Skin transcriptome analysis in Brangus cattle under heat stress.

Heat stress is a major factor that negatively affects animal welfare and production systems. Livestock should adapt to tropical and subtropical areas and to meet this, composite breeds have been developed. This work aimed to evaluate gene expression profiles in the skin of Brangus cattle under heat stress using a case-control design, and to correlate this with skin histological characteristics. Two groups of bulls were set using rectal temperature as a criterion to define stress conditions: stressed (N = 5) and non-stressed (N = 5) groups. Skin transcriptomics was performed and correlations between breed composition, phenotypic and skin histological traits were evaluated. Results showed 4309 differentially expressed genes (P < 0.01), 2113 downregulated and 2196 upregulated. Enrichment and ontology analyses revealed 132 GO terms and 67 pathways (P < 0.01), including thermogenesis, glycolysis, gluconeogenesis, mitochondrial activity, antioxidant and immune response, and apoptosis. The identity of the terms and pathways indicated the diversity of mechanisms directed to relieve the animals' suffering, acting from simple passive mechanisms (conduction, convection and radiation) to more complex active ones (behavioural changes, evaporation, vasodilation and wheezing). Furthermore, significant differences between phenotypic and skin histological traits and correlations between pairs of traits suggested a direction towards heat dissipation processes. In this sense, number of vessels was positively correlated with number of sweat glands (P < 0.001) and both were positively correlated with zebuine genetic content (P < 0.05 and P < 0.01, respectively), gland size was positively correlated with epidermal thickness and negatively with hair length (P < 0.05), and epidermal thickness was negatively correlated with gland-epidermis distance (P < 0.0005). These results support the notion that response to heat stress is physiologically complex, producing significant changes in the expression of genes involved in several biological pathways, while the animal's ability to face it depends greatly on their skin features.

Genetic evaluations of dairy goats with few pedigree data: different approaches to use molecular information.

One of the limitations of implementing animal breeding programs in small-scale or extensive production systems is the lack of production records and genealogical records. In this context, molecular markers could help to gain information for the breeding program. This study addresses the inclusion of molecular data into traditional genetic evaluation models as a random effect by molecular pedigree reconstruction and as a fixed effect by Bayesian clustering. The methods were tested for lactation curve traits in 14 dairy goat herds with incomplete phenotypic data and pedigree information. The results showed an increment of 37.3% of the relationships regarding the originals with MOLCOAN and clustering into five genetic groups. Data leads to estimating additive variance, error variance, and heritability with four different models, including pedigree and molecular information. Deviance Information Criterion (DIC) values demonstrate a greater fitting of the models that include molecular information either as fixed (genetic clusters) or as random (molecular matrix) effects. The molecular information of simple markers can complement genetic improvement strategies in populations with little information.

Development and growth of bovine calves demi-embryos.

The aim of this study was to investigate the growth and development of animals produced from demi-embryos and compare them with whole embryos from fetus to adult life. To achieve this, calves produced from fresh demi-embryos and whole embryos were individually transferred and monitored from 60 days of pregnancy until slaughter at 550 days. Ultrasound scans were conducted on fetuses at 60 and 90 days to evaluate the biparietal, abdominal, umbilical cord, orbital, and aorta diameters. Subsequently, morphological traits of newborn calves were measured at 0, 7, and 21 days (N = 18). Live weight was recorded at birth, weaning, and every 30 days thereafter until slaughter at 550 days. The growth curve of each group was modeled using logistic regression, and the factors of the respective functions were compared. As early as 60 days of pregnancy, ultrasound evaluations revealed no morphometric differences between fetuses produced from demi-embryos and those from whole embryos. This lack of differentiation persisted in the morphometric evaluations of newborns up to 21 days of age, as well as in live weight and the growth curve from birth to slaughter. Moreover, there were no significant differences between the groups in terms of rib eye area and fat thickness evolution. Consequently, individuals from demi-embryos exhibited no discernible disparities to those whole embryos in growth and development from 60 days of gestation, through birth, and into adulthood.

Coat score. A possible explanation for the zebuine selective sweep located on bovine chromosome 5: 47,670,001-48,100,000 bp.

Over 65% of the world's cattle population resides in warm areas where heat stress conditions limit the breed of European taurine cattle. Composite breeds were developed to retain the main traits of both parental breeds. The skin plays a central role in animal response to heat stress. Research on the genetic architecture of skin traits has identified genes and regions related to warm resistance skin features. The aim of this study was to determine whether the indicine proportion accounted for coat type or whether there were genes of large effect segregating in Brangus. Bulls (n = 108) were genotyped using microarrays and their coat score and hair length were evaluated. Indicine-taurine genome-wide composition was estimated and GWAS was performed. Although significant correlations between indicine proportion and traits were not observed, four windows of SNPs on BTA4 and BTA5 explained more than 2% of the trait variance. The GWAS for coat score in summer showed the main peak on BTA5:46,941,446-48,030,219 bp, accounting for 4.65% of the variance. Our results suggest that the variation in coat score and undercoat hair length in Argentinian Brangus bulls is associated with the presence of some particular gene variants, rather than with the whole indicine genetic content.

Genome-wide scan for signatures of selection in the Brangus cattle genome.

Brangus is a composite cattle breed developed with the objective of combining the advantages of Angus and Zebuine breeds (Brahman, mainly) in tropical climates. The aim of this work was to estimate breed composition both genome-wide and locally, at the chromosome level, and to uncover genomic regions evidencing positive selection in the Argentinean Brangus population/nucleus. To do so, we analysed marker data from 478 animals, including Brangus, Angus and Brahman. Average breed composition was 35.0% ± 9.6% of Brahman, lower than expected according to the theoretical fractions deduced by the usual cross-breeding practice in this breed. Local ancestry analysis evidenced that breed composition varies between chromosomes, ranging from 19.6% for BTA26 to 56.1% for BTA5. Using approaches based on allelic frequencies and linkage disequilibrium, genomic regions with putative selection signatures were identified in several chromosomes (BTA1, BTA5, BTA6 and BTA14). These regions harbour genes involved in horn development, growth, lipid metabolism, reproduction and immune response. We argue that the overlapping of a chromosome segment originated in one of the parental breeds and over-represented in the sample with the location of a signature of selection constitutes evidence of a selection process that has occurred in the breed since its take off in the 1950s. In this regard, our results could contribute to the understanding of the genetic mechanisms involved in cross-bred cattle adaptation and productivity in tropical environments.

Author Correction: The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Naturally monozygotic quadruplets in a Braford cow confirmed by DNA analysis: A case report.

Cattle are a monotocous species, despite naturally conceived multiple births are sometimes observed. Although the number of twins has consistently increased, triplet and quadruplet pregnancies represent 0.015% and 0.004% of the total births, respectively. Multiple births are the result of multiple ovulation and/or the spontaneous cleavage of one fertilized oocyte, which is known as monozygotic (MZ) twinning. In cattle, approximately 5% to 14% of all twin births are MZ, and births with more than two MZ calves are extremely rare. Monozygotic animals are genetically identical, and those derived from two or more zygotes are genetically different. Furthermore, the presence of placental vascular anastomosis can result in foetal chimerism. Notwithstanding, animals born as single calves can be chimeras when one of the foetal twins dies undetected in utero. Here, we used DNA testing to study the zygotic condition of an unusual female quadruplet born from a Braford cow bred in a multi-sire natural mating system without hormone stimulation. Two tissues with different embryological origin were sampled to test zygosity and possible chimerism. The results showed an identical genotype, confirming they all originated in an MZ pregnancy and suggesting the lack of chimerism in all animals. The use of MZ twins in breeding and selection systems provides an alternative to the conventional progeny testing. Some works have suggested a genetic background of MZ twins in humans. This female and her daughters could be the founders of a lineage to study the possible inheritance of MZ multiple births in cattle.

Application of longitudinal data analysis allows to detect differences in pre-breeding growing curves of 24-month calving Angus heifers under two pasture-based systems with differential puberty onset.

BACKGROUND: Longitudinal data analysis contributes to detect differences in the growing curve by exploiting all the information involved in repeated measurements, allowing to distinguish changes over time within individuals, from differences in the baseline levels among groups. In this research, longitudinal and cross-sectional analysis were compared to evaluate differences in growth in Angus heifers under two different grazing conditions, ad libitum (AG) and controlled (CG) to gain 0.5 kg day-1 . RESULTS: Longitudinal mixed models show differences in growing curve parameters between grazing conditions, that were not detected by cross-sectional analysis. Differences (P < 0.05) in first derivative of growth curves (daily gain) until 289 days were observed between treatments, AG being higher than CG. Correspondingly, pubertal heifer proportion was also higher in AG at the end of rearing (AG, 0.94; CG, 0.67). CONCLUSION: In longitudinal studies, the power to detect differences between groups increases by exploiting the whole information of repeated measures, modelling the relation between measurements performed on the same individual. Under a proper analysis, valid conclusion can be drawn with fewer animals in the trial, improving animal welfare and reducing investigation costs. © 2019 Society of Chemical Industry.

The genetic ancestry of American Creole cattle inferred from uniparental and autosomal genetic markers.

Cattle imported from the Iberian Peninsula spread throughout America in the early years of discovery and colonization to originate Creole breeds, which adapted to a wide diversity of environments and later received influences from other origins, including zebu cattle in more recent years. We analyzed uniparental genetic markers and autosomal microsatellites in DNA samples from 114 cattle breeds distributed worldwide, including 40 Creole breeds representing the whole American continent, and samples from the Iberian Peninsula, British islands, Continental Europe, Africa and American zebu. We show that Creole breeds differ considerably from each other, and most have their own identity or group with others from neighboring regions. Results with mtDNA indicate that T1c-lineages are rare in Iberia but common in Africa and are well represented in Creoles from Brazil and Colombia, lending support to a direct African influence on Creoles. This is reinforced by the sharing of a unique Y-haplotype between cattle from Mozambique and Creoles from Argentina. Autosomal microsatellites indicate that Creoles occupy an intermediate position between African and European breeds, and some Creoles show a clear Iberian signature. Our results confirm the mixed ancestry of American Creole cattle and the role that African cattle have played in their development.

The effect of the H-1 scaling factors τ and ω on the structure of H in the single-step procedure.

BACKGROUND: The single-step covariance matrix H combines the pedigree-based relationship matrix [Formula: see text] with the more accurate information on realized relatedness of genotyped individuals represented by the genomic relationship matrix [Formula: see text]. In particular, to improve convergence behavior of iterative approaches and to reduce inflation, two weights [Formula: see text] and [Formula: see text] have been introduced in the definition of [Formula: see text], which blend the inverse of a part of [Formula: see text] with the inverse of [Formula: see text]. Since the definition of this blending is based on the equation describing [Formula: see text], its impact on the structure of [Formula: see text] is not obvious. In a joint discussion, we considered the question of the shape of [Formula: see text] for non-trivial [Formula: see text] and [Formula: see text]. RESULTS: Here, we present the general matrix [Formula: see text] as a function of these parameters and discuss its structure and properties. Moreover, we screen for optimal values of [Formula: see text] and [Formula: see text] with respect to predictive ability, inflation and iterations up to convergence on a well investigated, publicly available wheat data set. CONCLUSION: Our results may help the reader to develop a better understanding for the effects of changes of [Formula: see text] and [Formula: see text] on the covariance model. In particular, we give theoretical arguments that as a general tendency, inflation will be reduced by increasing [Formula: see text] or by decreasing [Formula: see text].

Genetic Variation in FABP4 and Evaluation of Its Effects on Beef Cattle Fat Content.

FABP4 is a protein primarily expressed in adipocytes and macrophages that plays a key role in fatty acid trafficking and lipid hydrolysis. FABP4 gene polymorphisms have been associated with meat quality traits in cattle, mostly in Asian breeds under feedlot conditions. The objectives of this work were to characterize FABP4 genetic variation in several worldwide cattle breeds and evaluate possible genotype effects on fat content in a pasture-fed crossbred (Angus-Hereford-Limousin) population. We re-sequenced 43 unrelated animals from nine cattle breeds (Angus, Brahman, Creole, Hereford, Holstein, Limousin, Nelore, Shorthorn, and Wagyu) and obtained 22 single nucleotide polymorphisms (SNPs) over 3,164 bp, including four novel polymorphisms. Haplotypes and linkage disequilibrium analyses showed a high variability. Five SNPs were selected to perform validation and association studies in our crossbred population. Four SNPs showed well-balanced allele frequencies (minor frequency > 0.159), and three showed no significant deviations from Hardy-Weinberg proportions. SNPs showed significant effects on backfat thickness and fatty acid composition (P < 0.05). The protein structure of one of the missense SNPs was analyzed to elucidate its possible effect on fat content in our studied population. Our results revealed a possible blockage of the fatty acid binding site by the missense mutation.

Longitudinal data analysis of polymorphisms in the κ-casein and ß-lactoglobulin genes shows differential effects along the trajectory of the lactation curve in tropical dairy goats.

The κ-casein (CSN-3) and ß-lactoglobulin (BLG) genes are extensively polymorphic in ruminants. Several association studies have estimated the effects of polymorphisms in these genes on milk yield, milk composition, and cheese-manufacturing properties. Usually, these results are based on production integrated over the lactation curve or on cross-sectional studies at specific days in milk (DIM). However, as differential expression of milk protein genes occurs over lactation, the effect of the polymorphisms may change over time. In this study, we fitted a mixed-effects regression model to test-day records of milk yield and milk quality traits (fat, protein, and total solids yields) from Colombian tropical dairy goats. We used the well-characterized A/B polymorphisms in the CSN-3 and BLG genes. We argued that this approach provided more efficient estimators than cross-sectional designs, given the same number and pattern of observations, and allowed exclusion of between-subject variation from model error. The BLG genotype AA showed a greater performance than the BB genotype for all traits along the whole lactation curve, whereas the heterozygote showed an intermediate performance. We observed no such constant pattern for the CSN-3 gene between the AA homozygote and the heterozygote (the BB genotype was absent from the sample). The differences among the genotypic effects of the BLG and the CSN-3 polymorphisms were statistically significant during peak and mid lactation (around 40-160 DIM) for the BLG gene and only for mid lactation (80-145 DIM) for the CSN-3 gene. We also estimated the additive and dominant effects of the BLG locus. The locus showed a statistically significant additive behavior along the whole lactation trajectory for all quality traits, whereas for milk yield the effect was not significant at later stages. In turn, we detected a statistically significant dominance effect only for fat yield in the early and peak stages of lactation (at about 1-45 DIM). The longitudinal analysis of test-day records allowed us to estimate the differential effects of polymorphisms along the lactation curve, pointing toward stages that could be affected by the gene.

Genetic characterisation of PPARG, CEBPA and RXRA, and their influence on meat quality traits in cattle.

BACKGROUND: Peroxisome proliferator-activated receptor gamma (PPARG), CCAAT/enhancer binding protein alpha (CEBPA) and retinoid X receptor alpha (RXRA) are nuclear transcription factors that play important roles in regulation of adipogenesis and fat deposition. The objectives of this study were to characterise the variability of these three candidate genes in a mixed sample panel composed of several cattle breeds with different meat quality, validate single nucleotide polymorphisms (SNPs) in a local crossbred population (Angus - Hereford - Limousin) and evaluate their effects on meat quality traits (backfat thickness, intramuscular fat content and fatty acid composition), supporting the association tests with bioinformatic predictive studies. RESULTS: Globally, nine SNPs were detected in the PPARG and CEBPA genes within our mixed panel, including a novel SNP in the latter. Three of these nine, along with seven other SNPs selected from the Single Nucleotide Polymorphism database (SNPdb), including SNPs in the RXRA gene, were validated in the crossbred population (N = 260). After validation, five of these SNPs were evaluated for genotype effects on fatty acid content and composition. Significant effects were observed on backfat thickness and different fatty acid contents (P < 0.05). Some of these SNPs caused slight differences in mRNA structure stability and/or putative binding sites for proteins. CONCLUSIONS: PPARG and CEBPA showed low to moderate variability in our sample panel. Variations in these genes, along with RXRA, may explain part of the genetic variation in fat content and composition. Our results may contribute to knowledge about genetic variation in meat quality traits in cattle and should be evaluated in larger independent populations.

Association of a region of bovine chromosome 1 (BTA1) with age at puberty in Angus bulls.

Age at puberty is an important component of reproductive performance in cattle, so it is important to identify genes that contribute to the regulation of the onset of puberty and polymorphisms that explain differences between bulls. In a previous study, we found putative associations between age at puberty in Angus bulls and single-nucleotide polymorphisms (SNPs) in Chromosomes 1 and X. In the present work we aimed to confirm these findings in a larger sample of Angus bulls (n = 276). Four SNPs located in these regions were genotyped using SEQUENOM technology and the genotypes obtained were tested for association with age at puberty. The results showed that SNPs rs135953349 and rs110604205 on BTA1 were still significantly associated with age of puberty estimated at progressive sperm motility of 10% (P < 0.05). The association previously found on Chromosome X could not be confirmed. Analysis of the bovine genome revealed that the associated region (99.17-99.99 Mb) contained four predicted loci: myelodysplasia syndrome 1 (MDS1) and ecotropic virus integration site 1 (EVI1) complex locus (MECOM), eGF-like and EMI domain-containing 1 pseudogene-like (LOC100337483), microRNA mir-551b (MIR551B) and mCG140927-like (LOC100139843). The results obtained could contribute to the understanding of puberty regulation and could be useful for further identification and annotation of gene function in the context of reproduction.

Effectiveness of single-nucleotide polymorphisms to investigate cattle rustling.

Short tandem repeats (STR)s have been the eligible markers for forensic animal genetics, despite single-nucleotide polymorphisms (SNP)s became acceptable. The technology, the type, and amount of markers could limit the investigation in degraded forensic samples. The performance of a 32-SNP panel genotyped through OpenArrays(TM) (real-time PCR based) was evaluated to resolve cattle-specific forensic cases. DNA from different biological sources was used, including samples from an alleged instance of cattle rustling. SNPs and STRs performance and repeatability were compared. SNP call rate was variable among sample type (average = 80.18%), while forensic samples showed the lowest value (70.94%). The repeatability obtained (98.7%) supports the used technology. SNPs had better call rates than STRs in 12 of 20 casework samples, while forensic index values were similar for both panels. In conclusion, the 32-SNPs used are as informative as the standard bovine STR battery and hence are suitable to resolve cattle rustling investigations.

Characterization of the bovine gene LIPE and possible influence on fatty acid composition of meat.

LIPE is an intracellular neutral lipase, which is capable of hydrolyzing a variety of esters and plays a key role in the mobilization of fatty acids from diacylglycerols. The objectives of this study were to characterize the genetic polymorphism of bovine LIPE gene and to evaluate the possible association between three SNPs in the coding regions of this gene with the fatty acid composition of meat in a cattle population. Forty-three unrelated animals from different cattle breeds were re-sequenced and 21 SNPs were detected over approximately 2600 bp, five of these SNPs were novel. Three SNPs were selected, on the basis of evolutionary conservation, to perform validation and association studies in a crossbred cattle population. Our results may suggest a possible association of SNP1 with contents of oleic acid and total monounsaturated fatty acids (p < 0.01), and SNP2 and SNP3 with Heneicosylic acid content (p < 0.01), may be helpful to improve the quality of meat and improve health.

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd.

During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E(-42), respectively. Generally 2-3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ∼ 10(-11)). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).

Recent patents for detecting the species of origin in animal feedstuff, and raw and processed meat products.

The value of the traceability and labeling of food is attributable to two main aspects: health safety and/or product or process certification. The identification of the species related to meat production is still a major concern for economic, religious and health reasons. Many approaches and technologies have been used for species identification in animal feedstuff and food. The early methods for meat products identification include physical, anatomical, histological and chemical. Since 1970, a variety of methods were developed, these include electrophoresis (i.e. isoelectrofocusing), chromatography (i.e. HPLC), immunological techniques (i.e. ELISA), Nuclear Magnetic Resonance, Mass Spectrometry and PCR (DNA and RNA based methods). The recent patents on species detection in animal feedstuffs, raw meat and meat processed products, listed in this work, are mainly based on monoclonal antibodies and PCR, especially RT-PCR. The new developments under research are looking for more sensible, specific, less time consuming and quantitatively detection methods, which can be used in highly processed or heated treated meat food.

Association between GNRHR, LHR and IGF1 polymorphisms and timing of puberty in male Angus cattle.

BACKGROUND: In bovines, there are significant differences within and among beef breeds in the time when bulls reach puberty. Although the timing of puberty is likely to be a multigenic trait, previous studies indicate that there may also be single genes that exert major effects on the timing of puberty within the general population. Despite its economic importance, there are not many SNPs or genetic markers associated with the age of puberty in male cattle. In the present work, we selected three candidate genes, GNRHR, LHR and IGF1, and associated their polymorphisms with the age of puberty in Angus male cattle. RESULTS: After weaning, 276 Angus males were measured every month for weight (W), scrotal circumference (SC), sperm concentration (C) and percentage of motility (M). A total of 4 SNPs, two within GNRHR, one in LHR and one in IGF1 were genotyped using the pyrosequencing technique. IGF1-SnaBI SNP was significant associated (P < 0.01) with age at SC 28 cm, but it were not associated with age at M 10% and C 50 million. Genotype CC exhibited an average age at SC 28 cm of 7 and 11 days higher than CT (p = 0.037) and TT (p = 0.012), respectively. This SNP explained 1.5% of the genetic variance of age of puberty at SC28. LHR-I499L, GNRHR-SNP5 and GNRHR-SNP6 were not associated with any of the measurements. However, GNRHR haplotypes showed a suggestive association with age at SC 28 cm. CONCLUSIONS: The findings presented here could support the hypothesis that IGF1 is a regulator of the arrival to puberty in male calves and is involved in the events that precede and initiate puberty in bull calves. Given that most studies in cattle, as well as in other mammals, were done in female, the present results are the first evidence of markers associated with age at puberty in male cattle.

Animal markers assisted selection in South America: a point of view.

Genetic identification has been continuously evolving during the last century. The recent development of whole-genome projects allowed the discovery and characterization of a large number of single nucleotide polymorphisms (SNP). A number of high-throughput DNA methods has decreased the cost of DNA marker analysis and increased the amount of samples that can be processed at a time. Using this information and methods, many private and governmental laboratories offer a wide range of genetic tests, many of which have been patented. In the field of genetic resources, a significant amount of law-making has been developed at the international and regional levels. Many South American countries currently lack jurisprudence in relation to the protection of DNA sequences. In this paper, we compared laws related with life-form patents in some countries from South America. Nowadays, the knowledge and technology leveling of many of these countries allows marker assisted selection (MAS) programs to be applied. Herein, we resume the economical value of MAS. Finally, we present a point of view on the pertinence, viability and conditions for developing and applying MAS programs in South America.