Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

BACKGROUND

Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.

RESULTS

A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.

CONCLUSIONS

A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits

Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.

Genome-wide association studies for economically important traits in mink using copy number variation

Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.

Equine allergic skin diseases: Clinical consensus guidelines of the World Association for Veterinary Dermatology

BACKGROUND

Allergic skin diseases are common in horses worldwide. The most common causes are insect bites and environmental allergens.

OBJECTIVES

To review the current literature and provide consensus on pathogenesis, diagnosis, treatment and prevention.

MATERIALS AND METHODS

The authors reviewed the literature up to November 2022. Results were presented at North America Veterinary Dermatology Forum (2021) and European Veterinary Dermatology Congress (2021). The report was available to member organisations of the World Association for Veterinary Dermatology for feedback.

CONCLUSIONS AND CLINICAL RELEVANCE

Insect bite hypersensitivity (IBH) is the best characterised allergic skin disease. An immunoglobulin (Ig)E response against Culicoides salivary antigens is widely documented. Genetics and environmental factors play important roles. Tests with high sensitivity and specificity are lacking, and diagnosis of IBH is based on clinical signs, seasonality and response to insect control. Eosinophils, interleukin (IL)-5 and IL-31 are explored as therapeutic targets. Presently, the most effective treatment is insect avoidance. Existing evidence does not support allergen-specific immunotherapy (ASIT) using commercially available extracts of Culicoides. Hypersensitivity to environmental allergens (atopic dermatitis) is the next most common allergy. A role for IgE is supported by serological investigation, skin test studies and positive response to ASIT. Prospective, controlled, randomised studies are limited, and treatment relies largely on glucocorticoids, antihistamines and ASIT based on retrospective studies. Foods are known triggers for urticaria, yet their role in pruritic dermatitis is unknown. Recurrent urticaria is common in horses, yet our understanding is limited and focussed on IgE and T-helper 2 cell response. Prospective, controlled studies on treatments for urticaria are lacking. Glucocorticoids and antihistamines are primary reported treatments.

Identification of Copy Number Variations in Four Horse Breed Populations in South Korea

In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds.

Copy Number Variation (CNV): A New Genomic Insight in Horses

Simple Summary

This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response.

Abstract

Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.

Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse

In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of HSPA1A were significantly increased among the different heat shock durations. The expression level of NFKBIA and SOCS4 declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse.

CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly

Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.

A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes

BACKGROUND

In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K.

RESULTS

CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database.

CONCLUSIONS

This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.

Copy number variation: Characteristics, evolutionary and pathological aspects

Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.

Copy Number Variants in Four Italian Turkey Breeds

Simple Summary

Hybrid Turkey selection is focusing on meat production traits characterized by high genetic heritability; the strong directional selection is well known to produce a constant loss in genetic diversity. Genetic characterization is one of the essential activities in the management of populations at risk of extinction. In addition, the genetic structure at the population level and the relationships between individuals are nowadays analysable at the genomic level. In this paper, the genome of 4 different Italian turkey breeds included in the Autochthonous Italian Poultry Breeds Register are analysed in order to obtain a genome-wide Copy Number Variant scan to ameliorate the existing knowledge of the genomic structure of Italian local turkey breeds. Differences have been described at genomic level for physiological, reproductive, and behavioral traits. The analyzed breeds are clearly distinguishable at the genomic level, and their relationships are clearly linked to their geographical origin and to the history of the rural structure of their developing regions. Genome information based on Copy Number Variant (CNV) detection has generated important information in this study concerning the uniqueness of the Italian local turkey breeds.

Abstract

Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions.

A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing

Background

Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing.

Results

A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection.

Conclusions

In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07387-7.

Genetics of Immune Disease in the Horse

Host defenses against infection by viruses, bacteria, fungi, and parasites are critical to survival. It has been estimated that upwards of 7% of the coding genes of mammals function in immunity and inflammation. This high level of genomic investment in defense has resulted in an immune system characterized by extraordinary complexity and many levels of redundancy. Because so many genes are involved with immunity, there are many opportunities for mutations to arise that have negative effects. However, redundancy in the mammalian defense system and the adaptive nature of key immune mechanisms buffer the untoward outcomes of many such deleterious mutations.

Genetics of Skin Disease in Horses

Equine skin diseases are common, causing increased costs and reduced welfare of affected horses.Genetic testing, if available, can complement early detection, disease diagnosis, and clinical treatment and offers horse breeders the possibility to rule out carrier status. The mechanisms of complex disease can be investigated by using the latest state-of-the-art genomic technologies. Genome-based strategies may also serve as an efficient and cost-effective strategy for the management of the disease severity levels, with particular interest in complex traits such as insect bite hypersensitivity, chronic progressive lymphedema, and melanoma.

Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines

The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.

Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds

BACKGROUND

Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses.

RESULTS

We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs.

CONCLUSIONS

This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.

Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds

Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.

Expression analysis of miR-221-3p and its target genes in horses

BACKGROUND

A microRNA (miRNA) is a small non-coding RNA (ncRNA) approximately 20 nucleotides long and it affects gene expression through mRNA cleavage or translational repression. Horses (Equus caballus) have been domesticated and bred to enhance their speed for racing. It has been studied extensively with genetic diversity, origins and evolution.

OBJECTIVES

We examined expression patterns of miR-221-3p and its target gene CDKN1C in various horse tissues.

METHODS

We used bioinformatic tools to examine target gene, seed region and evolutionary conservation of miR-221-3p. The expression patterns of miR-221-3p and its target gene CDKN1C were analyzed by quantitative polymerase chain reaction (qPCR).

RESULTS

Among eight tissues of horse, miR-221-3p was highly expressed in cerebellum and spleen. On the other hand, only medulla was highly expressed in CDKN1C gene.

CONCLUSION

Our study provides expression data of miR-221-3p and CDKN1C gene in horse and suggests the fundamental information for future studies in relation to functional importance.