Previously imputed high-density genotypes, comprising 734,159 autosomal SNP genotypes from 638,662 cattle were available. An in-depth description of the pipeline used to impute the genotype data to high density is provided by Purfield et al. (2019b) (link). All 638,662 animals had been genotyped on one of the following panels: the Illumina HD panel (777,962 SNPs), the Illumina Bovine SNP50 panel (54,001 SNPs), or one of the custom Irish Dairy and Beef (IDB) genotype panels, namely the IDBV1 (16,662 SNPs), the IDBV2 (16,223 SNPs) or the IDBV3 (52,445 SNPs) panels. Imputation to high density was conducted for all genotyped animals using a two-step approach in FImpute2 (Sargolzaei et al., 2014 (link)). Only autosomal SNPs with a known chromosome and position were considered for imputation. In addition, all imputed animals and SNPs had a call rate ≥90%. The first step in the imputation process involved imputing animals genotyped on the IDB genotype panels to the Illumina Bovine SNP50 density. All animals with genotype information at the Bovine SNP50 density (imputed or not), were then imputed to high density using a multi-breed reference population of 5,504 high-density genotyped males specifically targeted for genotyping given their contribution to the Irish cattle population.
Bovinesnp50
Manufactured by Illumina
Sourced in United States
The BovineSNP50 is a high-density genotyping array designed for genome-wide association studies (GWAS) and genomic selection in cattle. The BovineSNP50 BeadChip allows for the simultaneous interrogation of approximately 54,000 single nucleotide polymorphisms (SNPs) distributed across the bovine genome.
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15 protocols using bovinesnp50
1
High-Density Genotype Imputation in Cattle
2
Genotyping Bovine Breeds for Genetic Analyses
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Animals, phenotypes and genotypes used in this study were a subset of those used in [12 (link)]. Briefly, we used data on 816 Brahman (BB) and 1028 Tropical Composite (TC) cows genotyped using either the BovineSNP50 [13 (link)] or the BovineHD (Illumina Inc., San Diego, CA, USA) that includes more than 770,000 SNPs. For animals that were genotyped with the lower density array, genotypes were imputed to higher-density based on the genotypes of relatives based on pedigree, as described previously [14 (link)]. The imputation was performed using 30 iterations of BEAGLE [15 (link)] within breeds, using 519 Brahman and 351 Tropical Composite animals genotyped using the BovineHD as reference. From the resulting 729,068 SNP genotypes per individual, we extracted the genotypes from 71,726 SNPs that were highly polymorphic in Bos indicus cattle (GGP Indicus HD Chip; http://www.neogeneurope.com/Agrigenomics/pdf/Slicks/NE_GeneSeekCustomChipFlyer.pdf ).
3
Genotyping and Imputation of Cattle Breeds
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The cattle were sourced from two populations, a Bos indicus (Brahman, n = 2112) and a cross-bred Bos taurus × Bos indicus (Tropical Composite, n = 2550) (Barwick et al., 2009 (link)). These animals were genotyped using either the BovineHD (Illumina, San Diego, California; BovineHD.pdf">http://res.illumina.com/documents/products/datasheets/datasheet_BovineHD.pdf ) or the BovineSNP50 (Illumina, San Diego, California) (Matukumalli et al., 2009 (link)). Genotypes acquired with the lower density panel were imputed to higher density using Beagle (Browning and Browning, 2011 (link)). The imputation process and quality control applied to genotypes were described previously (Bolormaa et al., 2013 (link)). In brief, imputations were done within breed applying 30 iterations of Beagle using related individuals that were genotyped using the BovineHD as reference. SNP and individuals were filtered using stringent quality control parameters. All SNP were mapped to the UMD 3.1 assembly of the bovine genome sequence up-dated from Zimin et al. (2009 (link)) (http://www.cbcb.umd.edu/research/bos_taurus_assembly.shtml ).
4
Genotyping and Imputation Workflow for Genomic Studies
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The Angus bulls that had RNA-Seq data, also had Illumina BovineSNP50 (liver samples) or Illumina BovineHD SNP genotypes (muscle samples). The low density SNP were imputed to high density (HD) genotypes using BEAGLE [25 (link)]. The Holsteins had BovineHD SNP genotypes, described by Pryce et al. (2012) [26 (link)]. Additionally, 45 Angus bulls with muscle samples also had whole genome sequence (WGS) data with an average coverage of 6.7 fold [27 (link)].
The animals in GWA studies had 729,068 SNP genotypes, genotyped using either HD chip or a lower density SNP chip and then imputed to HD using BEAGLE [25 (link)] as described by Bolormaa et al. (2014) [23 (link)].
The HD SNP genotypes of animals with RNA-Seq data and 5614 animals used in GWA study for RFI were imputed and phased to WGS of 28,899,038 SNPs using FImpute [28 (link)]. The WGS genotypes of 45 Angus bulls were also phased by FImpute. The reference genomes used for the imputation were WGS data in Run 4.0, 1000 bull genomes project [27 (link)], consisting of 27 breeds and 1147 sequenced animals, including 138 Angus (Black and Red) and 311 Holstein cattle (288 black and white and 23 red and white).
The animals in GWA studies had 729,068 SNP genotypes, genotyped using either HD chip or a lower density SNP chip and then imputed to HD using BEAGLE [25 (link)] as described by Bolormaa et al. (2014) [23 (link)].
The HD SNP genotypes of animals with RNA-Seq data and 5614 animals used in GWA study for RFI were imputed and phased to WGS of 28,899,038 SNPs using FImpute [28 (link)]. The WGS genotypes of 45 Angus bulls were also phased by FImpute. The reference genomes used for the imputation were WGS data in Run 4.0, 1000 bull genomes project [27 (link)], consisting of 27 breeds and 1147 sequenced animals, including 138 Angus (Black and Red) and 311 Holstein cattle (288 black and white and 23 red and white).
5
Bovine Genotyping for Genetic Analysis
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Animals were chosen according to convenience depending on availability at the time of sampling and their economic relevance in the herd. Blood samples from 1,224 animals (1,147 of them with phenotypic records) were obtained from the coccygeal vein using vacuum 4 mL tubes with EDTA. After collection, the samples were refrigerated at 4 °C and sent to AGROSAVIA’S animal genetics laboratory in Bogotá, Colombia for genotyping. The DNA was extracted with a commercial kit (MoBio Laboratories, Inc., Carlsbad, CA, USA). The samples were genotyped with the BovineLD (97), GGP Bovine LD (542), and BovineSNP50 (585) chips from Illumina. SNPs with call rates lower than 90% or MAF lower than 5%, and SNPs located in sex chromosomes as well as individuals with more than 10% missing SNP were excluded from the analysis. All genotypes were imputed to the highest density chip using the Fimpute program (Sargolzaei et al., 2014 (link)). The final genotype file contained 917 animals with 50,932 SNPs per animal.
6
Bovine Genotyping and Sample Collection
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All animal procedures implemented in this study were approved by the University of Nebraska-Lincoln Animal Care and Use Committee. All methods were performed in accordance with relevant guidelines and regulations. Methods are reported in the manuscript following the recommendations in the ARRIVE guidelines.
The blood obtained from 136 cows was centrifuged at 2500 × g for 10 min at room temperature. The buffy coat was collected and stored at − 80 °C. All samples were collected from October 2 to November 27 of 2018 at the Eastern Nebraska Research and Extension Center at the University of Nebraska-Lincoln. Cows were chosen to provide variation in age and ranged from 217 to 3,192 days (0.6 to 8.7 years) of age at the time of sample collection. Animal were from an admixed population comprised of purebred Angus and composites of differing proportions of Angus, Simmental, and Red Angus.
All animals were genotyped with the medium-density Illumina BovineSNP50 (~ 50 K SNPs) BeadChip (Illumina, San Diego, CA, USA). Genotype filtering included removing non-autosomal SNPs, SNPs with minor allele frequency < 0.02, and SNPs with Hardy–Weinberg equilibrium P-value > 10−5.
The blood obtained from 136 cows was centrifuged at 2500 × g for 10 min at room temperature. The buffy coat was collected and stored at − 80 °C. All samples were collected from October 2 to November 27 of 2018 at the Eastern Nebraska Research and Extension Center at the University of Nebraska-Lincoln. Cows were chosen to provide variation in age and ranged from 217 to 3,192 days (0.6 to 8.7 years) of age at the time of sample collection. Animal were from an admixed population comprised of purebred Angus and composites of differing proportions of Angus, Simmental, and Red Angus.
All animals were genotyped with the medium-density Illumina BovineSNP50 (~ 50 K SNPs) BeadChip (Illumina, San Diego, CA, USA). Genotype filtering included removing non-autosomal SNPs, SNPs with minor allele frequency < 0.02, and SNPs with Hardy–Weinberg equilibrium P-value > 10−5.
7
Genome-wide Haplotype Analysis for Fertility
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Most DNA used in this study was derived from a previous breed-based genome association study by Cole and colleagues [10] (link). Fine mapping of haplotypes affecting fertility was accomplished by checking for animals with crossover haplotypes and was made possible by monthly submissions of thousands of new Illumina BovineSNP50 [11] (link) animal genotypes to the United States Department of Agriculture, Agriculture Research Service (USDA, ARS) - Animal Improvement Programs Laboratory (AIPL) database by the U.S. dairy industry. Crossover events were detected by directly comparing progeny to parent haplotypes using findhap.f90 [12] on BovineSNP50 assay genotypes from 8,080 Brown Swiss and 111,886 Holsteins. Regions of partial homozygosity contained within the “original” 5 Mbp haplotypes were trimmed and removed from further consideration. For example, if a live animal received the original HH2 from one parent and the left-most 20 markers of HH2 from the other parent, the region containing those 20 homozygous markers was removed to reduce the haplotype length.
8
Genomic Evaluation of Dairy Cattle Systems
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A total of 625 HO and HO like unrelated cows and sires, born on or after 2005 and genotyped with the Illumina BovineSNP50 or BovineLD Bead Chips were used in this analysis. A total of 149 and 303 animals assigned to the Conv and Lowi systems, respectively, and 173 were from the Canadian and US HO populations. In addition, 162 Jersey (JE) and 86 Brown Swiss (BS) sires from Canada and US were included to help determine if crossbred cows were present in the populations. The animals from the Conv system originated from 16 herds in 6 states of Mexico (Aguascalientes, Guanajuato, Estado de México, Querétaro, San Luis Potosí, and Zacatecas) while the animals of the Lowi system were from 21 herds in 4 states (Estado de México, Jalisco, Puebla, and Tlaxcala). From the 6,836 common SNP markers in both the Illumina BovineSNP50 and the BovineLD Bead Chips a total of 6,617 SNP were included in the analysis after quality control. Markers with a minor allele frequency less than 2% and call rate less than 90% were excluded. Individuals with a call rate less than 90% were also excluded. Table 1 shows the number and frequency of markers per chromosome included in the analysis.
9
Genome-wide SNP genotyping in Holstein cattle
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The three studied populations consisted of Holstein animals from France (45,348), Holstein animals from the Netherlands (11,831), and Holstein-Friesian, Jersey, or crossbred individuals from New Zealand (58,474). Individuals were genotyped with the BovineSNP50 (54,001 SNPs, 111,597 individuals) or BovineHD (777,962 SNPs, 4056 individuals) genotyping arrays (Illumina). Markers common to both arrays were selected for further analysis. Monomorphic markers, with low call rate (below 0.95), or deviating from Hardy-Weinberg proportions (P-value < 1.0 × 10−5 in Holstein populations and < 1.0 × 10−8 in New Zealand crossbred population), or with >10 Mendelian inconsistencies were discarded. Thirty thousand eight hundred and seventy-four SNPs (30,127 on autosomes) and 115,653 animals with an individual call rate higher than 0.90 were kept for further analyses. Remaining Mendelian inconsistencies were erased.
10
Genotyping of Bovine SNPs in Jersey and Holstein
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Genotypes for SNPs on the Illumina Bovinesnp50 (Illumina Inc., San Diego, CA, USA) with 48,912 SNPs after quality control, were available on 595 New Zealand Jersey bulls and 5553 Dutch Holstein bulls. These SNPs had at least ten copies of the minor allele in a combined Dutch Holstein and New Zealand Jersey population, with a minor allele frequency (MAF) ranging from 0.009 to 0.5. Hereafter, we will refer to the New Zealand Jerseys as population and to the Dutch Holsteins as population .
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