Suitability of GWAS as a Tool to Discover SNPs Associated with Tick Resistance in Cattle: A Review

Applying the algorithm for Proven and young in GWAS Reveals high polygenicity for key traits in Nellore cattle

Background

Identifying genomic regions associated with traits of interest and their biological processes provides valuable insights into the phenotypic variability of these traits. This study aimed to identify candidate genes and genomic regions associated with 16 traits currently evaluated by the Brazilian Association of Zebu Breeders (ABCZ). These traits include reproductive traits such as age at first calving (AFC), stayability (STAY), and scrotal circumference at 365 (SC365) and 450 days (SC450). Growth traits include birthweight (BW), expected progeny difference for weight at 120days of age (EPD120), as well as weight at 120 (W120), 210 (W210), 365 (W365), and 450 days of age (W450). Carcass traits include body conformation (BC), finishing score (FS), marbling (MARB), muscularity (MUSC), finishing precocity (FP), and ribeye area (REA).

Methods

A dataset containing 304,782 Nellore cattle genotyped with 437,650 SNPs (after quality control) was used for this study. The Algorithm for Proven and Young (APY), implemented in the PREGSF90 software, was used to compute theG A P Y - 1 matrix using 36,000 core animals (which explained 98% of the variance in the genomic matrix). Subsequently, the SNP solutions were estimated by back-solving the Genomic Estimated Breeding Values (GEBVs) predicted by ABCZ using the single-step GBLUP method. Genomic regions were identified using sliding windows of 175 consecutive SNPs, and the top 1% genomic windows, ranked based on their proportion of the additive genetic variance, were used to annotate positional candidate genes and genomic regions associated with each of the 16 traits.

Results

The top 1% windows for all traits explained between 2.779% (STAY) to 3.158% (FP) of the additive genetic variance, highlighting the polygenic nature of these traits. Functional analysis of the candidate genes and genomic regions provided valuable insights into the genetic architecture underlying these traits in Nellore cattle. For instance, our results revealed genes with important functions for each trait, such as SERPINA14 (plays a key role for the endometrial epithelium) identified for AFC, HSPG2 (associated with morphological development and tissue differentiation) identified for BW, among others.

Conclusion

We identified genomic regions and candidate genes, some of which have been previously reported in the literature, while others are novel discoveries that warrant further investigation. These findings contribute to gene prioritization efforts, facilitating the identification of functional candidate genes that can enhance genomic selection strategies for economically important traits in Nellore cattle.

Genome-wide association analysis study on host resistance against the Aeromonas veronii of largemouth bass Micropterus salmoides

Largemouth bass (Micropterus salmoides) has become one of the most important freshwater economic fish farmed almost all over China in recent years. At the same time, the increasing outbreaks of diseases in its aquaculture process have caused substantial economic losses to this industry. However, at present, the genetic basis of disease resistance, including resistance against Aeromonas veronii infection, in largemouth bass is very limited. Therefore, a genome-wide association study (GWAS) on host resistance against the A. veronii of largemouth bass was conducted in the present study. A total of 627 largemouth bass were artificially challenged by A. veronii, among which 160 of the earliest deaths and 173 of the final survivals were genotyped. A total of 3076 high-quality SNPs were used for further analysis employing two analysis models, of which six shared SNPs were finally identified as significant molecular markers with the explaining phenotypic variance ranging from 2.28 % to 8.95 %. Furthermore, seven candidate genes were identified, including one gene, T-cell surface antigen CD2, which is directly involved in T cell activation and the cellular immune response. Additionally, the other identified genes play roles in critical processes such as cell survival, inflammatory responses, and signal transduction. This study lays a genetic foundation for research on largemouth bass disease resistance and studies related to A. veronii. It also contributes significantly to the future development of the commercial production of largemouth bass.

Application of Genomic Selection in Beef Cattle Disease Prevention

Genomic applications in beef cattle disease prevention have gained traction in recent years, offering new strategies for improving herd health and reducing economic losses in the livestock industry. Advances in genomics, including identification of genetic markers linked to disease resistance, provide powerful tools for early detection, selection, and management of cattle resistant to infectious diseases. By incorporating genomic technologies such as whole-genome sequencing, genotyping, and transcriptomics, researchers can identify specific genetic variants associated with resistance to pathogens like bovine respiratory disease and Johne's disease. These genomic insights allow for more accurate breeding programs aimed at enhancing disease resistance and overall herd resilience. Genomic selection, in particular, enables identification of individuals with superior genetic traits for immune function, reducing the need for antibiotic treatments and improving animal welfare. Moreover, precision medicine, powered by genomic data, supports development of tailored health management strategies, including targeted vaccination plans and antimicrobial stewardship. Incorporation of genomic tools in beef cattle management also offers the potential for early disease detection, facilitating proactive interventions that reduce the spread of infections. Despite challenges like cost, data interpretation and integration into current management systems, the potential advantages of genomic applications in disease prevention are substantial. As these technologies advance, they are anticipated to have crucial roles in improving sustainability (by enhancing herd performance), profitability (by improving overall herd longevity), and biosecurity (by decreasing the likelihood of disease outbreaks) of beef cattle production systems worldwide.

Exploring the biological responses involved in the genetic resistance to Rhipicephalus microplus in Argentine Creole cattle

The common cattle tick Rhipicephalus microplus causes severe limitations to livestock production. Bovine genetics could be a decisive component for the success or failure of control programs for ticks and diseases transmitted. The objective of this work was to detect chromosomal regions associated with host resistance to R. microplus through an associative mapping study using medium and high density microarrays in a population of Argentine Creole cattle. The phenotypic record of the number of ticks that completed their development on the host, after artificial infestations, was obtained during 2015 to 2020. Genomic DNA was extracted for genotyping from 192 animals using Affymetrix high (Axiom™ Bos 1) and medium density (ArBos1) microarrays. In an exploratory study, chromosomal regions containing putative quantitative trait loci (QTLs) were recognized on chromosomes 27, 11, 10, 9, 16, 13, 3, 19, 8 and 18, associated with the variation of R. microplus load. Gene ontology based on genes located on these regions revealed an enrichment of terms and pathways for the immune system, blood coagulation, tissue regeneration, endopeptidase activity and protein phosphorylation. The information obtained in this work constitutes a first report of QTLs for tick count in the Argentine Creole cattle, and contributes with the knowledge about the underlying process involved in tick resistance.

An overview of recent technological developments in bovine genomics

Cattle are regarded as highly valuable animals because of their milk, beef, dung, fur, and ability to draft. The scientific community has tried a number of strategies to improve the genetic makeup of bovine germplasm. To ensure higher returns for the dairy and beef industries, researchers face their greatest challenge in improving commercially important traits. One of the biggest developments in the last few decades in the creation of instruments for cattle genetic improvement is the discovery of the genome. Breeding livestock is being revolutionized by genomic selection made possible by the availability of medium- and high-density single nucleotide polymorphism (SNP) arrays coupled with sophisticated statistical techniques. It is becoming easier to access high-dimensional genomic data in cattle. Continuously declining genotyping costs and an increase in services that use genomic data to increase return on investment have both made a significant contribution to this. The field of genomics has come a long way thanks to groundbreaking discoveries such as radiation-hybrid mapping, in situ hybridization, synteny analysis, somatic cell genetics, cytogenetic maps, molecular markers, association studies for quantitative trait loci, high-throughput SNP genotyping, whole-genome shotgun sequencing to whole-genome mapping, and genome editing. These advancements have had a significant positive impact on the field of cattle genomics. This manuscript aimed to review recent advances in genomic technologies for cattle breeding and future prospects in this field.

Application of GWAS and mGWAS in Livestock and Poultry Breeding

In recent years, genome-wide association studies (GWAS) and metabolome genome-wide association studies (mGWAS) have emerged as crucial methods for investigating complex traits in animals and plants. These have played pivotal roles in research on livestock and poultry breeding, facilitating a deeper understanding of genetic diversity, the relationship between genes, and genetic bases in livestock and poultry. This article provides a review of the applications of GWAS and mGWAS in animal genetic breeding, aiming to offer reference and inspiration for relevant researchers, promote innovation in animal genetic improvement and breeding methods, and contribute to the sustainable development of animal husbandry.

Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle

Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.

Elucidation of novel SNPs affecting immune response to classical swine fever vaccination in pigs using immunogenomics approach

The host genetic makeup plays a significant role in causing the within-breed variation among individuals after vaccination. The present study was undertaken to elucidate the genetic basis of differential immune response between high and low responder Landlly (Landrace X Ghurrah) piglets vis-à-vis CSF vaccination. For the purpose, E2 antibody response against CSF vaccination was estimated in sampled animals on the day of vaccination and 21-day post-vaccination as a measure of humoral immune response. Double-digestion restriction associated DNA (ddRAD) sequencing was undertaken on 96 randomly chosen Landlly piglets using Illumina HiSeq platform. SNP markers were called using standard methodology. Genome-wide association study (GWAS) was undertaken in PLINK program to identify the informative SNP markers significantly associated with differential immune response. The results revealed significant SNPs associated with E2 antibody response against CSF vaccination. The genome-wide informative SNPs for the humoral immune response against CSF vaccination were located on SSC10, SSC17, SSC9, SSC2, SSC3 and SSC6. The overlapping and flanking genes (500Kb upstream and downstream) of significant SNPs were CYB5R1, PCMTD2, WT1, IL9R, CD101, TMEM64, TLR6, PIGG, ADIPOR1, PRSS37, EIF3M, and DNAJC24. Functional enrichment and annotation analysis were undertaken for these genes in order to gain maximum insights into the association of these genes with immune system functionality in pigs. The genetic makeup was associated with differential immune response against CSF vaccination in Landlly piglets while the identified informative SNPs may be used as suitable markers for determining variation in host immune response against CSF vaccination in pigs.

Current Status and Challenges Associated with Tick-Borne Pathogens and Diseases: Where Do We Stand?

Lyme Borreliosis (LB), caused by Borrelia burgdorferi sensu lato (s [...].

Tick and Tick-Borne Diseases: New Problems Providing New Possible Solutions

Ticks and tick-borne diseases are responsible for enormous losses in animal and human life, which do not seem to become better as new data show surprising connections [...].

Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science

Having played important roles in human growth and development, livestock animals are regarded as integral parts of society. However, industrialization has depleted natural resources and exacerbated climate change worldwide, spurring the emergence of various diseases that reduce livestock productivity. Meanwhile, a growing human population demands sufficient food to meet their needs, necessitating innovations in veterinary sciences that increase productivity both quantitatively and qualitatively. We have been able to address various challenges facing veterinary and farm systems with new scientific and technological advances, which might open new opportunities for research. Recent breakthroughs in multi-omics platforms have produced a wealth of genetic and genomic data for livestock that must be converted into knowledge for breeding, disease prevention and management, productivity, and sustainability. Vetinformatics is regarded as a new bioinformatics research concept or approach that is revolutionizing the field of veterinary science. It employs an interdisciplinary approach to understand the complex molecular mechanisms of animal systems in order to expedite veterinary research, ensuring food and nutritional security. This review article highlights the background, recent advances, challenges, opportunities, and application of vetinformatics for quality veterinary services.

Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences

Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.