Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle

Toll like receptor 4 (TLR4) gene polymorphism and its association with somatic cell score and milk production traits in Indian dromedary camels

Our study aimed to explore the genetic variation in the Toll-like receptor 4 (TLR4) gene and establish its association with somatic cell score (SCS) and milk production traits in four Indian camel breeds namely Bikaneri, Kachchhi, Jaisalmeri and Mewari. TLR4 gene fragment of 573 bp spanning 5' UTR, exon-1 and partial intron-1 region was amplified and genotyped using the PCR-sequence based typing method. Only one SNP located at position C472T was identified. Genotyping revealed two alleles (C and T) and three genotypes: CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.116, 0.326 and 0.558 and allele frequencies for C and T alleles were 0.279 and 0.721, respectively. Association study inferred that the effect of genotype on SCS, lactation yield (LY) and peak yield (PY) was non-significant however heterozygote (CT) genotypes recorded lower SCS and higher LY and PY. It can be concluded that the TLR4 gene possesses limited genetic variation, depicting polymorphism at a single locus in Indian camel breeds with a predominance of the TT genotype. The association study indicated that heterozygote animals possess better udder health and production performance, the statistical significance of which needs to be established using a large data set.

Association of Variants in Innate Immune Genes TLR4 and TLR5 with Reproductive and Milk Production Traits in Czech Simmental Cattle

Bovine genes TLR4 and TLR5, which encode antibacterial toll-like receptors, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle to identify variants associated with reproduction, udder health, and milk production traits. Variants were discovered by hybrid resequencing of 164 bulls using HiSeq X-Ten and PacBio technologies and then individually genotyped. Nominal p-values < 0.05 for associations were detected in 18 combinations between 14 polymorphisms and 15 traits using one-way analysis of variance (ANOVA). The TLR4 variants g.610C>T (rs43578094) and g.10310T>G (rs8193072) in reference AC000135.1 were strictly associated with the index of early reproductive disorders and maternal calving ease, respectively, at false discovery rate (FDR) < 0.05. A highly permissive false discovery rate cutoff of 0.6 separated seventeen combinations in both genes comprising eight positives. In the case of the TLR4 variant g.9422T>C (rs8193060), indications were obtained for the association with as many as four reproductive traits: incidence of cystic ovaries, early reproductive disorders, calving ease, and production longevity. The permissive FDR interpretation for the TLR5 data indicated associations with cyst incidence and early reproduction disorders with maternal calving ease. Moreover, three TLR5 polymorphisms correlated with milk production traits. The discrepancy of the observed associations with the predicted impacts of the SNPs on protein function points to the role of haplotypes. Nevertheless, this question should be resolved on a larger scale. The observed associations are endorsed by independent evidence from the published functional roles in other species and by the published QTL mapping data.

Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility

Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.

Candidate genes for mastitis resistance in dairy cattle: a data integration approach

BACKGROUND

Inflammation of the mammary tissue (mastitis) is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector. Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes. However, mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult. Currently, the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.

METHODS

To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci. Mastitis-associated candidate genes reported in association, expression, and mouse model studies were collected by searching the relevant literature and databases. The collected data were integrated into a single database, screened for overlaps, and used for gene set enrichment analysis.

RESULTS

The database contains candidate genes from association and expression studies and relevant transgenic mouse models. The 2448 collected candidate loci are evenly distributed across bovine chromosomes. Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL, revealing promising candidate genes for mastitis resistance.

CONCLUSION

Mastitis resistance is a complex trait influenced by numerous alleles. Based on the number of independent studies, we were able to prioritise candidate genes and propose a list of the 22 most promising. To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.

Combined effects of CXCL8 (IL-8) and CXCR2 (IL-8R) gene polymorphisms on deregressed MACE EBV indexes of milk-related traits in Simmental bulls

CXCL8 (also known as IL-8) is a member of the CXC subfamily of chemokines that binds two of the seven transmembrane G-protein-coupled receptors (GPCRs), CXCR1 and CXCR2, to mediate and regulate leucocyte accumulation and activation at sites of inflammation. They are known to play a critical role in both disease susceptibility and infection outcome. The aim of this study was to investigate the entire sequences of CXCL8 and CXCR2 genes in thirty-one Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, and for somatic cell score (SCS). Five new single nucleotide polymorphisms (SNPs) were found in CXCR2 gene. The analysis of association indicated that one SNP in CXCL8 and two in CXCR2 influenced the considered traits. To evaluate the existence of functional haplotypic effects, combinations among the three genomic variants (SNP 1 in CXCL8, SNP 6 and SNP 7 in CXCR2) were investigated. Four different haplotypic alleles were identified in the experimental population, one of which at a high frequency (61%). Bulls with Hap 4 (G-C-G at SNP 1, SNP 6, and SNP 7 respectively) had more favourable indexes for SCS (P < 0.05). These results suggest that the SNPs in CXCL8 and CXCR2 may be potential genetic markers to improve udder health in the Simmental breed.

Integrative analysis of transcriptomics and proteomics of longissimus thoracis of the Hu sheep compared with the Dorper sheep

Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep.

The variation in promoter sequences of the Akt3 gene between cow and buffalo revealed different responses against mastitis

BACKGROUND

Serine/threonine kinase 3 (AKT3) is a protein-coding gene that is associated with several cattle immune diseases including different tumors and cancers. The objective of this study was to investigate the differences in structures and functions of AKT3 of cow and buffalo cattle.

METHODS

The sequence differences of gene-coding sequence (CDS) and core promoter region of AKT3 in cow and buffalo were analyzed by using bioinformatics tools and PCR sequencing. Also, the functional analysis of promoter regulating gene expression by RT-PCR was performed using 500 Holstein cows and buffalos. And, evaluation of AKT3 inflammatory response to the lipopolysaccharide (LPS)-induced mastitis was performed between both species.

RESULTS

The results revealed the variation in 6 exons out of 13 exons of the two species of CDS. Also, 4 different regions in 3-kb promoters of the AKT3 gene were significantly different between cow and buffalo species, in which cow's AKT3 promoter sequence region was started from - 371 to - 1247, while in buffalo, the sequence was started from - 371 to - 969 of the promoter crucial region. Thus, the promoter was overexpressed in cows compared to buffaloes. As a result, significant differences (P < 0.05) between the two species in the AKT3 gene expression level related to the LPS stimulation in their mammary epithelial cell line.

CONCLUSIONS

This study emphasized the great importance of the structural differences of AKT3 between the animal species on their different responses against immune diseases like mastitis.

Bovine mastitis prevention and control in the post-antibiotic era

Mastitis is the most important disease in the dairy industry. Antibiotics are considered to be the first choice in the treatment of the disease. However, the problem of antibiotic residue and antimicrobial resistance, in addition to the impact of antibiotic abuse on public health, leads to many restrictions on uncontrolled antibiotic therapy in the dairy sector worldwide. Researchers have investigated novel therapeutic approaches to replace the use of antibiotics in mastitis control. These efforts, supported by the revolutionary development of nanotechnology, stem cell assays, molecular biological tools, and genomics, enabled the development of new approaches for mastitis-treatment and control. The present review discusses recent concepts to control mastitis such as breeding of mastitis-resistant dairy cows, the development of novel diagnostic and therapeutic tools, the application of communication technology as an educational and epidemiological tool, application of modern mastitis vaccines, cow drying protocols, teat disinfection, housing, and nutrition. These include the application of nanotechnology, stem cell technology, photodynamic and laser therapy or the use of traditional herbal medical plants, nutraceuticals, antibacterial peptides, bacteriocins, antibodies therapy, bacteriophages, phage lysins, and probiotics as alternatives to antibiotics.

Polymorphisms in TLR4 Gene Associated With Somatic Cell Score in Water Buffaloes (Bubalus bubalis)

Considering the importance of the diseases affecting the productive performance of animals in the dairy industry worldwide, it is necessary to implement tools that help to control and limit the occurrence of such diseases. As the increased somatic cell counts (SCC) are a direct expression of the inflammatory process, they are candidates to become the usual parameter for assessing udder health regarding milk quality and for monitoring mastitis incidences. Toll-Like Receptors are membrane proteins that play a key role in immunity, recognizing pathogens and, subsequently, activating immune responses. The present study was conducted to identify single nucleotide polymorphisms in the TLR4 gene of buffaloes and to analyze its associations with somatic cell counts. DNA samples of 120 Murrah buffaloes were used. The whole coding region of the TLR4 gene was amplified by polymerase chain reaction reactions and sequenced for polymorphism scanning. A total of 13 polymorphisms were identified for the sequenced regions of the TLR4, most of which are in the coding region. The association with the somatic cell score was highly significant (p < 0.001) for all identified polymorphisms of TLR4 gene (g.54621T>A, g.54429G>T, g.54407T>A, g.46616C>A, g.46613T>G, g.46612A>G, g.46611C>A, g.46609T>G, g.46541C>G, g.46526C>A, g.46516T>C, g.46376C>T, g.46372T>C). Therefore, it is suggested that the markers of the TLR4 gene can be used as molecular markers for mastitis resistance in buffaloes, due to their association with somatic cell counts.

A missense mutation in the coding region of the toll-like receptor 4 gene affects milk traits in Barki sheep

OBJECTIVE

Milk production is one of the most desirable traits in livestock. Recently, the toll-like receptor (TLR) has been identified as a candidate gene for milk traits in cows. So far, there is no information concerning the contribution of this gene in milk traits in sheep. This study was designed to investigate the TLR 4 gene polymorphisms in Barki ewes in Egypt and then correlate that with milk traits in order to identify potential single nucleotide polymorphisms (SNPs) for these traits in sheep.

METHODS

A part of the ovine TLR 4 gene was amplified in Barki ewes, to identify the SNPs. Consequently; Barki ewes were genotyped using polymerase chain reaction-single strand conformation polymorphism protocol. These genotypes were correlated with milk traits, which were the daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP).

RESULTS

Age and parity of the ewe had a significant effect (p<0.05 or p<0.01) on DMY, FP, and TSP. The direct sequencing identified a missense mutation located in the coding sequence of the gene (rs592076818; c.1710C>A) and was predicted to change the amino acid sequence of the resulted protein (p.Asn570Lys). The association analyses suggested a significant effect (p<0.05) of the TLR genotype on the FP and PP, while the DMY tended to be influenced as well (p = 0.07). Interestingly, the presence of the G allele tended to increase the DMY (+40.5 g/d) and significantly (p<0.05 or p<0.01) decreased the FP (-1.11%), PP (-1.21%), and TSP (-7.98%).

CONCLUSION

The results of this study suggested the toll-like receptor 4 (TLR4) as a candidate gene to improve milk traits in sheep worldwide, which will enhance the ability to understand the genetic architecture of genes underlying SNPs that affect such traits.

SERPINA1 gene identified in RNA-Seq showed strong association with milk protein concentration in Chinese Holstein cows

The detection of candidate genes and mutations associated with phenotypic traits is important for livestock animals. A previous RNA-Seq study revealed that SERPINA1 gene was a functional candidate that may affect milk protein concentration in dairy cows. To further confirm the genetic effect of SERPINA1 on milk protein traits, genetic polymorphisms were identified and genotype-phenotype associations were performed in a large Chinese Holstein cattle population. The entire coding region and the 5′-regulatory region (5′-UTR) of SERPINA1 was sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed model with a population encompassing 1,027 Chinese Holstein cows. A total of four SNPs were identified in SERPINA1, among which rs210222822 and rs41257068 presented in exons, rs207601878 presented in an intron, and rs208607693 was in the 5′-UTR. Analyses of pairwise D′ measures of linkage disequilibrium (LD) showed strong linkage among these four SNPs (D′ = 0.99–1.00), and a 9 Kb haplotype block involving three main haplotypes with GTGT, CCCC and CCGT was inferred. An association study revealed that all four single SNPs and their haplotypes had significant genetic effects on milk protein percentage, milk protein yield and milk yield (P = 0.0458 −  < 0.0001). The phenotypic variance ratio for all 11 significant SNP-trait pairs ranged from 1.01% to 7.54%. The candidate gene of SERPINA1 revealed by our previous RNA-Seq study was confirmed to have pronounced effect on milk protein traits on a genome level. Two SNPs (rs208607693 and rs210222822) presented phenotypic variances of approximately 7% and may be used as key or potential markers to assist selection for new lines of cows with high protein concentration.

SNP Diversity in CD14 Gene Promoter Suggests Adaptation Footprints in Trypanosome Tolerant N'Dama (Bos taurus) but not in Susceptible White Fulani (Bos indicus) Cattle

Immune response to infections has been shown to be mediated by genetic diversity in pattern recognition receptors, leading to disease tolerance or susceptibility. We elucidated naturally occurring variations within the bovine CD14 gene promoter in trypanosome-tolerant (N'Dama) and susceptible (White Fulani) cattle, with genomic and computational approaches. Blood samples were collected from White Fulani and N'Dama cattle, genomic DNA extracted and the entire promoter region of the CD14 gene amplified by PCR. We sequenced this region and performed in silico computation to identify SNP variants, transcription factor binding sites, as well as micro RNAs in the region. CD14 promoter sequences were compared with the reference bovine genome from the Ensembl database to identify various SNPs. Furthermore, we validated three selected N'Dama specific SNPs using custom Taqman SNP genotyping assay for genetic diversity. In all, we identified a total of 54 and 41 SNPs at the CD14 promoter for N'Dama and White Fulani respectively, including 13 unique SNPs present in N'Dama only. The significantly higher SNP density at the CD14 gene promoter region in N'Dama may be responsible for disease tolerance, possibly an evolutionary adaptation. Our genotype analysis of the three loci selected for validation show that mutant alleles (A/A, C/C, and A/A) were adaptation profiles within disease tolerant N'Dama. A similar observation was made for our haplotype analysis revealing that haplotypes H1 (ACA) and H2 (ACG) were significant combinations within the population. The SNP effect prediction revealed 101 and 89 new transcription factor binding sites in N'Dama and White Fulani, respectively. We conclude that disease tolerant N'Dama possessing higher SNP density at the CD14 gene promoter and the preponderance of mutant alleles potentially confirms the significance of this promoter in immune response, which is lacking in susceptible White Fulani. We, therefore, recommend further in vitro and in vivo study of this observation in infected animals, as the next step for understanding genetic diversity relating to varying disease phenotypes in both breeds.

Association of TLR gene variants in a Czech Red Pied cattle population with reproductive traits

The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.

Genomic Patterns of Homozygosity in Chinese Local Cattle

Genome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated F_ROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5-1 Mb, Medium 1-5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

Potential of TLR-gene diversity in Czech indigenous cattle for resistance breeding as revealed by hybrid sequencing

A production herd of Czech Simmental cattle (Czech Red Pied, CRP), the conserved subpopulation of this breed, and the ancient local breed Czech Red cattle (CR) were screened for diversity in the antibacterial toll-like receptors (TLRs), which are members of the innate immune system. Polymerase chain reaction (PCR) amplicons of TLR1, TLR2, TLR4, TLR5, and TLR6 from pooled DNA samples were sequenced with PacBio technology, with 3- 5 ×  coverage per gene per animal. To increase the reliability of variant detection, the gDNA pools were sequenced in parallel with the Illumina X-ten platform at low coverage ( 60 × per gene). The diversity in conserved CRP and CR was similar to the diversity in conserved and modern CRP, representing 76.4 % and 70.9 % of its variants, respectively. Sixty-eight (54.4 %) polymorphisms in the five TLR genes were shared by the two breeds, whereas 38 (30.4 %) were specific to the production herd of CRP; 4 (3.2 %) were specific to the broad CRP population; 7 (5.6 %) were present in both conserved populations; 5 (4.0 %) were present solely for the conserved CRP; and 3 (2.4 %) were restricted to CR. Consequently, gene pool erosion related to intensive breeding did not occur in Czech Simmental cattle. Similarly, no considerable consequences were found from known bottlenecks in the history of Czech Red cattle. On the other hand, the distinctness of the conserved populations and their potential for resistance breeding were only moderate. This relationship might be transferable to other non-abundant historical cattle breeds that are conserved as genetic resources. The estimates of polymorphism impact using Variant Effect Predictor and SIFT software tools allowed for the identification of candidate single-nucleotide polymorphisms (SNPs) for association studies related to infection resistance and targeted breeding. Knowledge of TLR-gene diversity present in Czech Simmental populations may aid in the potential transfer of variant characteristics from other breeds.

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle

We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.

Genetic Polymorphisms in LTF/EcoRI and TLR4/AluI loci as candidates for milk and reproductive performance assessment in Holstein cattle

The aim of this study was to explore the genetic polymorphisms in LTF/EcoRI and TLR4/AluI loci and their association with milk and reproductive performance in Holstein cattle. A randomly selected 800 Holstein dairy cows from two dairy farms (400 animals each) in Egypt were used. Based on the two farm records, association between LTF/EcoRI genotypes and milk performance traits (order of lactation, daily milk yield, days in milk, corrected milk at 305 day and dry period) was carried out. Meanwhile, exploring of TLR4/AluI genotypes effect was done on data for reproductive performance (age at first freshening, calving interval, number of services per conception, ovarian rebound and days open). DNA was extracted from blood samples collected from Holstein dairy cows of the both farms and restriction analysis of 301-bp PCR products of LTF gene revealed two genotypes: AA genotype (301 bp) and AB genotype (301, 201 and 100 bp). Meanwhile, restriction analysis of 382-bp PCR products of TLR4 gene digested with AluI yielded two alleles (A and B) and three genotypes (AA, AB and BB). The A allele was indicated by two bands at 300 and 82 bp, and the B allele resulted in three fragments of 160, 140 and 82 bp. There was a significant association (p ≤ 0.05) between LTF genotypes and milk performance traits except for days in milk. The TLR4 genotypes had significant effects (p ≤ 0.05) on age at first freshening, calving interval, number of services per conception, ovarian rebound and days open. Ordinal logistic regression statistical model also revealed that it is possible to calculate high reproductive performance traits and to predict favourable dairy cows based on LTF and TLR4 genotypes. This research reveals the effectiveness of LTF/EcoRI and TLR4/AluI loci as candidates for reproductive performance assessment in Holstein cattle.

Toll-like receptor 4 gene polymorphisms influence milk production traits in Chinese Holstein cows

The research reported in this Research Communication aimed to describe the influence of Toll-like receptor 4 gene polymorphisms on milk production traits in Chinese Holstein cows. Toll-like receptor 4 (TLR4) is an important member of the toll-like receptor gene family that is widely found in various organisms. Since TLR4 can identify molecular patterns from various pathogenic microorganisms and induce natural and acquired immunity, it plays an important role in disease resistance in dairy cows. Two single nucleotide polymorphisms (SNPs) of TLR4 (c.-226 G > C and c.2021 C > T) that were previously found to be associated with health traits were genotyped using Sequenom MassARRAY (Sequenom Inc., San Diego, CA) for Chinese Holstein cows (n = 866). The associations between SNPs or their haplotypes and milk production traits and somatic cell count were analyzed by the generalized linear model procedure of Statistics Analysis System software (SAS). The c.-226 G > C and c.2021 C > T showed low linkage disequilibrium (r2 = 0·192). There was no association between these two SNPs and SCC, but significant effects were found for SNP c.-226 G > C on test-day milk yield, fat content, protein content, and total solid and milk urea nitrogen (P T and the SNP haplotypes on test-day milk yield, fat content, protein content, lactose content and total solids (P C was located within several potential transcription factor binding sites, including transcription factor AP-2. The polymorphisms c.-226 G > C and c.2021 C > T had significant effects on the milk production for Chinese Holstein, and these SNP could be used for molecular marker-assisted selection of milk production.

Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed

Domestic animals can serve as model systems of adaptive introgression and their genomic signatures. In part, their usefulness as model systems is due to their well-known histories. Different breeding strategies such as introgression and artificial selection have generated numerous desirable phenotypes and superior performance in domestic animals. The modern Danish Red Dairy Cattle is studied as an example of an introgressed population. It originates from crossing the traditional Danish Red Dairy Cattle with the Holstein and Brown Swiss breeds, both known for high milk production. This crossing happened, among other things due to changes in the production system, to raise milk production and overall performance. The genomes of modern Danish Red Dairy Cattle are heavily influenced by regions introgressed from the Holstein and Brown Swiss breeds and under subsequent selection in the admixed population. The introgressed proportion of the genome was found to be highly variable across the genome. Haplotypes introgressed from Holstein and Brown Swiss contained or overlapped known genes affecting milk production, as well as protein and fat content (CD14, ZNF215, BCL2L12, and THRSP for Holstein origin and ITPR2, BCAT1, LAP3, and MED28 for Brown Swiss origin). Genomic regions with high introgression signals also contained genes and enriched QTL associated with calving traits, body confirmation, feed efficiency, carcass, and fertility traits. These introgressed signals with relative identity-by-descent scores larger than the median showing Holstein or Brown Swiss introgression are mostly significantly correlated with the corresponding test statistics from signatures of selection analyses in modern Danish Red Dairy Cattle. Meanwhile, the putative significant introgressed signals have a significant dependency with the putative significant signals from signatures of selection analyses. Artificial selection has played an important role in the genomic footprints of introgression in the genome of modern Danish Red Dairy Cattle. Our study on a modern cattle breed contributes to an understanding of genomic consequences of selective introgression by demonstrating the extent to which adaptive effects contribute to shape the specific genomic consequences of introgression.

Association of leptin, toll-like receptor 4, and chemokine receptor of interleukin 8 C-X-C motif single nucleotide polymorphisms with fertility traits in Czech Fleckvieh cattle

Objective

The use of genetic markers can help to enhance reproduction in cattle, which is a very important trait for profitability in dairy production systems. This study evaluated the association between genotypes of leptin (LEP), toll-like receptor 4 (TLR4), and chemokine receptor of interleukin 8 C-X-C motif (CXCR1) genes and fertility traits in Czech Fleckvieh cattle.

Methods

Phenotypic data from 786 Czech Fleckvieh cows raised on 5 farms in the Czech Republic were used, along with information from the 1st three parities. To determine genotype, the polymerase chain reaction– restriction fragment length polymorphism method was used.

Results

Except for LEP g.-963C>T, all studied genotype frequencies of single nucleotide polymorphisms (SNPs) were distributed according to the Hardy-Weinberg equilibrium. Two LEP SNPs (g.-963C>T and c.357C>T) were associated with the age at the 1st calving, days open (DO), pregnancy rate after 1st service (PR), and calving interval (CLI). In LEP g.-963C>T the TT genotype heifers firstly calved 24 days earlier than CC genotype and the CT genotype cow showed a tendency for shorter DO and higher PR. In LEP c.357C>T we observed longer CLI and DO period in TT cows. In general, we can propose the TT genotype of g.-963C>T as favorable and the TT genotype of c.357C>T as unfavorable for a cow’s fertility. Heterozygotes in TLR4 c.-226C>G were significantly associated with shorter CLI, and presented a nonsignificant tendency to be associated with higher PR. In CXCR1 c.777 C>G, we did not observe any relationship of this SNP with reproduction.

Conclusion

Overall, the results showed that LEP could be an effective marker for improving reproduction in Czech Fleckvieh cattle. This study also provides novel insights into the relationship between TLR4 and CXCR1 SNPs and reproduction in dual-purpose cattle.

CD14 gene polymorphisms associated with increased risk of bovine tuberculosis in Chinese Holstein cows

Cluster differentiation antigen 14 (CD14) is an important pattern recognition receptor protein in innate immunity. The aim of this study was to identify and assess the association of single-nucleotide polymorphisms (SNPs) in the CD14 gene with susceptibility to bovine tuberculosis (BTB) in Chinese Holstein cows. DNA samples from 517 Chinese Holstein cows (257 tuberculosis positive cases and 259 healthy controls) were collected from dairy farms in China. SNPs in the entire CD14 gene, including exonic regions, intronic regions and close to the 5'- and 3'-terminal untranslated regions, were detected by PCR, followed by direct sequencing. Five SNPs (-5C/T, 613G/A, 1023G/A, 1306G/A and 1326G/T) were found in the CD14 gene region. Significantly increased BTB susceptibility was evident in T allele carriers of -5C/T (P<0.001; odds ratio, OR 2.02; 95% confidence interval, CI 1.57-2.77), G allele carriers of 613G/A (P<0.001; OR 2.17, 95% CI 1.50-3.08) and TG haplotype carriers of both SNPs (P<0.001; OR 3.14, 95% CI 1.24-4.50). These results suggest that -5C/T and 613G/A are risk factors for BTB in Chinese Holstein cattle and might be used as candidate genetic markers in breeding cows with natural resistance to BTB.

Variation in the Toll-like Receptor 4 (TLR4) gene affects milk traits in dairy cows

The objective of this Research Communication was to use polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis to investigate a region of the bovine TLR4 gene (TLR4) in pasture-fed New Zealand (NZ) Holstein-Friesian × Jersey (HF × J) cross dairy cows and to determine whether gene variation was associated with milk production traits. Genetic variation was observed, with two variants (A and B) containing a single nucleotide polymorphism (SNP) (c.2021C/T) that was non-synonymous and putatively results in a p.Thr674Ile substitution in the transmembrane/cytoplasmic domain of TLR4. Variant A was associated with higher milk yields, but lower milk fat percentages, whereas B was associated with lower milk yields, but higher fat and protein percentages. Cows of genotype AA produced more milk than AB or BB cows, but the milk produced by AA cows contained less fat than AB or BB cows.

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.

Expression patterns of miR-146a and miR-146b in mastitis infected dairy cattle

This study reports a significant up-regulation of bta-miR-146a and bta-miR-146b expression levels in bovine mammary tissues infected with subclinical, clinical and experimental mastitis. Potential target genes are involved in multiple immunological pathways. These results suggest a regulatory function of both miRNAs for the bovine inflammatory response in mammary tissue.

Molecular characterization and combined genotype association study of bovine cluster of differentiation 14 gene with clinical mastitis in crossbred dairy cattle

Aim:

The present study was undertaken with the objectives to characterize and to analyze combined genotypes of cluster of differentiation 14 (CD14) gene to explore its association with clinical mastitis in Karan Fries (KF) cows maintained in the National Dairy Research Institute herd, Karnal.

Materials and Methods:

Genomic DNA was extracted using blood of randomly selected 94 KF lactating cattle by phenol-chloroform method. After checking its quality and quantity, polymerase chain reaction (PCR) was carried out using six sets of reported gene-specific primers to amplify complete KF CD14 gene. The forward and reverse sequences for each PCR fragments were assembled to form complete sequence for the respective region of KF CD14 gene. The multiple sequence alignments of the edited sequence with the corresponding reference with reported Bos taurus sequence (EU148610.1) were performed with ClustalW software to identify single nucleotide polymorphisms (SNPs). Basic Local Alignment Search Tool analysis was performed to compare the sequence identity of KF CD14 gene with other species. The restriction fragment length polymorphism (RFLP) analysis was carried out in all KF cows using Helicobacter pylori 188I (Hpy188I) (contig 2) and Haemophilus influenzae I (HinfI) (contig 4) restriction enzyme (RE). Cows were assigned genotypes obtained by PCR-RFLP analysis, and association study was done using Chi-square (χ²) test. The genotypes of both contigs (loci) number 2 and 4 were combined with respect to each animal to construct combined genotype patterns.

Results:

Two types of sequences of KF were obtained: One with 2630 bp having one insertion at 616 nucleotide (nt) position and one deletion at 1117 nt position, and the another sequence was of 2629 bp having only one deletion at 615 nt position. ClustalW, multiple alignments of KF CD14 gene sequence with B. taurus cattle sequence (EU148610.1), revealed 24 nt changes (SNPs). Cows were also screened using PCR-RFLP with Hpy188I (contig 2) and HinfI (contig 4) RE, which revealed three genotypes each that differed significantly regarding mastitis incidence. The maximum possible combination of these two loci shown nine combined genotype patterns and it was observed only eight combined genotypes out of nine: AACC, AACD, AADD, ABCD, ABDD, BBCC, BBCD, and BBDD. The combined genotype ABCC was not observed in the studied population of KF cows. Out of 94 animals, AACD combined genotype animals (10.63%) were found to be not affected with mastitis, and ABDD combined genotyped animals was observed having the highest mastitis incidence of 15.96%.

Conclusion:

AACD typed cows were found to be least susceptible to mastitis incidence as compared to other combined genotypes.

RNA-Seq reveals 10 novel promising candidate genes affecting milk protein concentration in the Chinese Holstein population

Paired-end RNA sequencing (RNA-Seq) was used to explore the bovine transcriptome from the mammary tissue of 12 Chinese Holstein cows with 6 extremely high and 6 low phenotypic values for milk protein percentage. We defined the differentially expressed transcripts between the two comparison groups, extremely high and low milk protein percentage during the peak lactation (HP vs LP) and during the non-lactating period (HD vs LD), respectively. Within the differentially expressed genes (DEGs), we detected 157 at peak lactation and 497 in the non-lactating period with a highly significant correlation with milk protein concentration. Integrated interpretation of differential gene expression indicated that SERPINA1, CLU, CNTFR, ERBB2, NEDD4L, ANG, GALE, HSPA8, LPAR6 and CD14 are the most promising candidate genes affecting milk protein concentration. Similarly, LTF, FCGR3A, MEGF10, RRM2 and UBE2C are the most promising candidates that in the non-lactating period could help the mammary tissue prevent issues with inflammation and udder disorders. Putative genes will be valuable resources for designing better breeding strategies to optimize the content of milk protein and also to provide new insights into regulation of lactogenesis.

Association of <i>TLR4</i> and <i>CARD15/NOD2</i> polymorphisms with SCC in Holstein–Friesian cattle

Abstract. Mastitis is one of the most important dairy cattle diseases which results in economic losses in dairy production. Mastitis cases can be classified as subclinical or clinical. All forms of mastitis lead to changes in milk composition and induce an increase in somatic cell count (SCC). SCC is a very important and basic indicator of udder health. An increase in SCC is usually caused by the immune response to the invasion of pathogens contributing to mastitis. The aim of this study was to investigate associations between the polymorphisms of selected genes (TLR4 and CARD15/NOD2) whose products are involved in the identification of pathogen-associated molecular patterns (PAMPs) during the innate immune response to infection, and immunity to mastitis expressed as SCC. The genes under study were also examined for epistatic effects as well as effects of interactions with parity and stages of lactation. In all the studied classes, allele G of TLR4 had a favourable additive effect with negative values, contributing to a lower lnSCC. Allele A of CARD15/NOD2 had a desirable additive effect which varied with time and the changing internal environment during lactation. With regard to the dominance effect, allele A of CARD15/NOD2 was found to be significantly associated with a higher SCC in milk in the first lactation and in the third stage of each single lactation. Moreover, statistically significant epistatic effects were found, in particular additive–additive and dominance–additive interactions were favourably associated with SCC which was lower than expected in the case of no epistasis.

Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

Aim:

An attempt has been made to study the toll-like receptors 4 (TLR4) gene polymorphism from cattle DNA to correlate with mastitis cows.

Materials and Methods:

In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR), respectively from Kankrej (22) and Triple cross (24) cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one.

Results:

Results showed that both alleles (A and B) of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ² test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p<0.05). Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS) indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05). Thus, the allele A might play an important role in mastitis resistance in cows.

Conclusion:

The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance.

A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure

Clinical mastitis (CM) is one of the health disorders with large impacts on dairy farming profitability and animal welfare. The objective of this study was to perform a genome-wide association study (GWAS) for CM in first-lactation Holstein. Producer-recorded mastitis event information for 103,585 first-lactation cows were used, together with genotype information on 1,361 bulls from the Illumina BovineSNP50 BeadChip. Single-step genomic-BLUP methodology was used to incorporate genomic data into a threshold-liability model. Association analysis confirmed that CM follows a highly polygenic mode of inheritance. However, 10-adjacent-SNP windows showed that regions on chromosomes 2, 14 and 20 have impacts on genetic variation for CM. Some of the genes located on chromosome 14 (LY6K, LY6D, LYNX1, LYPD2, SLURP1, PSCA) are part of the lymphocyte-antigen-6 complex (LY6) known for its neutrophil regulation function linked to the major histocompatibility complex. Other genes on chromosome 2 were also involved in regulating immune response (IFIH1, LY75, and DPP4), or are themselves regulated in the presence of specific pathogens (ITGB6, NR4A2). Other genes annotated on chromosome 20 are involved in mammary gland metabolism (GHR, OXCT1), antibody production and phagocytosis of bacterial cells (C6, C7, C9, C1QTNF3), tumor suppression (DAB2), involution of mammary epithelium (OSMR) and cytokine regulation (PRLR). DAVID enrichment analysis revealed 5 KEGG pathways. The JAK-STAT signaling pathway (cell proliferation and apoptosis) and the 'Cytokine-cytokine receptor interaction' (cytokine and interleukines response to infectious agents) are co-regulated and linked to the 'ABC transporters' pathway also found here. Gene network analysis performed using GeneMania revealed a co-expression network where 665 interactions existed among 145 of the genes reported above. Clinical mastitis is a complex trait and the different genes regulating immune response are known to be pathogen-specific. Despite the lack of information in this study, candidate QTL for CM were identified in the US Holstein population.

Associations between CXCR1 polymorphisms and pathogen-specific incidence rate of clinical mastitis, test-day somatic cell count, and test-day milk yield

The CXCR1 gene plays an important role in the innate immunity of the bovine mammary gland. Associations between single nucleotide polymorphisms (SNP) CXCR1c.735C>G and c.980A>G and udder health have been identified before in small populations. A fluorescent multiprobe PCR assay was designed specifically and validated to genotype both SNP simultaneously in a reliable and cost-effective manner. In total, 3,106 cows from 50 commercial Flemish dairy herds were genotyped using this assay. Associations between genotype and detailed phenotypic data, including pathogen-specific incidence rate of clinical mastitis (IRCM), test-day somatic cell count, and test-day milk yield (MY) were analyzed. Staphylococcus aureus IRCM tended to associate with SNP c.735C>G. Cows with genotype c.735GG had lower Staph. aureus IRCM compared with cows with genotype c.735CC (rate ratio = 0.35, 95% confidence interval = 0.14–0.90). Additionally, a parity-specific association between Staph. aureus IRCM and SNP c.980A>G was detected. Heifers with genotype c.980GG had a lower Staph. aureus IRCM compared with heifers with genotype c.980AG (rate ratio = 0.15, 95% confidence interval = 0.04–0.56). Differences were less pronounced in multiparous cows. Associations between CXCR1 genotype and somatic cell count were not detected. However, MY was associated with SNP c.735C>G. Cows with genotype c.735GG out-produced cows with genotype c.735CC by 0.8 kg of milk/d. Results provide a basis for further research on the relation between CXCR1 polymorphism and pathogen-specific mastitis resistance and MY.

Association of polymorphism harbored by tumor necrosis factor alpha gene and sex of calf with lactation performance in cattle

In a majority of mammals, male infants have heavier body mass and grow faster than female infants. Accordingly, male offspring nursing requires a much greater maternal energy contribution to lactation. It is possible that the maternal-fetal immunoendocrine dialog plays an important role in female preparation for lactation during pregnancy. Immune system genes are an integral part of gene regulatory networks in lactation and tumor necrosis factor alpha (TNFα) is a proinflammatory cytokine that also plays an important role in normal mammary gland development. The aim of this study was to evaluate the influence of the sex of calf and/or the -824A/G polymorphism in the promoter region of TNFα gene on milk performance traits in Black Pied cattle over the course of lactation. We also studied the allele frequency differences of -824A/G variants across several cattle breeds, which were bred in different climatic conditions. The G allele frequency decreased gradually over the course of lactation events in the Black Pied dairy cattle because of a higher culling rate of cows with the G/G genotype (p<0.001). In contrast to the genotypes A/A and A/G, cows with G/G genotype showed significant variability of milk and milk fat yield subject to sex of delivered calf. Milk yield and milk fat yield were significantly higher in the case of birth of a bull calf than with a heifer calf (p<0.03). The G allele frequency varies from 48% to 58% in Grey Ukrainian and Black Pied cattle to 77% in aboriginal Yakut cattle. Our results suggest that the TNFα -824A/G gene polymorphism may have an influence on the reproductive efforts of cows over the course of lactation events depending on the sex of progeny. Allocation of resources according to sex of the calf allows optimizing the energy cost of lactation. This may be a probable reason for high G allele frequency in Yakut cattle breeding in extreme environmental conditions. Similarly, the dramatic fall in milk production after birth of a heifer calf increases the probability of culling for the cows with the G/G genotype in animal husbandry.

A candidate gene association study for nine economically important traits in Italian Holstein cattle

We genotyped 58 single nucleotide polymorphisms (SNPs) in 25 candidate genes in about 800 Italian Holstein sires. Fifty-six (minor allele frequency >0.02) were used to evaluate their association with single traits: milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP), milk protein percentage (PP), milk somatic cell count (MSCC); and complex indexes: longevity, fertility and productivity-functionality type (PFT), using deregressed proofs, after adjustment for familial relatedness. Thirty-two SNPs were significantly associated (proportion of false positives <0.05) with different traits: 16 with MSCC, 15 with PY, 14 with MY, 12 with PFT, eight with longevity, eight with FY, eight with PP, five with FP and two with fertility. In particular, a SNP in the promoter region of the PRLR gene was associated with eight of nine traits. DGAT1 polymorphisms were highly associated with FP and FY. Casein gene markers were associated with several traits, confirming the role of the casein gene cluster in affecting milk yield, milk quality and health traits. Other SNPs in genes located on chromosome 6 were associated with PY, PP, PFT, MY (PPARGC1A) and MSCC (KIT). This latter association may suggest a biological link between the degree of piebaldism in Holstein and immunological functions affecting somatic cell count and mastitis resistance. Other significant SNPs were in the ACACA, CRH, CXCR1, FASN, GH1, LEP, LGB (also known as PAEP), MFGE8, SRC, TG, THRSP and TPH1 genes. These results provide information that can complement QTL mapping and genome-wide association studies in Holstein.

Polymorphism of cytokine and innate immunity genes associated with bovine brucellosis in cattle

Genetic susceptibility to brucellosis is multifactorial, and it is known that impairment of the immune system could contribute to risk for getting brucellosis. The aim of the study was to find association of bovine brucellosis with 20 SNPs pertaining to bovine cytokine (IFNG, IFNGR1, IFNGR2, TNFA) and innate immunity (SLC11A1, TLR1, TLR4, and TLR9) genes using PCR-RFLP genotyping technique and it was observed that SLC11A1 (+1066 C/G), TLR1 (+1446 C/A), TLR1 (+1380 G/A), TLR4 (+10 C/T) and TLR4 (+399 C/T) loci were significantly (P≤0.05) associated with bovine brucellosis. The odds ratios (OR) of CG and CC genotypes versus GG genotype were 0.31 (0.12-0.82; 95% CI) and 0.18 (0.03-1.06; 95% CI) at SLC11A1 (+1066 C/G) locus in cases of brucellosis affected cattle. For TLR1 (+1380 G/A) locus, the OR for AG and AA genotypes versus GG genotypes were 0.15 (0.05-0.44; 95% CI) and 0.26 (0.04-1.47; 95% CI) which indicated that proportion of GG homozygote was significantly higher in brucellosis affected animals as compared to control. At TLR1 (+1446 C/A) locus the OR of AC genotype versus CC genotype was 0.24 (0.08-0.68; 95% CI) which revealed that relative proportion CC genotypes was significantly higher in case population. The TLR4 (+10 C/T) locus had three genotypes (TT, CT and CC) where OR of CT and CC genotypes versus TT genotype were near to zero. The OR of CT genotypes versus CC genotypes was 8.25 (0.94-71.92; 95% CI) at TLR4 (+399 C/T) locus and indicated that CT genotype had higher odds of bovine brucellosis than control animals.

Splicing variants of SERPINA1 gene in ovine milk: characterization of cDNA and identification of polymorphisms

The serine protease inhibitor, clade A, member 1 (SERPINA1) is the gene for a protein called alpha-1-antitrypsin (AAT), which is a member of the serine protease inhibitor (serpin) superfamily of proteins. By conformational change, serpins control several chemical reactions inhibiting the activity of proteases. AAT is the most abundant endogenous serpin in blood circulation and it is present in relatively high concentration in human milk as well as in bovine and porcine colostrum. Here we report for the first time the molecular characterization and sequence variability of the ovine SERPINA1 cDNA and gene. cDNAs from mammary gland and from milk were PCR amplified, and three different transcripts (1437, 1166 and 521bp) of the SERPINA1 gene were identified. We amplified and sequenced different regions of the gene (5' UTR, from exon 2 to exon 5 and 3' UTR), and we found that the exon-intron structure of the gene is similar to that of human and bovine. We detected a total of 97 SNPs in cDNAs and gene sequences from 10 sheep of three different breeds. In adult sheep tissues a SERPINA1 gene expression analysis indicated a differential expression of the three different transcripts. The finding reported in this paper will aid further studies on possible involvement of the SERPINA1 gene in different physiological states and its possible association with production traits.

Pathogen-group specific association between CXCR1 polymorphisms and subclinical mastitis in dairy heifers

The chemokine (C-X-C motif) receptor 1 (CXCR1) gene encodes the homonymous receptor for interleukin 8 (IL8) on polymorphonuclear neutrophilic leucocytes (PMNL). Binding causes migration from blood to milk, activation and prolonged survival of PMNL, a crucial process in the innate immune defence of the bovine mammary gland against invading mastitis-causing pathogens. The main objective of this study was to screen the entire coding region of the CXCR1 gene for polymorphisms and to analyse their association with udder health of dairy heifers. One-hundred-and-forty Belgian Holstein heifers originating from 20 commercial dairy farms were genotyped by DNA sequencing. Detailed phenotypic data on udder health was available including quarter bacteriological culture results and somatic cell count (SCC) in early lactation and composite milk SCC during first lactation. In total, 16 polymorphisms (including 8 missense mutations) were detected. Polymorphism c.980A>G was associated with pathogen-group specific IMI: heifers with genotype AG were less likely to have an IMI due to major mastitis pathogens compared with heifers with genotype GG but did not have less IMI by coagulase-negative staphylococci, so-called minor pathogens. CXCR1 genotype was neither associated with quarter SCC in early lactation nor with composite SCC during lactation. Although mastitis susceptibility is influenced by many factors, some genetic polymorphisms potentially have major effects on udder health of heifers, as was shown here. These results trigger us to further study the relationship between CXCR1 polymorphisms and mastitis susceptibility in both observational and experimental trials.

Characterization of the bovine innate immune response in milk somatic cells following intramammary infection with Streptococcus dysgalactiae subspecies dysgalactiae

The innate immune response of milk somatic cells in cows to Streptococcus dysgalactiae ssp. dysgalactiae was investigated by deliberate intramammary challenge. Cows were challenged with 2,500 colony-forming units of Strep. dysgalactiae DPC 5435, previously isolated from a clinical mastitis case. Eight of the 9 cows treated showed clinical signs of mastitis (swollen udders, increased somatic cell score, and clotted milk) within 1 wk of challenge. Messenger RNA levels of IL-1β and toll-like receptor 4 (TLR4) in milk somatic cells increased approximately 40 fold within 48 h of infusion, whereas tumor necrosis factor α increased 16 fold within the same time frame. Interestingly, cows homozygous for the G allele of the C-X-C chemokine receptor type 1 (CXCR1)-777 polymorphism had higher IL-8 and CXCR1 transcript abundance at 24h postinfusion compared with cows homozygous for the C allele. The difference in expression of these genes at this critical time point may influence the severity of disease within different genotypes.

Association of TLR4 polymorphisms with subclinical mastitis in Brazilian holsteins

The identification of dairy cows with greater or lower potential to develop mastits has been pursued for many years among different segments of the milk industry, including governmental organizations. Genomic studies have suggested that Single Nucleotide Polymorphisms (SNPs) within the pattern recognition receptors (PRR) could lead to different responses to pathogens, and consequently result in mastitis resistance or susceptibility. To investigate whether toll like receptor 4 (TLR4) gene is associated with subclinical mastitis in Holstein cows from a property in the state of Goiás, Brazil, TaqMan allelic discrimination and somatic cell count were performed. One hundred and fifty milk samples were analyzed for SCC and centesimal composition. Twenty percent of those samples with SCC above 200,000 (n=13) were screened for real-time PCR identification of microorganisms and blood samples were genotyped for TLR4 SNPs. There was a higher prevalence of Gram-positive bacteria in the analyzed samples (88.9%) and animals that had the combined genotypes AACCCC, GGTCGG and GACCGC presented the lowest somatic cell scores, and consequently those genotypes have the potential to be applied as molecular markers for assisted animal selection to improve milk quality.

Identification of single nucleotide polymorphisms in the bovine Toll-like receptor 1 gene and association with health traits in cattle

Bovine mastitis remains the most common and costly disease of dairy cattle worldwide. A complementary control measure to herd hygiene and vaccine development would be to selectively breed cattle with greater resistance to mammary infection. Toll-like receptor 1 (TLR1) has an integral role for the initiation and regulation of the immune response to microbial pathogens, and has been linked to numerous inflammatory diseases. The objective of this study was to investigate whether single nucleotide polymorphisms (SNPs) within the bovine TLR1 gene (boTLR1) are associated with clinical mastitis (CM).Selected boTLR1 SNPs were analysed within a Holstein Friesian herd. Significant associations were found for the tagging SNP -79 T > G and the 3'UTR SNP +2463 C > T. We observed favourable linkage of reduced CM with increased milk fat and protein, indicating selection for these markers would not be detrimental to milk quality. Furthermore, we present evidence that some of these boTLR1 SNPs underpin functional variation in bovine TLR1. Animals with the GG genotype (from the tag SNP -79 T > G) had significantly lower boTLR1 expression in milk somatic cells when compared with TT or TG animals. In addition, stimulation of leucocytes from GG animals with the TLR1-ligand Pam3csk4 resulted in significantly lower levels of CXCL8 mRNA and protein.SNPs in boTLR1 were significantly associated with CM. In addition we have identified a bovine population with impaired boTLR1 expression and function. This may have additional implications for animal health and warrants further investigation to determine the suitability of identified SNPs as markers for disease susceptibility.

Genetics of primary glaucoma

PURPOSE OF REVIEW

To provide an overview of the genetics of the primary open-angle glaucomas with particular attention to congenital, infantile, and juvenile forms.

RECENT FINDINGS

Mutations in CYP1B1, in addition to being the most common identifiable cause of autosomal recessive primary congenital/infantile glaucoma, can infrequently underlie juvenile and even primary adult-onset open-angle glaucoma, particularly in certain consanguineous populations. In 2009, patients diagnosed with congenital/infantile glaucoma were found to have recessive mutations in a second gene, LTBP2, with a phenotypic spectrum that includes primary megalocornea, spherophakia with ectopia lentis, and lens-related glaucoma. The most common identifiable cause of primary juvenile open-angle glaucoma across most populations remains heterozygous (autosomal dominant) MYOC mutation, underlying up to one-third of cases and possibly sometimes involved in earlier and later onset glaucomas Although primary adult-onset open-angle glaucoma usually does not follow simple Mendelian genetics and is etiologically complex, genome-wide association studies are uncovering genetic susceptibility factors. In some cases, primary adult-onset open-angle glaucoma can be caused by heterozygous mutation in MYOC, OPTN, or WDR36. In addition, in 2009, heterozygous NTF4 mutation was associated with the phenotype in a small percentage of patients from a German cohort.

SUMMARY

Seemingly unaffected siblings of children with CYP1B1-related primary congenital/infantile glaucoma should undergo genetic testing because of variable expressivity for the phenotype; such testing should also be considered for other asymptomatic relatives, especially in consanguineous families. In western populations, dominant MYOC mutation remains a common cause of primary open-angle juvenile glaucoma and infrequently can be implicated in congenital/infantile or adult-onset forms; identified families should undergo genetic counseling. Primary adult-onset open-angle glaucoma rarely follows simple Mendelian genetics, but genomic studies in different populations are revealing potential genetic risk factors for the phenotype.