Genetic disorders in beef cattle: a review

Comparing genomic studies in animal breeding and human genetics: focus on disease-related traits in livestock - A review

Genomic studies of diseases can be divided into two types: i) analyses that reveal causal genes by focusing on linkage disequilibrium between observed and causal variants and ii) those that simultaneously assess numerous genetic markers to estimate the polygenic effects of a particular genomic region or entire genome. The field of human genetics has emphasized the discovery of causal genes, but these represent only a fraction of the total genetic variance. Therefore, alternative approaches, such as the polygenic risk score, which estimates the genetic risk for a given trait or disease based on all genetic markers (rather than on known causal variants only), have begun to garner attention. In many respects, these human genetic methods are similar to those originally developed for the estimation of breeding values (i.e., total additive genetic effects) in livestock. However, despite these similarities in methods, the fields of human and animal genetics still differ markedly in terms of research objectives, target populations, and other characteristics. For example, livestock populations have continually been selected and inbred throughout their history; consequently, their effective population size has shrunk and preferred genes (such as those influencing disease resistance and production traits) have accumulated in the modern breeding populations. By examining the characteristics of these two fields, particularly from the perspectives of disease and disease resistance, this review aims to improve understanding of the intrinsic differences between genomic studies using human compared with livestock populations.

Distribution of Recessive Genetic Defect Carriers in Holstein Friesian Cattle: A Polish Perspective

Genetic disorders are caused by a hereditary change in the structure of DNA that may hurt the health and life of animals. Several recessive haplotypes and a few causative mutations are known in Holstein Friesian cattle: CDH (Holstein cholesterol deficiency), haplotypes with a homozygous deficiency in Holstein (HH1, HH3, HH4, HH5, HH6, HH7), BLAD (bovine leukocyte adhesion deficiency), DUMPS (deficiency of uridine monophosphate synthase), FXI (factor XI deficiency), HHM (mule foot, syndactyly), and BC (citrullinaemia). From a breeding point of view, these genetic diseases have highly negative effects and are a significant problem for breeders, exposing them to economic losses and hurting animal welfare. This study aimed to characterize the Polish population of Holstein Friesian dairy cattle, considering the carrier status of twelve selected genetic defects. This study was based on genotype data collected from 78,884 cows and 691 bulls of the Holstein Friesian variety. The studies were performed using Illumina Infinium microarrays. Among both bulls and cows, the highest numbers of carriers were detected for HH5 (appropriately 6.7% and 5.4%). The lowest numbers of carriers were detected for DUMPS, factor XI, and HHM. The study revealed one calf suffering from cholesterol deficiency.

Future Directions for Ruminant Genomics

The current article is a forward-looking synopsis to provide insights into the current state of the industry and some areas where future work may hold additional promise. The integration of genomics into the dairy and beef industries is multifaceted and will impact production gains, identification and management of genetic diseases, and streamlined breeding and selection approaches. Veterinarians are uniquely poised to educate clients, integrate genomic data with existing metrics, and assist in decision-making that will impact the future shape of the global herd.

Genetics and Genomics 101

Genetic mutations, both favorable and unfavorable, are the raw material for improvement in livestock populations. The random inheritance of these mutations is essential for generating progenies with genetic potential greater than their parents. These mutations can act either in a simple manner, such that a single alteration disrupts phenotype, or in a complex manner where hundreds or thousands of mutations of small effect create a continuous distribution of phenotypes. Selection tools leverage phenotypic records, pedigrees, and genomics to estimate the genetic potential of individual animals. This more accurate accounting of genetic potential has generated enormous gains in livestock populations.

Improving laboratory animal genetic reporting: LAG-R guidelines

The biomedical research community addresses reproducibility challenges in animal studies through standardized nomenclature, improved experimental design, transparent reporting, data sharing, and centralized repositories. The ARRIVE guidelines outline documentation standards for laboratory animals in experiments, but genetic information is often incomplete. To remedy this, we propose the Laboratory Animal Genetic Reporting (LAG-R) framework. LAG-R aims to document animals' genetic makeup in scientific publications, providing essential details for replication and appropriate model use. While verifying complete genetic compositions may be impractical, better reporting and validation efforts enhance reliability of research. LAG-R standardization will bolster reproducibility, peer review, and overall scientific rigor.

Enhancing sustainability through resource efficiency in beef production systems using a sliding time window-based approach and frame scores

The food needs of the increasing global population, inefficiencies in supply chains, customer expectations and environmental concerns are the challenges to meeting resource-intensive protein needs sustainably. Collectively, this increases the need to enhance sustainability in the beef sector. This study proposes a sliding time-window-based multi-period livestock production model using mixed-integer linear programming (MILP) to simultaneously balance economic and environmental losses. It identifies the optimal finishing time using frame score (FS) and feed conversion ratio (FCR), targeting flexibility by allowing variable growth periods to reduce food/nutritional losses while meeting the variability in demands with minimum inventory levels. Furthermore, sequencing and assigning animals to facilities with optimum separation time is applied to avoid bad handling of animals and ensure quality meat with hygienic standards for longer shelf life. The system boundary of the proposed model includes beef farms and processing facilities. Compared to the recently proposed batch processing models over seven months with a herd size of 1980 animals, the findings reduce the average forage needed by ∼126.90 kips and methane emissions by ∼2560 kg, with a significant benefit in terms of the live animals' weight gain by ∼10,276 lbs.

Effects of the F94L myostatin gene mutation in beef × dairy crossed cattle on strip loin steak dimensionality, shear force, and sensory attributes

Carcasses (n = 115) from steers resulting from the mating of four Limousin × Angus sires heterozygous for the F94L myostatin mutation to Jersey, Jersey × Holstein, and Holstein dams were utilized to evaluate the effects of one copy of the F94L allele on strip loin dimensionality, Warner-Bratzler shear force and slice shear force, and sensory panel ratings. In phase I of a two-phase study, 57 carcasses from two sires were utilized to obtain samples of longissimus dorsi (LD), psoas major (PM), gluteus medsius (GM), semitendinosus (ST), serratus ventralis, triceps brachii, and biceps femori muscles, which were vacuum packaged, aged until 10 d postmortem, and frozen. Frozen strip loins were cut into 14, 2.5-cm-thick steaks each, and individual strip loin steaks were imaged at a fixed height on a gridded background and processed through image analysis software. In phase II, to obtain a greater power of test for LD palatability attributes, 58 additional carcasses from three sires were utilized to obtain LD samples only for sensory panel and shear force analysis. Cooked steak sensory attributes evaluated by trained panelists were tenderness, juiciness, beef flavor, browned flavor, roasted flavor, umami flavor, metallic flavor, fat-like flavor, buttery flavor, sour flavor, oxidized flavor, and liver-like flavor. In strip loin steaks from carcasses with one F94L allele, LD muscle area was larger in steaks 4, 5, 7, 8, and 9, and steaks 1, 6, 7, and 9 were less angular than those from carcasses with no F94L allele (P < 0.05). Of the seven muscles observed, there were no shear force differences between F94L genotypes (P > 0.20). F94L genotype did not affect sensory panel ratings of LD and GM steaks (P > 0.07). Cooked ST steaks from carcasses with one F94L rated lower in fat-like flavor compared to those from carcasses with no F94L allele (P = 0.035). Cooked PM steaks from carcasses with one F94L allele rated lower in juiciness, fat-like flavor, buttery flavor, and umami flavor compared to those with no copies of the F94L (P < 0.04). In summary, one copy of the F94L allele utilized in beef × dairy cross steers improved strip loin steak dimensionality, did not affect cooked steak tenderness across seven muscles, and decreased fat-associated flavors in the PM and ST. The use of F94L homozygous terminal beef sires would be an easily implemented strategy for dairy producers to improve steak portion size and shape in carcasses from nonreplacement calves.

Effects of the F94L myostatin gene mutation in beef × dairy crossed cattle on muscle fiber type, live performance, carcass characteristics, and boxed beef and retail cut yields

Producer live performance data and carcasses from steers (n = 116) resulting from the mating of four Limousin/Angus sires heterozygous for the F94L myostatin mutation to Jersey/Holstein dams were utilized to evaluate the effects of one copy of the F94L allele on live performance, carcass traits and USDA grades, and boxed beef and retail yields. Slaughter data were collected at time of harvest and carcass data were collected 48 hours postmortem. One side from each of the 58 carcasses was fabricated into boxed beef and retail cuts by experienced lab personnel 5-8 d postmortem. One copy of the F94L allele did not affect gestation length, birth weight, percentage of unassisted births, feedlot average daily gain, live weight at harvest, hot carcass weight, or dressing percentage (P > 0.05). Muscle fiber analysis indicated that the increase in muscularity by the F94L allele in the semitendinosus and longissimus was likely due to hyperplasia as there was a 19% increase in the quantity of myosin heavy chain type IIA and IIX fibers in the semitendinosus (P < 0.05) with no effect on muscle fiber size (P > 0.05). Carcasses from steers with one F94L allele had larger ribeye areas (99.2 vs. 92.3 sq.cm.), greater ribeye width:length ratios (0.498 vs. 0.479), lower USDA yield grades (2.21 vs. 2.66), and lower marbling scores (438 vs. 480) (P < 0.05). Additionally, for boxed beef yields, one F94L allele, vs. zero F94L alleles, increased (P < 0.05) 85/15 trimmings (+0.59%), top round (+0.28%), strip loin (+0.12%), eye round (+0.11%), tenderloin (+0.07%), boneless foreshank (+0.07%), cap/wedge (+0.06%), and tri-tip (+0.04%). Overall, carcasses from steers with one F94L allele had a greater boxed beef yield (+1.06%), boxed beef plus 85/15 trimmings yield (+1.65%), and total retail cuts plus ground beef 85/15 yield (+1.78%) than carcasses from steers with zero F94L alleles (P < 0.05). One copy of the F94L allele utilized in beef-on-dairy breeding system had no significant impact on live performance traits but resulted in lower marbling scores and increased muscularity as evidenced through larger, more beef-shaped ribeyes, lower USDA yield grades, and greater carcass cutout yields (both boxed beef and retail yields).

Comparative analysis of allele frequencies for DNA polymorphisms associated with disease and economically important traits in the genomes of Russian and foreign cattle breeds

The genetic makeup of a breed including its genetic differences from other breeds determines its appearance and characteristics, including economically important traits and resistance to pathologies. To date, many loci controlling significant phenotypes have been identified, which is successfully used in the world practice of marker-assisted selection to improve breed properties. The aim of this study was a comparative analysis of frequencies for known causative nucleotide substitutions, insertions and deletions associated with disease and economically important traits in Russian and foreign cattle breeds. As a result, we identified frequencies of these DNA polymorphisms in the populations of Russian cattle breeds, compared them with those of foreign populations of the same breed, as well as other foreign breeds. Our results indicate similarities in frequencies for most of such alleles within breeds (populations of Russian and foreign breeding), as well as the relationship between the causative allele prevalence and the presence of phenotypic traits under the effect. We also found an excess of some undesirable alleles in the Russian cattle populations, which should be paid attention to when designing breeding programs. We found that the alleles increasing fertility in the Hereford breed have a higher frequency in the Russian Hereford population compared to the foreign counterpart. Interestingly, unlike for the European breeds, for Asian Turano-Mongolian Wagyu and Yakut cattle, there was a less clear link between phenotypic traits and frequencies of known causative alleles. Our work points to specific genetic variants that could be used to improve and/or maintain the performance of certain cattle breeds bred in the Russian Federation.

From Mendel laws to whole genetic association study to decipher the swine mulefoot phenotype

The swine mulefoot (SM) is a rare condition characterized by a non-cloven hoof due to the partial or total fusion of the phalanges. No comprehensive study has been conducted to identify associated markers with this phenotype until now. We aimed to characterize the association between SNP and the mulefoot phenotype using a Genome-Wide Association Study (GWAS). An experimental population was produced using a half-sib mating where the male had the mulefoot phenotype and the females (n = 6) had cloven hoofs. The cross resulted in 27 (47%) animals with the mulefoot characteristic and 30 (53%) normal animals, indicating the possible dominant gene action. Animals were further genotyped using the Illumina PorcineSNP50k BeadChip, and SNPs were tested for associations. Twenty-nine SNPs located on the SSC15, SSC4, and SSCX were associated with the mulefoot phenotype (p-value <5 × 10^-5). Six markers were found in the intronic regions of VWC2L, CATIP, PDK3, PCYT1B, and POLA1 genes. The marker rs81277626, on SSC15:116,886,110 bp, is located in the Von Willebrand Factor C Domain (VWC2L), a possible functional candidate gene. The VWC2L is part of a biological process involved with the bone morphogenetic protein (BMP) signaling pathway, previously associated with syndactyly in other species. In conclusion, the identified markers suggest the involvement of the VWC2L gene in the SM phenotype in this population.

Frequency of genotypic markers for genetic disorders, colour, polledness, and major genes in Blanco Orejinegro cattle

The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.

Unintended consequences of selection for increased production on the health and welfare of livestock

Modern farming technologies, including quantitative selection and breeding methods in farm animal species, resulted in increased production and efficiency. Selection for increased output in both intensive and extensive production systems has trade-offs and negative outcomes, often more pronounced in intensive systems. Animal welfare and health are often adversely affected and this influences sustainable production. The relative importance of animal welfare differs among developed and developing countries due to the level of economic development, food security and education, as well as religious and cultural practices which presents challenges for sound scientific research. Due to breeding goals in the past set on growth performance, traits such as fertility, welfare and health have been neglected. Fertility is the single most important trait in all livestock species. Reduced fertility and lameness, claw health and mastitis results in unnecessary culling and reduced longevity. Selection pressure for growth accompanied with inbreeding has resulted in a number of genetic defects in beef, sheep and pigs. This review demonstrated the importance of inclusion of animal welfare concepts into breeding objectives and selection strategies. Accurate phenotyping of welfare traits is a limiting factor in the implementation of mitigating strategies, which include diagnostic testing, control of inbreeding and genomic selection.

Mandibulofacial Dysostosis Attributed to a Recessive Mutation of CYP26C1 in Hereford Cattle

In spring 2020, six Hereford calves presented with congenital facial deformities attributed to a condition we termed mandibulofacial dysostosis (MD). Affected calves shared hallmark features of a variably shortened and/or asymmetric lower mandible and bilateral skin tags present 2–10 cm caudal to the commissure of the lips. Pedigree analysis revealed a single common ancestor shared by the sire and dam of each affected calf. Whole-genome sequencing (WGS) of 20 animals led to the discovery of a variant (Chr26 g. 14404993T>C) in Exon 3 of CYP26C1 associated with MD. This missense mutation (p.L188P), is located in an α helix of the protein, which the identified amino acid substitution is predicted to break. The implication of this mutation was further validated through genotyping 2 additional affected calves, 760 other Herefords, and by evaluation of available WGS data from over 2500 other individuals. Only the affected individuals were homozygous for the variant and all heterozygotes had at least one pedigree tie to the suspect founder. CYP26C1 plays a vital role in tissue-specific regulation of retinoic acid (RA) during embryonic development. Dysregulation of RA can result in teratogenesis by altering the endothelin-1 signaling pathway affecting the expression of Dlx genes, critical to mandibulofacial development. We postulate that this recessive missense mutation in CYP26C1 impacts the catalytic activity of the encoded enzyme, leading to excess RA resulting in the observed MD phenotype.

Genome-Wide Identification of Discriminative Genetic Variations in Beef and Dairy Cattle via an Information-Theoretic Approach

Analyzing the associations between genotypic changes and phenotypic traits on a genome-wide scale can contribute to understanding the functional roles of distinct genetic variations during breed development. We performed a whole-genome analysis of Angus and Jersey cattle breeds using conditional mutual information, which is an information-theoretic method estimating the conditional independency among multiple factor variables. The proposed conditional mutual information-based approach allows breed-discriminative genetic variations to be explicitly identified from tens of millions of SNP (single nucleotide polymorphism) positions on a genome-wide scale while minimizing the usage of prior knowledge. Using this data-driven approach, we identified biologically relevant functional genes, including breed-specific variants for cattle traits such as beef and dairy production. The identified lipid-related genes were shown to be significantly associated with lipid and triglyceride metabolism, fat cell differentiation, and muscle development. In addition, we confirmed that milk-related genes are involved in mammary gland development, lactation, and mastitis-associated processes. Our results provide the distinct properties of Angus and Jersey cattle at a genome-wide level. Moreover, this study offers important insights into discovering unrevealed genetic variants for breed-specific traits and the identification of genetic signatures of diverse cattle breeds with respect to target breed-specific properties.

Domestication leads to increased predation susceptibility

Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.

Screening genetic diseases prevalence in Braunvieh cattle

Heritable abnormalities can cause a reduction in productive performance, structural defects, or death of the animal. There are reports of hereditary abnormalities in Braunvieh cattle from several countries, but no evidence was found on their existence in Mexico. In this study, 28 genes associated with hereditary diseases were screened with the GGP-LD 30K array (GeneSeek^®) in 300 Mexican registered Braunvieh animals. Allelic frequencies of the markers associated with illness were obtained for the following: citrullinaemia, spinal dysmyelination, spinal muscular atrophy, Brows Swiss fertility haplotype 2, congenital muscular dystonia, epidermolysis bullosa, Pompes, maple syrup urine, syndactyly, Weaver syndrome, crooked tail, deficiency of uridine monophosphate synthase, hypotrichosis, Marfan syndrome, and weak calf syndrome. The allelic frequency values were low for all the analysed loci (from 0.0015 to 0.0110), with exception of syndactyly (0.4145). Although homozygous animals for these genetic conditions were detected, no physical or physiological abnormalities associated with the clinical form of the diseases were observed in the sampled animals. Markers associated with a crooked tail, deficiency of uridine monophosphate synthase, hypotrichosis, Marfan syndrome, and weak calf syndrome were absent. The studied Mexican Braunvieh population does not present clinical or subclinical effects for ten diseases in homozygous animals. However, since the assessed animals are considered as breeding stock, the monitoring of carrier animals might be periodically necessary.

Deciphering signature of selection affecting beef quality traits in Angus cattle

Artificial selection towards a desired phenotype/trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a cross-population composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A-H and A-J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A-H) and five (A-J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.