Fine-mapping thePOLLlocus in Brahman cattle yields the diagnostic markerCSAFG29

The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock

Oxford Nanopore Technologies' MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the recent African swine fever outbreak in China and providing a diagnostic tool for disease in the cassava plant in Eastern Africa. Here we review the current applications of Oxford Nanopore sequencing in livestock, then focus on proposed applications in livestock agriculture for rapid diagnostics, base modification detection, reference genome assembly and genomic prediction. In particular, we propose a future application: 'crush-side genotyping' for real-time on-farm genotyping for extensive industries such as northern Australian beef production. An initial in silico experiment to assess the feasibility of crush-side genotyping demonstrated promising results. SNPs were called from simulated Nanopore data, that included the relatively high base call error rate that is characteristic of the data, and calling parameters were varied to understand the feasibility of SNP calling at low coverages in a heterozygous population. With optimised genotype calling parameters, over 85% of the 10,000 simulated SNPs were able to be correctly called with coverages as low as 6×. These results provide preliminary evidence that Oxford Nanopore sequencing has potential to be used for real-time SNP genotyping in extensive livestock operations.

Characterization of the poll allele in Brahman cattle using long-read Oxford Nanopore sequencing

Brahman cattle (Bos indicus) are well adapted to thrive in tropical environments. Since their introduction to Australia in 1933, Brahman's ability to grow and reproduce on marginal lands has proven their value in the tropical beef industry. The poll phenotype, which describes the absence of horns, has become desirable in the cattle industry for animal welfare and handler safety concerns. The poll locus has been mapped to chromosome one. Four alleles, each a copy number variant, have been reported across this locus in B. indicus and Bos taurus. However, the causative mutation in Brahman cattle has not been fully characterized. Oxford Nanopore Technologies' minION sequencer was used to sequence four homozygous poll (PcPc), four homozygous horned (pp), and three heterozygous (Pcp) Brahmans to characterize the poll allele in Brahman cattle. A total of 98 Gb were sequenced and an average coverage of 3.33X was achieved. Read N50 scores ranged from 9.9 to 19 kb. Examination of the mapped reads across the poll locus revealed insertions approximately 200 bp in length in the poll animals that were absent in the horned animals. These results are consistent with the Celtic poll allele, a 212-bp duplication that replaces 10 bp. This provides direct evidence that the Celtic poll allele is segregating in the Australian Brahman population.

Optimized Genetic Testing for Polledness in Multiple Breeds of Cattle

Many breeds of modern cattle are naturally horned, and for sound husbandry management reasons the calves frequently undergo procedures to physically remove the horns by disbudding or dehorning. These procedures are however a welfare concern. Selective breeding for polledness - absence of horns - has been effective in some cattle breeds but not in others (Bos indicus genotypes) due in part to the complex genetics of horn phenotype. To address this problem different approaches to genetic testing which provide accurate early-in-life prediction of horn phenotype have been evaluated, initially using microsatellites (MSAT) and more recently single nucleotide polymorphism (SNP). A direct gene test is not effective given the genetic heterogeneity and large-sized sequence variants associated with polledness in different breeds. The current study investigated 39,943 animals of multiple breeds to assess the accuracy of available poll testing assays. While the standard SNP-based test was an improvement on the earlier MSAT haplotyping method, 1999 (9.69%) out of 20,636 animals tested with this SNP-based assay did not predict a genotype, most commonly associated with the Indicus-influenced breeds. The current study has developed an optimized poll gene test that resolved the vast majority of these 1999 unresolved animals, while the predicted genotypes of those previously resolved remained unchanged. Hence the optimized poll test successfully predicted a genotype in 99.96% of samples assessed. We demonstrated that a robust set of 5 SNPs can effectively determine P_C and P_F alleles and eliminate the ambiguous and undetermined results of poll gene testing previously identified as an issue in cattle.

The role of molecular genetics in livestock production

Genetic variations that lead to easy-to-identify phenotypic changes have always been of interest to livestock breeders since domestication. Molecular genetics has opened up possibilities for identifying these variations and understanding their biological and population effects. Moreover, molecular genetics is part of the most diverse approaches and applications in animal production nowadays, including paternity testing, selection based on genetic variants, diagnostic of genetic diseases, reproductive biotechniques, fraud identification, differentiation of hybrids, parasite identification, genetic evaluation, diversity studies, and genome editing, among others. Therefore, the objective of this review was to describe the different applications of molecular genetics in livestock production, contextualising them with examples and highlighting the importance of the study of these topics and their applications.

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Brahman cattle have a Bos indicus and Bos taurus mosaic genome, as a result of the process used to create the breed (repeat backcrossing of Bos taurus females to Bos indicus bulls). With the aim of identifying Bos taurus segments in the Brahman genome at sequence level resolution, we sequenced the genomes of 46 influential Brahman bulls. Using 36 million variants identified in the sequences, we searched for regions close to fixation for Bos indicus or Bos taurus segments that were longer than expected by chance (from simulation of the breed formation history of Brahman cattle). Regions close to fixation for Bos indicus content were enriched for protein synthesis genes, while regions of higher Bos taurus content included genes of the G-protein coupled receptor family (including genes implicated in puberty, such as THRS). The region with the most extreme Bos taurus enrichment was on chromosome 14 surrounding PLAG1. The introgressed Bos taurus allele at PLAG1 increases stature and the high frequency of the allele likely reflects strong selection for the trait. Finally, we provide evidence that the polled mutation in Brahmans, a desirable trait under very strong recent selection, is of Celtic origin and is introgressed from Bos taurus.

Climate Adaptation of Tropical Cattle

There is sustained growth in the number of tropical cattle, which represent more than half of all cattle worldwide. By and large, most research in tropical areas is still focused on breeds of cattle, their particular advantages or disadvantages in tropical areas, and the tropical forages or feeds that could be usefully fed to them. A consistent issue for adaptation to climate is the heat of tropical environments. Changing the external characteristics of the animal, such as color and coat characteristics, is one way to adapt, and there are several major genes for these traits. However, further improvement in heat tolerance and other adaptation traits will need to use the entire genome and all physical and physiological systems. Apart from the response to heat, climate forcing through methane emission identifies dry season weight loss as an important if somewhat neglected trait in climate adaptation of cattle. The use of genome-estimated breeding values in tropical areas is in its infancy and will be difficult to implement, but will be essential for rapid, coordinated genetic improvement. The difficulty of implementation cannot be exaggerated and may require major improvements in methodology.

Genome-wide Association Study Identifies Loci for the Polled Phenotype in Yak

The absence of horns, known as the polled phenotype, is an economically important trait in modern yak husbandry, but the genomic structure and genetic basis of this phenotype have yet to be discovered. Here, we conducted a genome-wide association study with a panel of 10 horned and 10 polled yaks using whole genome sequencing. We mapped the POLLED locus to a 200-kb interval, which comprises three protein-coding genes. Further characterization of the candidate region showed recent artificial selection signals resulting from the breeding process. We suggest that expressional variations rather than structural variations in protein probably contribute to the polled phenotype. Our results not only represent the first and important step in establishing the genomic structure of the polled region in yak, but also add to our understanding of the polled trait in bovid species.

Evaluation of breeding strategies for polledness in dairy cattle using a newly developed simulation framework for quantitative and Mendelian traits

Background

Intensified selection of polled individuals has recently gained importance in predominantly horned dairy cattle breeds as an alternative to routine dehorning. The status quo of the current polled breeding pool of genetically-closely related artificial insemination sires with lower breeding values for performance traits raises questions regarding the effects of intensified selection based on this founder pool.

Methods

We developed a stochastic simulation framework that combines the stochastic simulation software QMSim and a self-designed R program named QUALsim that acts as an external extension. Two traits were simulated in a dairy cattle population for 25 generations: one quantitative (QMSim) and one qualitative trait with Mendelian inheritance (i.e. polledness, QUALsim). The assignment scheme for qualitative trait genotypes initiated realistic initial breeding situations regarding allele frequencies, true breeding values for the quantitative trait and genetic relatedness. Intensified selection for polled cattle was achieved using an approach that weights estimated breeding values in the animal best linear unbiased prediction model for the quantitative trait depending on genotypes or phenotypes for the polled trait with a user-defined weighting factor.

Results

Selection response for the polled trait was highest in the selection scheme based on genotypes. Selection based on phenotypes led to significantly lower allele frequencies for polled. The male selection path played a significantly greater role for a fast dissemination of polled alleles compared to female selection strategies. Fixation of the polled allele implies selection based on polled genotypes among males. In comparison to a base breeding scenario that does not take polledness into account, intensive selection for polled substantially reduced genetic gain for this quantitative trait after 25 generations. Reducing selection intensity for polled males while maintaining strong selection intensity among females, simultaneously decreased losses in genetic gain and achieved a final allele frequency of 0.93 for polled.

Conclusions

A fast transition to a completely polled population through intensified selection for polled was in contradiction to the preservation of high genetic gain for the quantitative trait. Selection on male polled genotypes with moderate weighting, and selection on female polled phenotypes with high weighting, could be a suitable compromise regarding all important breeding aspects.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0228-7) contains supplementary material, which is available to authorized users.

A Meta-Assembly of Selection Signatures in Cattle

Since domestication, significant genetic improvement has been achieved for many traits of commercial importance in cattle, including adaptation, appearance and production. In response to such intense selection pressures, the bovine genome has undergone changes at the underlying regions of functional genetic variants, which are termed “selection signatures”. This article reviews 64 recent (2009–2015) investigations testing genomic diversity for departure from neutrality in worldwide cattle populations. In particular, we constructed a meta-assembly of 16,158 selection signatures for individual breeds and their archetype groups (European, African, Zebu and composite) from 56 genome-wide scans representing 70,743 animals of 90 pure and crossbred cattle breeds. Meta-selection-scores (MSS) were computed by combining published results at every given locus, within a sliding window span. MSS were adjusted for common samples across studies and were weighted for significance thresholds across and within studies. Published selection signatures show extensive coverage across the bovine genome, however, the meta-assembly provides a consensus profile of 263 genomic regions of which 141 were unique (113 were breed-specific) and 122 were shared across cattle archetypes. The most prominent peaks of MSS represent regions under selection across multiple populations and harboured genes of known major effects (coat color, polledness and muscle hypertrophy) and genes known to influence polygenic traits (stature, adaptation, feed efficiency, immunity, behaviour, reproduction, beef and dairy production). As the first meta-assembly of selection signatures, it offers novel insights about the hotspots of selective sweeps in the bovine genome, and this method could equally be applied to other species.

A Prototype Tool to Enable Farmers to Measure and Improve the Welfare Performance of the Farm Animal Enterprise: The Unified Field Index

Schemes for the assessment of farm animal welfare and assurance of welfare standards have proliferated in recent years. An acknowledged short-coming has been the lack of impact of these schemes on the welfare standards achieved on farm due in part to sociological factors concerning their implementation. Here we propose the concept of welfare performance based on a broad set of performance attributes of an enterprise and describe a tool based on risk assessment and benchmarking methods for measuring and managing welfare performance. The tool termed the Unified Field Index is presented in a general form comprising three modules addressing animal, resource, and management factors. Domains within these modules accommodate the principle conceptual perspectives for welfare assessment: biological functioning; emotional states; and naturalness. Pan-enterprise analysis in any livestock sector could be used to benchmark welfare performance of individual enterprises and also provide statistics of welfare performance for the livestock sector. An advantage of this concept of welfare performance is its use of continuous scales of measurement rather than traditional pass/fail measures. Through the feedback provided via benchmarking, the tool should help farmers better engage in on-going improvement of farm practices that affect animal welfare.

Associations of single nucleotide polymorphisms in candidate genes with the polled trait in Datong domestic yaks

The domestic yak (Bos grunniens) is an iconic symbol of animal husbandry at high altitudes. Yaks exhibit unique external characteristics including long hair and large horns. However, hornless yaks can be found in different breeds and different populations. The hornless trait is also known as polled, and the POLL locus has been fine-mapped to chromosome 1 in cattle (Bos taurus), although the underlying genetic basis of the polled trait is still unclear in the yak. Thus, we performed an association study to identify the genetic polymorphisms responsible for the polled trait in the yak. Fifty polled Datong domestic yaks and 51 horned individuals were selected randomly from a huge herd and were used as the case and control groups respectively for the association analysis. Twelve genes located in the candidate region of the POLL locus in cattle were used as references to detect DNA polymorphisms related to yak polledness, which were analyzed by sequencing and a high-resolution melting test. We applied Fisher's exact test and haplotype analysis to show that a 147-kb segment that included three protein-coding genes C1H21orf62, GCFC1 and SYNJ1 was the most likely location of the POLL mutation in domestic yaks.

Validation of genome-wide association studies (GWAS) results

Validation of the results of genome-wide association studies or genomic selection studies is an essential component of the experimental program. Validation allows users to quantify the benefit of applying gene tests or genomic prediction, relative to the costs of implementing the program. Further, if implemented, an appropriate weight in a selection index can only be derived if estimates of the accuracy of genomic predictions are available. In this chapter the reasons for validation are explored, and a range of commonly encountered scenarios described. General principles are stated, and options for performing validation discussed. Designs for validation are heavily dependent on the availability of phenotyped animals, and also on the pedigree structures that characterize the breeding program. Consequently, there is no single plan that is always applicable, and a custom plan often must be developed.