A. L. Van Eenennaam

Hot topic: Performance of bovine high-density genotyping platforms in Holsteins and Jerseys

Two high-density single nucleotide polymorphism (SNP) genotyping arrays have recently become available for bovine genomic analyses, the Illumina High-Density Bovine BeadChip Array (777,962 SNP) and the Affymetrix Axiom Genome-Wide BOS 1 Array (648,874 SNP). These products each have unique design and chemistry attributes, and the extent of marker overlap and their potential utility for quantitative trait loci fine mapping, detection of copy number variation, and multibreed genomic selection are of significant interest to the cattle community. This is the first study to compare the performance of these 2 arrays. Deoxyribonucleic acid samples from 16 dairy cattle (10 Holstein, 6 Jersey) were used for the comparison. An independent set of DNA samples taken from 46 Jersey cattle and 18 Holstein cattle were used to ascertain the amount of SNP variation accounted by the 16 experimental samples. Data were analyzed with SVS7 software (Golden Helix Inc., Bozeman, MT) to remove SNP having a call rate less than 90%, and linkage disequilibrium pruning was used to remove linked SNP (r² ≥ 0.9). Maximum, average, and median gaps were calculated for each analysis based on genomic position of SNP on the bovine UMD3.1 genome assembly. All samples were successfully genotyped (≥ 98% SNP genotyped) with both platforms. The average number of genotyped SNP in the Illumina platform was 775,681 and 637,249 for the Affymetrix platform. Based on genomic position, a total of 107,896 SNP were shared between the 2 platforms; however, based on genotype concordance, only 96,031 SNP had complete concordance at these loci. Both Affymetrix BOS 1 and Illumina BovineHD genotyping platforms are well designed and provide high-quality genotypes and similar coverage of informative SNP. Despite fewer total SNP on BOS 1, 19% more SNP remained after linkage disequilibrium pruning, resulting in a smaller gap size (5.2 vs. 6.9 kb) in Holstein and Jersey samples relative to BovineHD. However, only 224,115 Illumina and 241,038 Affymetrix SNP remained following removal of SNP with a minor allele frequency of zero in Holstein and Jersey samples, resulting in an average gap size of 11,887 bp and 11,018 bp, respectively. Combining the 354,348 informative (r² ≥ 0.9), polymorphic (minor allele frequency ≥ 0), unique SNP data from both platforms decreased the average gap size to 7,560 bp. Genome-wide copy number variant analyses were performed using intensity files from both platforms. The BovineHD platform provided an advantage to the copy number variant data compared with the BOS 1 because of the larger number of SNP, higher intensity signals, and lower background effects. The combined use of both platforms significantly improved coverage over either platform alone and decreased the gap size between SNP, providing a valuable tool for fine mapping quantitative trait loci and multibreed animal evaluation.

Accuracy of genomic breeding values in multibreed beef cattle populations derived from deregressed breeding values and phenotypes.

Genomic selection involves the assessment of genetic merit through prediction equations that allocate genetic variation with dense marker genotypes. It has the potential to provide accurate breeding values for selection candidates at an early age and facilitate selection for expensive or difficult to measure traits. Accurate across-breed prediction would allow genomic selection to be applied on a larger scale in the beef industry, but the limited availability of large populations for the development of prediction equations has delayed researchers from providing genomic predictions that are accurate across multiple beef breeds. In this study, the accuracy of genomic predictions for 6 growth and carcass traits were derived and evaluated using 2 multibreed beef cattle populations: 3,358 crossbred cattle of the U.S. Meat Animal Research Center Germplasm Evaluation Program (USMARC_GPE) and 1,834 high accuracy bull sires of the 2,000 Bull Project (2000_BULL) representing influential breeds in the U.S. beef cattle industry. The 2000_BULL EPD were deregressed, scaled, and weighted to adjust for between- and within-breed heterogeneous variance before use in training and validation. Molecular breeding values (MBV) trained in each multibreed population and in Angus and Hereford purebred sires of 2000_BULL were derived using the GenSel BayesCπ function (Fernando and Garrick, 2009) and cross-validated. Less than 10% of large effect loci were shared between prediction equations trained on (USMARC_GPE) relative to 2000_BULL although locus effects were moderately to highly correlated for most traits and the traits themselves were highly correlated between populations. Prediction of MBV accuracy was low and variable between populations. For growth traits, MBV accounted for up to 18% of genetic variation in a pooled, multibreed analysis and up to 28% in single breeds. For carcass traits, MBV explained up to 8% of genetic variation in a pooled, multibreed analysis and up to 42% in single breeds. Prediction equations trained in multibreed populations were more accurate for Angus and Hereford subpopulations because those were the breeds most highly represented in the training populations. Accuracies were less for prediction equations trained in a single breed due to the smaller number of records derived from a single breed in the training populations.

Precision genetics for complex objectives in animal agriculture

ABSTRACT Indirect modification of animal genomes by interspecific hybridization, cross-breeding, and selection has produced an enormous spectrum of phenotypic diversity over more than 10,000 yr of animal domestication. Using these established technologies, the farming community has successfully increased the yield and efficiency of production in most agricultural species while utilizing land resources that are often unsuitable for other agricultural purposes. Moving forward, animal well-being and agricultural sustainability are moral and economic priorities of consumers and producers alike. Therefore, these considerations will be included in any strategy designed to meet the challenges produced by global climate change and an expanding world population. Improvements in the efficiency and precision of genetic technologies will enable a timely response to meet the multifaceted food requirements of a rapidly increasing world population.

Feedlot efficiency implications on greenhouse gas emissions and sustainability 1

The term sustainable has many meanings, but in agriculture it generally refers to some balance between environmental, social, and economic goals. The objective of this project was to quantify inputs and outputs to assess the sustainability implications of 2 feedlot cattle management systems: Never Ever 3 (NE3) and a conventional (CON) system using metabolic modifiers. Angus-cross steers (n=104) were stratified by BW (337 kg ± 17) and randomly assigned to 4 pens per treatment group. The NE3 cattle received no feed additives or implants, whereas CON were implanted with 100 mg of trenbolone acetate and 14 mg of estradiol benzoate on d 1 and 70, and were additionally fed monensin [330 mg/(animal·d)] and tylosin phosphate [90 mg/(animal·d)] in their ration throughout the course of the study, and ractopamine hydrochloride at 254 mg/(animal·d) for the last 29 d on feed. Cattle were shipped on a constant average pen weight basis (596 kg ± 32 BW). The CON cattle had greater ADG (1.81 vs. 1.35 kg, P < 0.01) and were on feed fewer days (146 vs. 188 d, P < 0.01) than the NE3 cattle. No significant differences were observed in HCW (P = 0.072) or dressing percentage (P=0.62) between treatments (P > 0.05); however, CON carcasses averaged larger ribeye area (87 vs. 80 cm(2), P < 0.01), greater Warner-Bratzler shear force measurement (WBSF; 3.46 vs. 3.19 kg, P < 0.01), and smaller USDA marbling score (5.4 vs. 6.2, P < 0.01), and less backfat thickness (1.64 vs. 1.84 cm, P < 0.05) and yield grade (3.38 vs. 3.95, P < 0.01) than NE3 carcasses. Overall, CON cattle consumed 393 kg less DM in the feedlot (1,250 vs. 1,643 kg; P < 0.05). No treatment effects were observed for daily methane (CH(4); P=0.62) or nitrous oxide (N(2)O; P=0.7) emissions per steer. Assuming a constant emission rate on a DMI basis throughout the course of the feedlot trial, CON feedlot management resulted in a 31% decrease in emissions per finished steer compared with NE3 management. Expressing CH(4) emissions on a carbon dioxide equivalent (CO(2)-eq) basis revealed a 1.10-kg CO(2)-eq difference per kilogram BW gain (5.02 kg of NE3 vs. 3.92 kg of CON) between the 2 feedlot management systems. Although the metabolic modifiers resulted in additional costs for the CON treatment group, the cost per kilogram of feedlot BW gain was significantly less (

Karyotype of the American Green Sturgeon

1.12/kg vs.

The value of using DNA markers for beef bull selection in the seedstock sector.

1.35/kg; P < 0.05) than NE3. Both production systems satisfied some sustainability criteria, although neither concurrently fulfilled all of the environmental, social, and economic goals of agricultural sustainability.

Genetic parameters for carnitine, creatine, creatinine, carnosine, and anserine concentration in longissimus muscle and their association with palatability traits in Angus cattle.

Abstract We report the first karyological analysis of the rare American green sturgeon Acipenser medirostris. We found a mean chromosome number of 249 ± 8 (range, 234–263) with both between- and within-animal variation in chromosome number. Approximately one half of the karyotype comprises very small microchromosomes and the majority of the macrochromosomes are metacentric and submetacentric.

Genetic parameters for concentrations of minerals in longissimus muscle and their associations with palatability traits in Angus cattle

The objective of this study was to estimate the value derived from using DNA information to increase the accuracy of beef sire selection in a closed seedstock herd. Breeding objectives for commercial production systems targeting 2 diverse markets were examined using multiple-trait selection indexes developed for the Australian cattle industry. Indexes included those for both maternal (self-replacing) and terminal herds targeting either a domestic market, where steers are finished on pasture, or the export market, where steers are finished on concentrate rations in feedlots and marbling has a large value. Selection index theory was used to predict the response to conventional selection based on phenotypic performance records, and this was compared with including information from 2 hypothetical marker panels. In 1 case the marker panel explained a percentage of additive genetic variance equal to the heritability for all traits in the breeding objective and selection criteria, and in the other case to one-half of this amount. Discounted gene flow methodology was used to calculate the value derived from the use of superior bulls selected using DNA test information and performance recording over that derived from conventional selection using performance recording alone. Results were ultimately calculated as discounted returns per DNA test purchased by the seedstock operator. The DNA testing using these hypothetical marker panels increased the selection response between 29 to 158%. The value of this improvement above that obtained using traditional performance recording ranged from

Genetic polymorphisms in bovine transferrin receptor 2 (TFR2) and solute carrier family 40 (iron-regulated transporter), member 1 (SLC40A1) genes and their association with beef iron content.

89 to 565 per commercial bull, and

Genome-wide association study of concentrations of iron and other minerals in longissimus muscle of Angus cattle.

5,332 to 27,910 per stud bull. Assuming that the entire bull calf crop was tested to achieve these gains, the value of the genetic gain derived from DNA testing ranged from