Genome-wide association study of infectious bovine keratoconjunctivitis in Angus cattle

A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned?

The Brangus cattle were developed to utilize the superior traits of Angus and Brahman cattle. Their genetic compositions are expected to be stabilized at 3/8 Brahman and 5/8 Angus. Previous studies have shown more than expected Angus lineage with Brangus cattle, and the reasons are yet to be investigated. In this study, we revisited the breed compositions for 3,605 Brangus cattle from three perspectives: genome-wise (GBC), per chromosomes (CBC), and per chromosome segments (SBC). The former (GBC) depicted an overall picture of the “mosaic” genome of the Brangus attributable to their ancestors, whereas the latter two criteria (CBC and SBC) corresponded to local ancestral contributions. The average GBC for the 3,605 Brangus cattle were 70.2% Angus and 29.8% Brahman. The K-means clustering supported the postulation of the mixture of 1/2 Ultrablack (UB) animals in Brangus. For the non-UB Brangus animals, the average GBC were estimated to be 67.4% Angus and 32.6% Brahman. The 95% confidence intervals of their overall GBC were 60.4%–73.5% Angus and 26.5%–39.6% Brahman. Possibly, genetic selection and drifting have resulted in an approximately 5% average deviation toward Angus lineage. The estimated ancestral contributions by chromosomes were heavily distributed toward Angus, with 27 chromosomes having an average Angus CBC greater than 62.5% but only two chromosomes (5 and 20) having Brahman CBC greater than 37.5%. The chromosomal regions with high Angus breed proportions were prevalent, tending to form larger blocks on most chromosomes. In contrast, chromosome segments with high Brahman breed proportion were relatively few and isolated, presenting only on seven chromosomes. Hence, genomic hitchhiking effects were strong where Angus favorable alleles resided but weak where Brahman favorable alleles were present. The functions of genes identified in the chromosomal regions with high (≥75%) Angus compositions were diverse yet may were related to growth and body development. In contrast, the genes identified in the regions with high (≥37.5%) Brahman compositions were primarily responsible for disease resistance. In conclusion, we have addressed the questions concerning the Brangus genetic make-ups. The results can help form a dynamic picture of the Brangus breed formation and the genomic reshaping.

Genome-wide association study of resistance/susceptibility to infectious bovine keratoconjunctivitis in Brazilian Hereford cattle

Genome-wide association studies were conducted to identify the more informative genomic regions and SNPs, as well as to identify candidate genes associated with infectious bovine keratoconjunctivitis (IBK) resistance/susceptibility in Hereford cattle. A Bayes B statistical approach was initially applied in genome-wide association studies by using deregressed estimated breeding values for IBK resistance/susceptibility. To estimate the combined effect of a genomic region that is potentially associated with QTL, 2504 non-overlapping 1-Mb windows that varied in SNP number were defined, with the most informative 24 windows including 427 SNPs and explaining more than 20% of the estimated genetic variance for IBK resistance/susceptibility. These regions were explored with respect to their biological functions through functional analysis to map potential candidate genes. The significant SNPs were mapped on chromosomes 1, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 18, 20, 23, and 28, and candidate genes were detected as related to the IBK. Most informative SNPs in term of genetic variance were located in proximity of genes related to phenotypic expression of lesions and biological processes associated to the IBK. Knowledge about phenotypic and genomic variation generated in the present study can be used to on design selection strategies to improve the resistance to IBK of Hereford cattle herds.

Risk factors associated with pinkeye in Australian cattle

Pinkeye is the most important bovine ocular disease worldwide and a major welfare and economic concern to the Australian cattle industry. Pinkeye can occur in epidemic proportions, but severity and susceptibility vary within and between herds, indicating that the disease is multifactorial. This study was conducted to identify the on-farm risk factors associated with pinkeye disease in Australian cattle. Data were gathered from cattle farmers using a custom designed online questionnaire. Farmer responses suitable for assessment (n = 999) were analysed with descriptive, univariable and multivariable logistic regression to evaluate the association of 26 explanatory variables with pinkeye within-herd prevalence. Results revealed that farm location, farm grazing area, farmer-reported dust levels, fly levels, rain levels, animal zebu content and cattle age were significantly associated with pinkeye prevalence. More specifically, having a farm located in southern Australia, of smaller grazing area with cattle ≤ 2 years of age, was associated with a higher pinkeye prevalence. Pinkeye prevalence was also greater if respondents ranked their farms as having high fly levels compared to moderate and low fly levels, respectively and on farms ranked low for rainfall compared to moderate and high rainfall, respectively. Those that ranked their farms as having high dust levels had more pinkeye compared to moderate and low dust levels, but moderate dust levels were protective compared to low dust levels. The results confirm that pinkeye disease is multifactorial and is associated with a range of host and environmental factors. These findings should be used to assist in the control of the disease and improve pinkeye outcomes in Australian cattle.

Component Causes of Infectious Bovine Keratoconjunctivitis: The Role of Genetic Factors in the Epidemiology of Infectious Bovine Keratoconjunctivitis

The purpose of this article is to discuss the host as a cause of infectious bovine keratoconjunctivitis (IBK). The focus is on the host genetics rather than characteristics of the host, such as age, sex, and season of birth. From 4 conducted studies, estimates of IBK heritability are generally less than 0.15, except for some estimates for Herefords and Angus cattle around 0.2 and 1 study reporting a heritability of 0.33. These magnitudes of heritability are typically described as low to moderate. Quantitative trait locus on chromosome 1, 2, 12, 13, 20, and 21 has been associated with IBK resistance.

Future Directions for Research in Infectious Bovine Keratoconjunctivitis

In this article, the authors summarize the future needs from a research perspective to make the greatest gains. They discuss the areas of research: diagnosis, epidemiology, economic impact, prevention, and treatment. In some areas, simple studies with little cost could be conducted that would quickly add to the evidence base. In other areas, substantial investment is needed if new study approaches, which do not repeat past studies' failures, are to be conducted. To maximize the value of research funding, it is essential to critically evaluate the information gains from prior studies and ensure that studies increase knowledge incrementally.

Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea)

Large yellow croaker is an important marine culture species in China. Recently, the large yellow croaker industry is threatened by various disease problems, especially for the white spot disease, which is caused by parasite Cryptocaryon irritans. In the current study, we conducted a genome-wide association study (GWAS) for C. irritans resistance in two large yellow croaker populations (n = 264 and n = 480, respectively). We identified 15 QTL with explained genetic variance ranging from 1 to 8% in the two populations. One QTL on chromosome 23 was shared by the two populations, and three QTL had been reported in the previous study. We identified a lot of biological pathways associated with C. irritans resistance, such as hormone transport, response to bacterium, apoptotic process, acute inflammatory response to antigenic stimulus, and NF-kappa B signaling pathway. The genes casp8 and traf6 involved in regulatory network for apoptosis and inflammation were identified to be candidate genes for C. irritans resistance. Our results showed the complex polygenic architecture of resistance of large yellow croaker against C. irritans. These results would be helpful for the researches of the molecular mechanism of C. irritans resistance and genome-assisted breeding of large yellow croaker.

Insights into adaption and growth evolution: a comparative genomics study on two distinct cattle breeds from Northern and Southern China

Mongolian cattle (MG, Bos taurus) and Minnan cattle (MN, Bos indicus) are two different breeds of Chinese indigenous cattle, representing North type and South type, respectively. However, their value and potential have not yet been discovered at the genomic level. In this study, 26 individuals of MN and MG were sequenced for the first time at an average of 13.9- and 12.8-fold, respectively. Large numbers of different variations were identified. In addition, the analyses of phylogenetic and population structure showed that these two cattle breeds are distinct from each other, and results of linkage disequilibrium analysis revealed that these two cattle breeds have undergone various degrees of intense natural or artificial selection. Subsequently, 496 and 306 potential selected genes (PSRs) were obtained in MN and MG, containing 1,096 and 529 potential selected genes (PSGs), respectively. These PSGs, together with the analyzed copy number variation (CNV)-related genes, showed potential relations with their phenotypic characteristics, including environmental adaptability (e.g., DVL2, HSPA4, CDHR4), feed efficiency (e.g., R3HDM1, PLAG1, XKR4), and meat/milk production (e.g., PDHB, LEMD3, APOF). The results of this study help to gain new insights into the genetic characteristics of two distinct cattle breeds and will contribute to future cattle breeding.

Copy number variation detection in Chinese indigenous cattle by whole genome sequencing

Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.

Similar Genetic Architecture with Shared and Unique Quantitative Trait Loci for Bacterial Cold Water Disease Resistance in Two Rainbow Trout Breeding Populations

Bacterial cold water disease (BCWD) causes significant mortality and economic losses in salmonid aquaculture. In previous studies, we identified moderate-large effect quantitative trait loci (QTL) for BCWD resistance in rainbow trout (Oncorhynchus mykiss). However, the recent availability of a 57 K SNP array and a reference genome assembly have enabled us to conduct genome-wide association studies (GWAS) that overcome several experimental limitations from our previous work. In the current study, we conducted GWAS for BCWD resistance in two rainbow trout breeding populations using two genotyping platforms, the 57 K Affymetrix SNP array and restriction-associated DNA (RAD) sequencing. Overall, we identified 14 moderate-large effect QTL that explained up to 60.8% of the genetic variance in one of the two populations and 27.7% in the other. Four of these QTL were found in both populations explaining a substantial proportion of the variance, although major differences were also detected between the two populations. Our results confirm that BCWD resistance is controlled by the oligogenic inheritance of few moderate-large effect loci and a large-unknown number of loci each having a small effect on BCWD resistance. We detected differences in QTL number and genome location between two GWAS models (weighted single-step GBLUP and Bayes B), which highlights the utility of using different models to uncover QTL. The RAD-SNPs detected a greater number of QTL than the 57 K SNP array in one population, suggesting that the RAD-SNPs may uncover polymorphisms that are more unique and informative for the specific population in which they were discovered.

Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle

Background

Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations.

Results

Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained).

Conclusions

Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3754-y) contains supplementary material, which is available to authorized users.

Whole genome sequencing of Guzerá cattle reveals genetic variants in candidate genes for production, disease resistance, and heat tolerance

In bovines, artificial selection has produced a large number of breeds which differ in production, environmental adaptation, and health characteristics. To investigate the genetic basis of these phenotypical differences, several bovine breeds have been sequenced. Millions of new SNVs were described at every new breed sequenced, suggesting that every breed should be sequenced. Guzerat or Guzerá is an indicine breed resistant to drought and parasites that has been the base for some important breeds such as Brahman. Here, we describe the sequence of the Guzerá genome and the in silico functional analyses of intragenic breed-specific variations. Mate-paired libraries were generated using the ABI SOLiD system. Sequences were mapped to the Bos taurus reference genome (UMD 3.1) and 87% of the reference genome was covered at a 26X. Among the variants identified, 2,676,067 SNVs and 463,158 INDELs were homozygous, not found in any database searched, and may represent true differences between Guzerá and B. taurus. Functional analyses investigated with the NGS-SNP package focused on 1069 new, non-synonymous SNVs, splice-site variants (including acceptor and donor sites, and the conserved regions at both intron borders, referred to here as splice regions) and coding INDELs (NS/SS/I). These NS/SS/I map to 935 genes belonging to cell communication, environmental adaptation, signal transduction, sensory, and immune systems pathways. These pathways have been involved in phenotypes related to health, adaptation to the environment and behavior, and particularly, disease resistance and heat tolerance. Indeed, 105 of these genes are known QTLs for milk, meat and carcass, production, reproduction, and health traits. Therefore, in addition to describing new genetic variants, our approach provided groundwork for unraveling key candidate genes and mutations.

Pain and sickness behavior associated with corneal lesions in dairy calves

Infectious bovine keratoconjunctivitis (IBK) is a common corneal disease of calves that adversely affects animal welfare by causing pain and weight loss. Identifying behavioral indicators of pain and sickness in calves with IBK is necessary for designing studies that aim to identify effective means of pain mitigation. Consistent with principles of the 3Rs for animal use in research, data from a randomized blinded challenge study was used to identify and describe variation of behaviors that could serve as reliable indicators of pain and sickness in calves with corneal injuries. Behavioral observations were collected from 29 Holstein calves 8 to 12 weeks of age randomly allocated to one of three treatments: (1) corneal scarification only, (2) corneal scarification with inoculation with Moraxella bovoculi and (3) corneal scarification with inoculation with Moraxella bovis. Behavior was continuously observed between time 1230 - 1730 h on day -1 (baseline time period) and day 0 (scarification time period). Corneal scarification and inoculation occurred between 0800 - 1000 h on day 0. Frequency of head-directed behaviors (head shaking, head rubbing, head scratching) and durations of head rubbing, feeding, standing with head lifted, lying with head lifted and sleeping were compared between study days and groups. Following scarification, the frequency of head-directed behavior significantly increased (p = 0.0001), as did duration of head rubbing (p=0.02). There was no significant effect of trial, trial day, treatment or treatment-day interaction on other behaviors studied. Our study demonstrated that head-directed behavior, such as head shaking, rubbing and scratching, was associated with scarification of eyes using an IBK challenge model, but sickness behavior was not observed.

Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle

Background

Meat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF.

Results

Twenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥ 1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle.

Conclusions

The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.

The application of genome-wide SNP genotyping methods in studies on livestock genomes

Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.