Development of a genetic tool for determining breed purity of cattle

Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

The Revolution of Animal Genomics in Forensic Sciences

Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.

Balancing at the Borderline of a Breed: A Case Study of the Hungarian Short-Haired Vizsla Dog Breed, Definition of the Breed Profile Using Simple SNP-Based Methods

The aim of this study was to determine the breed boundary of the Hungarian Short-haired Vizsla (HSV) dog breed. Seventy registered purebred HSV dogs were genotyped on approximately 145,000 SNPs. Principal Component Analysis (PCA) and Admixture analysis certified that they belong to the same population. The outer point of the breed demarcation was a single Hungarian Wire-haired Vizsla (HWV) individual, which was the closest animal genetically to the HSV population in the PCA analysis. Three programs were used for the breed assignment calculations, including the widely used GeneClass2.0 software and two additional approaches developed here: the 'PCA-distance' and 'IBS-central' methods. Both new methods calculate a single number that represents how closely a dog fits into the actual reference population. The former approach calculates this number based on the PCA distances from the median of HSV animals. The latter calculates it from identity by state (IBS) data, measuring the distance from a central animal that is the best representative of the breed. Having no mixed-breed dogs with known HSV genome proportion, admixture animals were simulated by using data of HSV and HWV individuals to calibrate the inclusion/exclusion probabilities for the assignment. The numbers generated from these relatively simple calculations can be used by breeders and clubs to keep their populations under genetic supervision.

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.

Genomic breed composition of pure registered Brazilian Gir

INTRODUCTION

Gir is a Bos indicus breed originally from India, first imported to Brazil in 1850. High-performance Dairy Gir has been systematically selected in Brazil from its arrival. Since the major phenotypic difference between Gir in India and Brazil is a higher milk production in the former, it is speculated that Brazilian Gir was strategically crossed with Holstein or another Bos taurus to improve milk yield. This study evaluated the purity of Brazilian Gir breed stocks from BASA Farms in Brazil, trying to identify possible admixture events with other cattle breeds based on DNA analysis.

MATERIALS AND METHODS

The population included 1061 pure registered individuals genotyped using two commercial platforms with 37 k and 25 k SNPs. Admixture analysis was performed individually to estimate levels of genomic composition derived from six different reference populations, three indicine and three taurine breeds.

RESULTS

A Gir ancestry of 99% or higher was found for 94.2% of the population, while the remaining showed levels of non-Gir ancestry up to 6.8%. Only five individuals were identified with possible taurine ancestry, all of them exhibiting levels lower than 2%. The remaining non-Gir ancestry identified was derived from indicine breeds. The levels of admixture observed in the population were from low to non-detectable. No consistent patterns of admixture were observed indicating sustained introgression of taurine lines as means of genetic improvement.

CONCLUSION

According to these results, genetic improvement achieved by Brazilian Gir breeders is the result of within-breed selection methods applied intensively over the past five decades, rather than the result from sustained introgression.

Opportunities of Genomics for the Use of Semen Cryo-Conserved in Gene Banks

Shortly after the introduction of cryo-conserved semen in the main farm animal species, gene banks were founded. Safeguarding farm animal genetic diversity for future use was and is the main objective. A sampling of sires was based on their pedigree and phenotypic information. Nowadays, DNA information from cryo-conserved sires and from animals in the living populations has become available. The combination of their DNA information can be used to realize three opportunities: 1) to make the gene bank a more complete archive of genetic diversity, 2) to determine the history of the genetic diversity from the living populations, and 3) to improve the performance and genetic diversity of living populations. These three opportunities for the use of gene bank sires in the genomic era are outlined in this study, and relevant recent literature is summarized to illustrate the great value of a gene bank as an archive of genetic diversity.

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

Simple Summary

Over the last century, genetic diversity in the cattle species has been affected by the replacement of many local, dual-purpose breeds with a few specialized, high-output dairy breeds. This replacement caused a sharp decline in the population size of local breeds. In the Netherlands, the local Dutch Friesian breed has gradually been replaced by the Holstein Friesian. This resulted in a rapid decrease in numbers of the Dutch Friesian breed with an associated risk of loss of genetic diversity due to drift. The objective of this study is to investigate genomewide genetic diversity between a group of historic and recent Dutch Friesian bulls and a group of recently used Holstein Friesian bulls. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has some unique genetic identity (12% of the single nucleotide polymorphism were group-specific). The genetic diversity of the Dutch Friesians reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors has not increased. Genetically, the recent Dutch Friesians were slightly more different from Holstein Friesians than the historic Dutch Friesians. Our results also highlighted the presence of several genomic regions that differentiated between the groups.

Abstract

Over the last century, genetic diversity in many cattle breeds has been affected by the replacement of traditional local breeds with just a few milk-producing breeds. In the Netherlands, the local Dutch Friesian breed (DF) has gradually been replaced by the Holstein Friesian breed (HF). The objective of this study is to investigate genomewide genetic diversity between a group of historically and recently used DF bulls and a group of recently used HF bulls. Genetic material of 12 historic (hDF), 12 recent DF bulls (rDF), and 12 recent HF bulls (rHF) in the Netherlands was sequenced. Based on the genomic information, different parameters—e.g., allele frequencies, inbreeding coefficient, and runs of homozygosity (ROH)—were calculated. Our findings showed that a large amount of diversity is shared between the three groups, but each of them has a unique genetic identity (12% of the single nucleotide polymorphisms were group-specific). The rDF is slightly more diverged from rHF than hDF. The inbreeding coefficient based on runs of homozygosity (Froh) was higher for rDF (0.24) than for hDF (0.17) or rHF (0.13). Our results also displayed the presence of several genomic regions that differentiated between the groups. In addition, thirteen, forty-five, and six ROH islands were identified in hDF, rDF, and rHF, respectively. The genetic diversity of the DF breed reduced over time, but this did not lead to higher inbreeding levels—especially, inbreeding due to recent ancestors was not increased.

The Use of Genomic Information for the Conservation of Animal Genetic Diversity

The conservation of genetic diversity, both among and within breeds, is a costly process. Therefore, choices between breeds and animals within breeds are unavoidable, either for conservation in vitro (gene banks) or in vivo (maintaining small populations alive). Nowadays, genomic information on breeds and individual animals is the standard for the choices to be made in conservation. Genomics may accurately measure the genetic distances among breeds and the relationships among animals within breeds. Homozygosity at loci and at parts of chromosomes is used to measure inbreeding. In addition, genomics can be used to detect potentially valuable rare alleles and haplotypes, their carriers in these breeds and can facilitate in vivo or in vitro conservations of these genomic regions.

Genomic diversity and breed composition of Vietnamese smallholder dairy cows

Vietnamese smallholder dairy cows (VDC) are the result of crossbreeding between different zebu (ZEB) and taurine dairy breeds through many undefined generations. Thus, the predominant breed composition of VDC is currently unknown. This study aimed to evaluate the level of genetic diversity and breed composition of VDC. The SNP data of 344 animals from 32 farms located across four dairy regions of Vietnam were collected and merged with genomic reference data, which included three ZEB breeds: Red Sindhi, Sahiwal and Brahman, three taurine breeds: Holstein (HOL), Jersey (JER) and Brown Swiss (BSW), and a composite breed: Chinese Yellow cattle. Diversity and admixture analyses were applied to the merged data set. The VDC were not excessively inbred, as indicated by very low inbreeding coefficients (Wright's F_IS ranged from -0.017 to 0.003). The genetic fractions in the test herds suggested that the VDC are primarily composed of HOL (85.0%); however, JER (6.0%), BSW 5.3%) and ZEB (4.5%) had also contributed. Furthermore, major genotype groupings in the test herds were pure HOL (48%), B3:15/16HOL_1/16ZEB (22%) and B2:7/8HOL_1/8ZEB (12%). The genetic makeup of the VDC is mainly components of various dairy breeds but also has a small percentage of ZEB; thus, the VDC could be a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.

Development of a genomic tool for breed assignment by comparison of different classification models: Application to three local cattle breeds

Assignment of individual cattle to a specific breed can often not rely on pedigree information. This is especially the case for local breeds for which the development of genomic assignment tools is required to allow individuals of unknown origin to be included to their herd books. A breed assignment model can be based on two specific stages: (a) the selection of breed-informative markers and (b) the assignment of individuals to a breed with a classification method. However, the performance of combination of methods used in these two stages has been rarely studied until now. In this study, the combination of 16 different SNP panels with four classification methods was developed on 562 reference genotypes from 12 cattle breeds. Based on their performances, best models were validated on three local breeds of interest. In cross-validation, 14 models had a global cross-validation accuracy higher than 90%, with a maximum of 98.22%. In validation, best models used 7,153 or 2,005 SNPs, based on a partial least squares-discriminant analysis (PLS-DA) and assigned individuals to breeds based on nearest shrunken centroids. The average validation sensitivity of the first two best models for the three local breeds of interest were 98.33% and 97.5%. Moreover, results reported in this study suggest that further studies should consider the PLS-DA method when selecting breed-informative SNPs.

Genome-wide selection of discriminant SNP markers for breed assignment in indigenous sheep breeds

The assignment of an individual to the true population of origin is one of the most important applications of genomic data for practical use in animal breeding. The aim of this study was to develop a statistical method and then, to identify the minimum number of informative SNP markers from high-throughput genotyping data that would be able to trace the true breed of unknown samples in indigenous sheep breeds. The total numbers of 217 animals were genotyped using Illumina OvineSNP50K BeadChip in Zel, Lori-Bakhtiari, Afshari, Moqani, Qezel and a wild-type Iranian sheep breed. After SNP quality check, the principal component analysis (PCA) was used to determine how the animals allocated to the groups using all genotyped markers. The results revealed that the first principal component (PC1) separated out the two domestic and wild sheep breeds, and all domestic breeds were separated from each other for PC2. The genetic distance between different breeds was calculated using FST and Reynold methods and the results showed that the breeds were well differentiated. A statistical method was developed using the stepwise discriminant analysis (SDA) and the linear discriminant analysis (LDA) to reduce the number of SNPs for discriminating 6 different Iranian sheep populations and K-fold cross-validation technique was employed to evaluate the potential of a selected subset of SNPs in assignment success rate. The procedure selected reduced pools of markers into 201 SNPs that were able to exactly discriminate all sheep populations with 100% accuracy. Moreover, a discriminate analysis of principal components (DAPC) developed using 201 linearly independent SNPs revealed that these markers were able to assign all individuals into true breed. Finally, these 201 identified SNPs were successfully used in an independent out-group breed consisting of 96 samples of Baluchi sheep breed and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. In general, the results of this study indicated that the combined use of the SDA and LDA techniques represents an efficient strategy for selecting a reduced pool of highly discriminant markers.

Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe

Background

Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful.

Results

Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility.

Conclusions

This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

BACKGROUND

Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows.

METHODS

Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny.

RESULTS

For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2.

CONCLUSIONS

The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products

Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.