. During the gastrointestinal proteolysis of A1 beta-casein in humans this difference results in the release of beta-casomorphin-7, an opioid which may lead to severe effects on human health, causing various ailments (type-1 diabetes mellitus, ischemic heart disease, arteriosclerosis, sudden infant death syndrome, autism, schizophrenia, gastrointestinal digestive discomfort, as well as increased gastrointestinal transit time). By contrast, A2 beta-casein cannot exert these effects owing to its different composition and metabolism. Furthermore, studies have shown that it can influence milk productivity traits. Our research aimed to screen the frequency of A1 and A2 alleles of beta-casein gene in a population of Serbian Holstein-Friesian cows and to detect how the genotypes influence milk production, and milk protein and fat yields. Out of 106 animals, 13 (12.26%) were of A1A1 genotype, 58 (54.72%) of A1A2, and 35 (33.02%) of A2A2 genotype. Milk yield was significantly (P<0.01) higher in A2A2 compared to both A1A1 and A1A2 genotypes. Milk protein concentrations were significantly (P<0.01) higher in A2A2 compared to A1A2 genotype, while milk fat concentrations were significantly (P<0.01) higher in A2A2 compared to both A1A1 and A1A2 genotypes.

Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits

Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.

DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN)

Casein proteins were repeatedly examined for protein polymorphisms and frequencies in diverse cattle breeds. The occurrence of casein variants in Holstein Friesian, the leading dairy breed worldwide, is well known. The frequencies of different casein variants in Holstein are likely affected by selection for high milk yield. Compared to Holstein, only little is known about casein variants and their frequencies in German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind,” DSN). The DSN population was a main genetic contributor to the current high-yielding Holstein population. The goal of this study was to investigate casein (protein) variants and casein haplotypes in DSN based on the DNA sequence level and to compare these with data from Holstein and other breeds. In the investigated DSN population, we found no variation in the alpha-casein genes CSN1S1 and CSN1S2 and detected only the CSN1S1*B and CSN1S2*A protein variants. For CSN2 and CSN3 genes, non-synonymous single nucleotide polymorphisms leading to three different β and κ protein variants were found, respectively. For β-casein protein variants A¹, A², and I were detected, with CSN2*A¹ (82.7%) showing the highest frequency. For κ-casein protein variants A, B, and E were detected in DSN, with the highest frequency of CSN3*A (83.3%). Accordingly, the casein protein haplotype CSN1S1*B-CSN2*A¹-CSN1S2*A-CSN3*A (order of genes on BTA6) is the most frequent haplotype in DSN cattle.

Options for genetic improvement of milk composition

Genetic improvement is constrained by the long-term and cumulate nature of genetic improvement, by the economic rewards for making genetic change and by the variances and covariances among traits of interest. Genetic change is cumulate, so that small annual changes make substantial differences over time. This cumulate nature of genetic improvement dictates the importance of identifying long-term goals driven by robust economic signals and then adhering to them. The economic rewards for genetic improvement will ultimately determine the uptake and therefore the success of any breeding program. In developed countries the value of milk can be divided between the weight of water, fat and protein produced. Water generally has a negative value due the cost of handling, removal and disposal. Fat and protein have varying values depending on the market, but both will always have underlying positive values. Genetic variances and covariances among the aggregate composition traits, water, fat and protein, are such that simultaneous increase in the yield of all three is considerably easier than improvement of just one, or improvement of one while decreasing others. Selection for simultaneous increase of fat and protein percentage will also be successful, but at the price of not increasing fat and protein yield nearly as rapidly as when selecting directly on yield traits. In virtually all developed countries, the optimum selection goal will be for some combination of increased fat and protein yield that may lead to a gradual increase in the protein to fat ratio. Genetic polymorphisms in several protein genes have been associated with yield and with milk processing properties, but are unlikely to play more than a minor role in overall selection. There is some evidence of genetic variation in milk fat composition, but the level of variation and economic incentives for change mean that selection for milk fat composition is not worthwhile. Thus, with the exception of very slow changes in the water to fat to protein yield ratio, genetic improvement does not seem a particularly suitable route for altering milk composition.

The influence of casein haplotype on quality, coagulation, and yield traits of milk from Italian Holstein cows

The aim of this work was to investigate the effect of casein haplotype (CSN1S1, CSN2, and CSN3) on quality, coagulation, and yield traits of milk from Italian Holstein cows. The casein haplotype was determined by isoelectric focusing; milk clotting properties were determined by using a mechanical lacto-dynamographic instrument; and the yields of pressed and pasta filata cheeses were expressed as kilograms of cheese per 100kg of milk processed. Statistical analysis showed a significant effect of the casein haplotype. In particular, BB-A(1)A(1)-AA milk showed the highest fat content (4.01g/100g), whereas BB-A(2)A(2)-BB milk had a higher protein content, the best coagulation characteristics, and the highest yields in pressed and pasta filata cheeses, and, consequently, better ability to retain fat and protein in the curd. The results of this study suggest that knowledge of milk protein polymorphisms not only allows the production of milk with specific qualitative and quantitative characteristics, but it could also be used as a specific marker within a breed to identify milk suitable for cheesemaking, which confers an economical advantage for dairy producers.

Comparative screening of single nucleotide polymorphisms in β-casein and κ-casein gene in different livestock breeds of India

The most polymorphic milk protein gene is β-casein; 13 protein variants are known in cattle. Milk protein genetic polymorphism has received considerable research interest in recent years because of possible associations between milk protein and economically important traits in livestock. The present study was undertaken to explore the genetic polymorphisms in exon 7 of β-casein and exon 4 of κ-casein genes in Arunachali yaks (Bos grunniens), Sahiwal (Bos indicus) cattle, malpura sheep (Ovis aries) and Gaddi goat (Capra hircus). Results of the study revealed presence of 11 SNP variants in all livestock species. Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus. These variations are found to be synonymous in nature as these variations do not result in their corresponding amino acids. A total of five polymorphic sites have been described at the κ-casein (CSN3) locus in the Indian domestic Gaddi goat (Capra hircus) when compared with exotic goat (X60763) while sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637). These results highlight the importance of taking into consideration the CSN3 SNPs when performing selection for milk composition in dairy livestock breeds.

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This is first comparative sequence analysis of Beta casein and kappa casein genes in different livestock breeds of India.

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Total 11 SNPs variants were found in all livestock species studied, namely, Bos indicus, Bos grunniens, Ovis aries and Capra hircus.

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Four SNPs were observed in Bos indicus; two SNPs in Bos grunniens; three SNPs in Ovis aries and three SNPs in Capra hircus.

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Homology of 99% with Bos taurus and Bos indicus, 97% with Bubalus bubaline, 99% with Bos grunniens, 95% with Ovis aries, 95% with Capra hircus.

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Sequence analysis of κ-casein gene in sheep showed three novel nucleotide changes in malpura sheep when compared with the exotic sheep (AY237637).

Go with the flow-biology and genetics of the lactation cycle

Lactation is a dynamic process, which evolved to meet dietary demands of growing offspring. At the same time, the mother's metabolism changes to meet the high requirements of nutrient supply to the offspring. Through strong artificial selection, the strain of milk production on dairy cows is often associated with impaired health and fertility. This led to the incorporation of functional traits into breeding aims to counteract this negative association. Potentially, distributing the total quantity of milk per lactation cycle more equally over time could reduce the peak of physiological strain and improve health and fertility. During lactation many factors affect the production of milk: food intake; digestion, absorption, and transportation of nutrients; blood glucose levels; activity of cells in the mammary gland, liver, and adipose tissue; synthesis of proteins and fat in the secretory cells; and the metabolic and regulatory pathways that provide fatty acids, amino acids, and carbohydrates. Whilst the endocrine regulation and physiology of the dynamic process of milk production seems to be understood, the genetics that underlie these dynamics are still to be uncovered. Modeling of longitudinal traits and estimating the change in additive genetic variation over time has shown that the genetic contribution to the expression of a trait depends on the considered time-point. Such time-dependent studies could contribute to the discovery of missing heritability. Only very few studies have estimated exact gene and marker effects at different time-points during lactation. The most prominent gene affecting milk yield and milk fat, DGAT1, exhibits its main effects after peak production, whilst the casein genes have larger effects in early lactation. Understanding the physiological dynamics and elucidating the time-dependent genetic effects behind dynamically expressed traits will contribute to selection decisions to further improve productive and healthy breeding populations.

Construction of Foot-and-mouth disease virus 2A-based bicistronic expression vector and coexpression of two genes in goat mammary epithelial cells

Using animal mammary glands as bioreactors for producing commercially important proteins is a cutting-edge direction in the field of biotechnology development and application. Dairy goats are an important dairy livestock, with roughage-resistance, fast propagation, long lactation periods and high milk production per bodyweight; these characteristics make dairy goats ideal for use as mammary gland bioreactors. Foot-and-mouth disease virus 2A (FMDV 2A) is an efficient viral cleavage element that mediates proteolytic cleavage independent of the presence of other FMDV sequences. It is often incorporated into recombinant vectors to generate cleavage in the presence of heterologous sequences. To achieve specific co-expression of two heterologous genes in goat mammary gland epithelial (GMGE) cells, a mammary gland-specific bicistronic expression vector, pFIEβ, containing the β-casein 5′ flanking sequence and FMDV 2A, was successfully constructed and the specific expression of human interleukin 2 (hIL-2) and enhanced green fluorescent protein (EGFP) was conducted in primary GMGE cells. Another bicistronic expression vector, pFIEC, driven by the cytomegalovirus promoter, was constructed as a positive control. In cells transfected with pFIEβ and pFIEC, RT-PCR verified the existence of recombinant fusion mRNA of hIL-2 upstream of EGFP within the FMDV 2A cassette fragment and western blot analysis showed the existence of the fusion between hIL-2 and EGFP. It is concluded that FMDV 2A generated specific co-expression of multiple genes for the first time in primary GMGE cells driven by the β-casein promoter.

Molecular characterization of a long range haplotype affecting protein yield and mastitis susceptibility in Norwegian Red cattle

Background

Previous fine mapping studies in Norwegian Red cattle (NRC) in the region 86-90.4 Mb on Bos taurus chromosome 6 (BTA6) has revealed a quantitative trait locus (QTL) for protein yield (PY) around 88 Mb and a QTL for clinical mastitis (CM) around 90 Mb. The close proximity of these QTLs may partly explain the unfavorable genetic correlation between these two traits in NRC. A long range haplotype covering this region was introduced into the NRC population through the importation of a Holstein-Friesian bull (1606 Frasse) from Sweden in the 1970s. It has been suggested that this haplotype has a favorable effect on milk protein content but an unfavorable effect on mastitis susceptibility. Selective breeding for milk production traits is likely to have increased the frequency of this haplotype in the NRC population.

Results

Association mapping for PY and CM in NRC was performed using genotypes from 556 SNPs throughout the region 86-97 Mb on BTA6 and daughter-yield-deviations (DYDs) from 2601 bulls made available from the Norwegian dairy herd recording system. Highest test scores for PY were found for single-nucleotide polymorphisms (SNPs) within and surrounding the genes CSN2 and CSN1S2, coding for the β-casein and α_S2-casein proteins. High coverage re-sequencing by high throughput sequencing technology enabled molecular characterization of a long range haplotype from 1606 Frasse encompassing these two genes. Haplotype analysis of a large number of descendants from this bull indicated that the haplotype was not markedly disrupted by recombination in this region. The haplotype was associated with both increased milk protein content and increased susceptibility to mastitis, which might explain parts of the observed genetic correlation between PY and CM in NRC. Plausible causal polymorphisms affecting PY were detected in the promoter region and in the 5'-flanking UTR of CSN1S2. These polymorphisms could affect transcription or translation of CSN1S2 and thereby affect the amount of α_S2-casein in milk.

Highest test scores for CM were found in the region 89-91 Mb on BTA6, very close to a cluster of genes coding for CXC chemokines. Expression levels of some of these CXC chemokines have previously been shown to increase in bovine mammary gland cell lines after exposure to bacterial cell wall components.

Conclusion

Molecular characterization of the long range haplotype from the Holstein-Friesian bull 1606 Frasse, imported into NRC in the 1970s, revealed polymorphisms that could affect transcription or translation of the casein gene CSN1S2. Sires with this haplotype had daughters with significantly elevated milk protein content and selection for milk production traits is likely to have increased the frequency of this haplotype in the NRC population. The haplotype was also associated with increased mastitis susceptibility, which might explain parts of the genetic correlation between PY and CM in NRC.

QTL mapping in outbred half-sib families using Bayesian model selection

In this article, we propose a model selection method, the Bayesian composite model space approach, to map quantitative trait loci (QTL) in a half-sib population for continuous and binary traits. In our method, the identity-by-descent-based variance component model is used. To demonstrate the performance of this model, the method was applied to map QTL underlying production traits on BTA6 in a Chinese half-sib dairy cattle population. A total of four QTLs were detected, whereas only one QTL was identified using the traditional least square (LS) method. We also conducted two simulation experiments to validate the efficiency of our method. The results suggest that the proposed method based on a multiple-QTL model is efficient in mapping multiple QTL for an outbred half-sib population and is more powerful than the LS method based on a single-QTL model.

Molecular characterization and phylogenetic analysis of a yak (Bos grunniens) κ-casein cDNA from lactating mammary gland

κ-Casein is one of the major proteins in the milk of mammals. It plays an important role in determining the size and specific function of milk micelles. We have previously identified and characterized a genetic variant of yak κ-casein by evaluating genomic DNA. Here, we isolate and characterize a yak κ-casein cDNA harboring the full-length open reading frame (ORF) from lactating mammary gland. Total RNA was extracted from mammary tissue of lactating female yak, and the κ-casein cDNA were synthesized by RT-PCR technique, then cloned and sequenced. The obtained cDNA of 660-bp contained an ORF sufficient to encode the entire amino acid sequence of κ-casein precursor protein consisting of 190 amino acids with a signal peptide of 21 amino acids. Yak κ-casein has a predicted molecular mass of 19,006.588 Da with a calculated isoelectric point of 7.245. Compared with the corresponding sequences in GenBank of cattle, buffalo, sheep, goat, Arabian camel, horse, and rabbit, yak κ-casein sequence had identity of 64.76-98.78% in cDNA, and identity of 44.79-98.42% and similarity of 53.65-98.42% in deduced amino acids, revealing a high homology with the other livestock species. Based on κ-casein cDNA sequences, the phylogenetic analysis indicated that yak κ-casein had a close relationship with that of cattle. This work might be useful in the genetic engineering researches for yak κ-casein.

Casein haplotypes and their association with milk production traits in Norwegian Red cattle

A high resolution SNP map was constructed for the bovine casein region to identify haplotype structures and study associations with milk traits in Norwegian Red cattle. Our analyses suggest separation of the casein cluster into two haplotype blocks, one consisting of the CSN1S1, CSN2 and CSN1S2 genes and another one consisting of the CSN3 gene. Highly significant associations with both protein and milk yield were found for both single SNPs and haplotypes within the CSN1S1-CSN2-CSN1S2 haplotype block. In contrast, no significant association was found for single SNPs or haplotypes within the CSN3 block. Our results point towards CSN2 and CSN1S2 as the most likely loci harbouring the underlying causative DNA variation. In our study, the most significant results were found for the SNP CSN2_67 with the C allele consistently associated with both higher protein and milk yields. CSN2_67 calls a C to an A substitution at codon 67 in β-casein gene resulting in histidine replacing proline in the amino acid sequence. This polymorphism determines the protein variants A1/B (CSN2_67 A allele) versus A2/A3 (CSN2_67 C allele). Other studies have suggested that a high consumption of A1/B milk may affect human health by increasing the risk of diabetes and heart diseases. Altogether these results argue for an increase in the frequency of the CSN2_67 C allele or haplotypes containing this allele in the Norwegian Red cattle population by selective breeding.

Sequence analysis of UTR and coding region of kappa-casein gene of Indian riverine buffalo (Bubalus bubalis)

In this study, complete nucleotide as well as derived amino acid sequence characterization of water buffalo (Bubalus bubalis) kappa-casein gene has been presented. Kappa-casein cDNA clones were identified and isolated from a buffalo lactating mammary gland cDNA library. Sequence analysis of kappa-casein cDNA revealed 850 nucleotides with an open reading frame (ORF) of 573 nucleotides, encoding mature peptide of 169 amino acids. The 5' untranslated region (UTR) comprised 71 nucleotides, while 3' UTR was of 206 nucleotides. A total of 11 nucleotide and seven amino acid changes were observed in, buffalo (Bubalus bubalis) as compared to cattle (Bos taurus), sheep (Ovis aries) and goat (Capra hircus). Among these nucleotide changes, eight were unique in buffalo as they were fully conserved in cattle, sheep and goat. Majority of the nucleotide changes and all the amino acid changes; 14 (Asp-Glu), 19(Asp/Ser-Asn), 96(Ala-Thr), 126(Ala-Val), 128(Ala/Gly-Val), 156(Ala/Pro-Val) and 168(Ala/Glu-Val) were limited to exon IV. Three glycosylation sites, Thr 131, Thr 133 and Thr 142 reported in cattle and goat kappa-casein gene were also conserved in buffalo, however, in sheep Thr 142 was replaced by Ala. Chymosin hydrolysis site, between amino acids Phe 105 and Met 106, important for rennet coagulation process, were found to be conserved across four bovid species. Buffalo kappa-casein with the presence of amino acids Thr 136 and Ala 148 seems to be an intermediate of "A" and "B" variants of cattle. Comparison with other livestock species revealed buffalo kappa-casein sharing maximum nucleotide (95.5%) and amino acid (92.6%) similarity with cattle, whereas with pig it showed least sequence similarity of 76.0% and 53.2%, respectively. Phylogenetic analysis based on both nucleotide and amino acid sequence indicated buffalo kappa-casein grouping with cattle, while sheep and goat forming a separate cluster close to them. The non-ruminant species viz. camel, horse and pig were distantly placed, in separate lineages.

Detection of Quantitative Trait Loci Affecting Milk Production Traits on Bovine Chromosome 6 in a Chinese Holstein Population by the Daughter Design

Fourteen microsatellite markers with a coverage of 63.5 cM on bovine chromosome 6 were selected, and 26 sire families with 2,260 daughters were analyzed for mapping quantitative trait loci (QTL) affecting 5 milk production traits in a Chinese Holstein population. In the analyses across 26 families and within the largest significant families with a one-QTL model fitted, a QTL near BMS470 was detected that affected fat yield at the 5% experiment-wide significance level. When a 2-QTL model was fitted in the across-family analysis, it was found that there might exist 2 QTL affecting the 3 yield traits, although the exact or empirical thresholds for the significance testing were unknown. In all analyses, the results for milk yield and protein yield were generally consistent, which might have resulted from the same genetic background for milk and protein yield.

Quantitative trait loci affecting milk production traits in Finnish Ayrshire dairy cattle

A whole genome scan of Finnish Ayrshire was conducted to map quantitative trait loci (QTL) affecting milk production. The analysis included 12 half-sib families containing a total of 494 bulls in a granddaughter design. The families were genotyped with 150 markers to construct a 2764 cM (Haldane) male linkage map. In this study interval mapping with multiple-marker regression approach was extended to analyse multiple chromosomes simultaneously. The method uses identified QTL on other chromosomes as cofactors to increase mapping power. The existence of multiple QTL on the same linkage group was also analyzed by fitting a two-QTL model to the analysis. Empirical values for chromosome-wise significance thresholds were determined using a permutation test. Two genome-wise significant QTL were identified when chromosomes were analyzed individually, one affecting fat percentage on chromosome (BTA) 14 and another affecting fat yield on BTA12. The cofactor analysis revealed in total 31 genome-wise significant QTL. The result of two-QTL analysis suggests the existence of two QTL for fat percentage on BTA3. In general, most of the identified QTL confirm results from previous studies of Holstein-Friesian cattle. A new QTL for all yield components was identified on BTA12 in Finnish Ayrshire.

A whole genome scan for quantitative trait loci affecting milk protein percentage in Israeli-Holstein cattle, by means of selective milk DNA pooling in a daughter design, using an adjusted false discovery rate criterion

Selective DNA pooling was employed in a daughter design to screen all bovine autosomes for quantitative trait loci (QTL) affecting estimated breeding value for milk protein percentage (EBVP%). Milk pools prepared from high and low daughters of each of seven sires were genotyped for 138 dinucleotide microsatellites. Shadow-corrected estimates of sire allele frequencies were compared between high and low pools. An adjusted false discovery rate (FDR) method was employed to calculate experimentwise significance levels and empirical power. Significant associations with milk protein percentage were found for 61 of the markers (adjusted FDR = 0.10; estimated power, 0.68). The significant markers appear to be linked to 19--28 QTL. Mean allele substitution effects of the putative QTL averaged 0.016 (0.009--0.028) in units of the within-sire family standard deviation of EBVP% and summed to 0.460 EBVP%. Overall QTL heterozygosity was 0.40. The identified QTL appear to account for all of the variation in EBVP% in the population. Through use of selective DNA pooling, 4400 pool data points provided the statistical power of 600,000 individual data points.

Associations between casein haplotypes and first lactation milk production traits in Finnish Ayrshire cows

The objective of this study was to estimate the effects of beta-kappa-casein (CN) haplotypes on first-lactation milk production traits. The beta-kappa-CN haplotypes were deduced using information on beta- and kappa-CN genotypes of cows and their sires for 16,973 Finnish Ayrshire cows that had at least nine paternal half sibs. Effects of CN haplotypes on milk production traits were estimated for one haplotype at a time using an animal model, which included the fixed effects for calving year and month, age at calving, days open, beta-lactoglobulin, and a beta-kappa-CN haplotype. Differences in milk production traits were also estimated between haplotype combinations A1A+A2B and A1B+A2A within beta-kappa-CN genotype A1A2AB and between combinations A1E+A2A and A1A+A2E within genotype A1A2AE. The beta-kappa-CN haplotypes A2A and A2B were associated with high milk and protein yields and low fat content, and those that included the beta-CN A1 allele were associated with low yields and high fat content. Protein content was affected by the kappa-CN locus; haplotype A1B was associated with high protein content and A1E was with low protein content. The haplotype combination A1A+A2B was associated with 140 kg more milk yield (P = 0.045) and 0.03 percentage units less protein content (P = 0.055) than combination A1B+A2A, and combination A1A+A2E showed 0.02 percentage units greater protein content (P = 0.098) than A1E+A2A. These results indicate that genes linked to the CN loci contribute to the variation in milk yield and protein content.

Detection of putative loci affecting milk, health, and conformation traits in a US Holstein population using 105 microsatellite markers

Quantitative trait loci affecting milk yield, health, and conformation traits were studied for eight large US Holstein grandsire families by using the granddaughter design. A total of 105 microsatellite markers, located throughout the bovine genome, were selected for the scan. The data analyzed include genotypes for 35 markers in eight families not previously reported and genotypes for 70 markers reported previously in seven of those families. Analyses of markers previously reported were updated. Effects of marker alleles were analyzed for 38 traits, including traits for milk production, somatic cell score, productive life, conformation, calving ease, and 16 canonical traits derived from conformation and production traits. Permutation tests were used to calculate empirical trait-wise error rates. A trait-wise critical value of P = 0.1 was used to determine significance. Eight putative quantitative trait loci associated with 7 of the 35 new markers were identified within specific families. Two of these markers were associated with differences in strength and rump angle on chromosomes 4 and 9, respectively. Different markers were associated with protein percentage, milk yield, and somatic cell score on chromosomes 6, 7, and 10 in different families. Differences in the canonically transformed traits were associated with markers on chromosomes 5, 6, and 9. Additional marker-trait combinations were identified in the across-family tests, including effects on chromosomes 3, 4, and 9 for protein percentage, body depth, and canonical conformation traits, respectively. Additional markers are being added to allow interval analysis for putative quantitative trait loci that have been identified and to increase marker density.

Associations between casein haplotypes and milk production traits of Swiss Brown cattle

Effects of casein haplotypes and beta-lactoglobulin (LG) genotypes on milk protein fractions and on daughter yield deviations for milk performance traits were estimated from a daughter design. Offspring of seven Swiss Brown sires with the haplotypes B-A-B-A and B-A-B-B for alpha s1-, alpha s2-, beta-, and kappa-caseins were selected. The milk of daughter groups with paternal haplotype B-A-B-A was associated with lower casein content and higher whey protein content compared with B-A-B-B. Because of these contrary effects, the true protein content was not affected by the paternal haplotypes. The effects of maternal haplotypes were significant on true protein and casein content but not on whey protein content. The beta-LG genotypes had highly significant effects on casein and whey protein content. The effect of beta-LG BB was positive on casein and negative on whey protein content compared with beta-LG AA; the effect of beta-LG AB was intermediate. No significant effects of paternal haplotypes were found for daughter yield deviation on kilograms of milk, fat, and protein or percentages of fat and protein. The effects of the beta-LG genotypes were, independent of the parental haplotypes, close to significant on daughter yield deviation for percentage of protein. The beta-LG BB tended to be associated with a higher protein content compared with beta-LG AA. The effects for beta-LG genotypes showed additive gene effects. The analysis of paternal haplotypes within sires revealed a contrary effect of haplotypes for two of the seven sires for casein content. The paternal haplotypes within sire showed, although not significant, that haplotypes of the two sires had a contrary effect on daughter yield deviation for percentage of protein as well.

Detection of putative loci affecting milk, health, and type traits in a US Holstein population using 70 microsatellite markers in a genome scan

Quantitative trait loci affecting milk yield, health, and type traits were studied for seven large U.S. Holstein grandsire families using the granddaughter design. Seventy microsatellite markers located throughout the genome were selected for the quantitative trait loci scan. Effects of marker alleles were analyzed for 30 traits (21 type traits, 5 milk traits, 2 calving ease triats, and somatic cell score and productive life) and 16 canonical traits derived from type and production traits. Previously we reported results from 36 of these markers but have re-evaluated those results using a more robust analysis method. We report results from all 70 markers using permutation tests to calculate experiment-wise significance values, replacing the less stringent comparison-wise values previously reported. With this new methodology we detected 9 putative quantitative trait loci within specific families. Four markers were associated with effects on type traits on chromosomes 4, 5, 14, and 23. Two markers were associated with effects on protein percentage on chromosomes 6 and 14, and 3 markers were associated with effects on productive life on chromosomes 2, 21, and 23. Although these initial 70 microsatellite markers have been completed in the 7 Holstein families, additional markers will need to be added to allow interval analysis of areas where putative QTL have been identified and to increase marker density where needed.

Detection of QTL for milk production traits in cattle by application of a specifically developed marker map of BTA6

Interval mapping was carried out to identify quantitative trait loci (QTL) for milk production traits in five granddaughter design families of the German Holstein population. Fourteen randomly generated markers spanning the whole of BTA6 and six targeted microsatellite markers from BTA6q21-31 were included in the analysis. In one family a QTL with effects on milk fat yield and milk protein yield was mapped to the interval TGLA37-FBN13 (3 CM proximal to FBN13, lodscore 3.22) in the middle part of the chromosome. Although there are several reports about QTL with effects on milk production traits on BTA6 in the literature, a QTL with effects on milk fat and milk protein yield has not been previously described.

Genetic variability and population structure in loci related to milk production traits in native Argentine Creole and commercial Argentine Holstein cattle

Many cattle breeds have been subjected to high selection pressure for production traits. Consequently, population genetic structure and allelic distribution could differ in breeds under high selection pressure compared to unselected breeds. Analysis of <FONT FACE="Symbol">k</font>-casein, <FONT FACE="Symbol">a</font>S1-casein and prolactin gene frequencies was made for Argentine Creole (AC) and Argentine Holstein (AH) cattle herds. The calculated FST values measured the degree of genetic differentiation of subpopulations, depending on the variances of gene frequencies.The AC breed had considerably more variation among herds at the <FONT FACE="Symbol">a</font>S1-casein and <FONT FACE="Symbol">k</font>-casein loci. Conservation strategies should consider the entire AC population in order to maintain the genetic variability found in this native breed.

Associations between milk protein polymorphism and first lactation milk production traits in Finnish Ayrshire cows

Genotypic effects of beta-casein (CN), kappa-CN, and beta-lactoglobulin (LG) on milk, fat, and protein production and fat and protein percentages were estimated for 18,686 Finnish Ayrshire cows in first lactation using an animal model. Casein genotype effects were estimated including individual beta-CN and kappa-CN simultaneously in a model and then as composite beta-kappa-CN. The A2 allele of beta-CN and the A allele of kappa-CN, as well as the A1 allele of beta-CN and the B or E allele of kappa-CN, appeared together more frequently than was expected. Because of linkage disequilibrium in the casein loci and, consequently, unbalanced data, some contradictory effects of casein genotypes were obtained with the two models. A well-founded way to estimate the effects of casein genotypes was to use beta-kappa-CN genotypes. Composite casein genotypes including the A2 allele of beta-CN were associated with the highest milk and protein production and the lowest fat content, those including the B allele of kappa-CN with the highest protein content, and those including the E allele of kappa-CN with the lowest protein content. The effect of the beta-kappa-CN genotypes on protein content was moderately strong, and the effect was somewhat smaller for other traits. The AA genotype of beta-LG had a favorable effect on milk and protein production, and the BB genotype had a favorable effect on fat content.

A search for quantitative trait loci for milk production traits on chromosome 6 in Finnish Ayrshire cattle

Cattle chromosome 6 was scanned with 11 markers, ten microsatellites and the casein haplotype, to identify quantitative trait loci (QTLs) affecting the following milk production traits: milk yield, fat percentage, fat yield, protein percentage and protein yield. Twelve Finnish Ayrshire half-sib families with a total of 480 sons were genotyped and used in a grand-daughter design. Interval mapping was performed with a multiple-marker regression approach with a one-QTL and a two-QTL model, and the significance threshold values were determined empirically using a permutation test. Across-family analysis with the one-QTL model revealed an effect on protein percentage (P < 0.05) and on milk yield (P < 0.05). The analysis with the two-QTL model identified significant effects (P < 0.05) on protein percentage, milk yield, and fat yield. Comparing these two cases, the results suggest the existence of two QTLs on chromosome 6 with an effect on milk production traits. One of the QTLs was located around the casein genes. As the other QTL was similar in location and effect to a QTL found previously in Holstein-Friesians, an identity-by-descent approach could be applied to fine map this region.

Comparison of milk protein allele frequencies in Nordic cattle breeds

Allele frequencies at four milk protein loci were studied in five modern and 17 old Nordic cattle breeds in order to reveal variants that are characteristic for these populations. The B allele of CSN3, which has been associated with improved manufacturing properties of milk, showed significantly lower frequencies in modern production breeds than in old breeds of interest for conservation purposes. Characteristic frequencies of CSN1S1 (C), CSN2 (A2) and CSN3 (B) were found in Icelandic cattle, Swedish Mountain cattle, Northern Finncattle and Western Fjord cattle, which indicate a common origin of these populations. Further comparisons of allele frequencies in old Nordic breeds suggest sorting of these breeds into two groups with a northern and southern geographic location.

Quantitative trait locus mapping in dairy cattle by means of selective milk DNA pooling using dinucleotide microsatellite markers: analysis of milk protein percentage

"Selective DNA pooling" accomplishes quantitative trait locus (QTL) mapping through densitometric estimates of marker allele frequencies in pooled DNA samples of phenotypically extreme individuals. With poly(TG) microsatellites, such estimates are confounded by "shadow" ("stutter") bands. A correction procedure was developed on the basis of an observed linear regression between shadow band intensity and allele TG repeat number. Using this procedure, a selective DNA pooling study with respect to milk protein percentage was implemented in Israel-Holstein dairy cattle. Pools were prepared from milk samples of high and low daughters of each of seven sires and genotyped with respect to 11 markers. Highly significant associations with milk protein percentage were found for 5 of the markers; 4 of these markers confirmed previous reports. Selective DNA pooling accessed 80.6 and 48.3%, respectively, of the information that would have been available through individual selective genotyping or total population genotyping. In effect, the statistical power of 45,600 individual genotypings was obtained from 328 pool genotypings. This methodology can make genome-wide mapping of QTL accessible to moderately sized breeding organizations.