E. Casas

Selection and use of SNP markers for animal identification and paternity analysis in U.S. beef cattle

Abstract. DNA marker technology represents a promising means for determining the genetic identity and kinship of an animal. Compared with other types of DNA markers, single nucleotide polymorphisms (SNPs) are attractive because they are abundant, genetically stable, and amenable to high-throughput automated analysis. In cattle, the challenge has been to identify a minimal set of SNPs with sufficient power for use in a variety of popular breeds and crossbred populations. This report describes a set of 32 highly informative SNP markers distributed among 18 autosomes and both sex chromosomes. Informativity of these SNPs in U.S. beef cattle populations was estimated from the distribution of allele and genotype frequencies in two panels: one consisting of 96 purebred sires representing 17 popular breeds, and another with 154 purebred American Angus from six herds in four Midwestern states. Based on frequency data from these panels, the estimated probability that two randomly selected, unrelated individuals will possess identical genotypes for all 32 loci was 2.0 × 10−13 for multi-breed composite populations and 1.9 × 10−10 for purebred Angus populations. The probability that a randomly chosen candidate sire will be excluded from paternity was estimated to be 99.9% and 99.4% for the same respective populations. The DNA immediately surrounding the 32 target SNPs was sequenced in the 96 sires of the multi-breed panel and found to contain an additional 183 polymorphic sites. Knowledge of these additional sites, together with the 32 target SNPs, allows the design of robust, accurate genotype assays on a variety of high-throughput SNP genotyping platforms.

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

Linkage mapping bovine EST-based SNP

BackgroundExisting linkage maps of the bovine genome primarily contain anonymous microsatellite markers. These maps have proved valuable for mapping quantitative trait loci (QTL) to broad regions of the genome, but more closely spaced markers are needed to fine-map QTL, and markers associated with genes and annotated sequence are needed to identify genes and sequence variation that may explain QTL.ResultsBovine expressed sequence tag (EST) and bacterial artificial chromosome (BAC)sequence data were used to develop 918 single nucleotide polymorphism (SNP) markers to map genes on the bovine linkage map. DNA of sires from the MARC reference population was used to detect SNPs, and progeny and mates of heterozygous sires were genotyped. Chromosome assignments for 861 SNPs were determined by twopoint analysis, and positions for 735 SNPs were established by multipoint analyses. Linkage maps of bovine autosomes with these SNPs represent 4585 markers in 2475 positions spanning 3058 cM . Markers include 3612 microsatellites, 913 SNPs and 60 other markers. Mean separation between marker positions is 1.2 cM. New SNP markers appear in 511 positions, with mean separation of 4.7 cM. Multi-allelic markers, mostly microsatellites, had a mean (maximum) of 216 (366) informative meioses, and a mean 3-lod confidence interval of 3.6 cM Bi-allelic markers, including SNP and other marker types, had a mean (maximum) of 55 (191) informative meioses, and were placed within a mean 8.5 cM 3-lod confidence interval. Homologous human sequences were identified for 1159 markers, including 582 newly developed and mapped SNP.ConclusionAddition of these EST- and BAC-based SNPs to the bovine linkage map not only increases marker density, but provides connections to gene-rich physical maps, including annotated human sequence. The map provides a resource for fine-mapping quantitative trait loci and identification of positional candidate genes, and can be integrated with other data to guide and refine assembly of bovine genome sequence. Even after the bovine genome is completely sequenced, the map will continue to be a useful tool to link observable phenotypes and animal genotypes to underlying genes and molecular mechanisms influencing economically important beef and dairy traits.

Use of bovine EST data and human genomic sequences to map 100 gene-specific bovine markers

Abstract. A system to use bovine EST data in conjunction with human genomic sequence to improve the bovine linkage map over the entire genome or on specific chromosomes was evaluated. Bovine EST sequence was used to provide primer sequences corresponding to bovine genes, while human genomic sequence directed primer design to flank introns and produce amplicons of appropriate size for efficient direct sequencing. The sequence tagged sites (STS) produced in this way from the four sires of the MARC reference families were examined for single nucleotide polymorphisms (SNPs) that could be used to map the corresponding genes. With this approach, along with a primer/extension mass spectrometry SNP genotyping assay, 100 ESTs were placed on the bovine genetic linkage map. The first 70 were chosen at random from bovine EST–human genomic comparisons. An additional 30 ESTs were successfully mapped to bovine Chromosome 19 (BTA19), and comparison of the resulting BTA19 map to the position of the corresponding human orthologs on the HSA17 draft sequences revealed differences in the spacing and order of genes. Over 80% of successful amplicons contained SNPs, indicating that this is an efficient approach to generating EST-associated genetic markers. We have demonstrated the feasibility of constructing a linkage map based on SNPs associated with ESTs and the plausibility of utilizing EST, comparative mapping information, and human sequence data to target regions of the bovine genome for SNP marker development.

Prevalence of the prion protein gene E211K variant in U.S. cattle

BackgroundIn 2006, an atypical U.S. case of bovine spongiform encephalopathy (BSE) was discovered in Alabama and later reported to be polymorphic for glutamate (E) and lysine (K) codons at position 211 in the bovine prion protein gene (Prnp) coding sequence. A bovine E211K mutation is important because it is analogous to the most common pathogenic mutation in humans (E200K) which causes hereditary Creutzfeldt – Jakob disease, an autosomal dominant form of prion disease. The present report describes a high-throughput matrix-associated laser desorption/ionization-time-of-flight mass spectrometry assay for scoring the Prnp E211K variant and its use to determine an upper limit for the K211 allele frequency in U.S. cattle.ResultsThe K211 allele was not detected in 6062 cattle, including those from five commercial beef processing plants (3892 carcasses) and 2170 registered cattle from 42 breeds. Multiple nearby polymorphisms in Prnp coding sequence of 1456 diverse purebred cattle (42 breeds) did not interfere with scoring E211 or K211 alleles. Based on these results, the upper bounds for prevalence of the E211K variant was estimated to be extremely low, less than 1 in 2000 cattle (Bayesian analysis based on 95% quantile of the posterior distribution with a uniform prior).ConclusionNo groups or breeds of U.S. cattle are presently known to harbor the Prnp K211 allele. Because a carrier was not detected, the number of additional atypical BSE cases with K211 will also be vanishingly low.

Effect of bovine respiratory disease and overall pathogenic disease incidence on carcass traits.

The objective this study was to evaluate the effects of incidence of bovine respiratory disease (BRD) and overall incidence of pathogenic diseases (IPD) on carcass traits. Two independent populations were used. The first population included crossbred steers (GPE7; n = 642) derived from sires of 7 Bos taurus breeds: Angus, Charolais, Gelbvieh, Hereford, Limousin, Red Angus, and Simmental. The second population included crossbred steers (GPE8; n = 621) derived from tropically adapted Bos taurus breeds and Bos indicus-influenced breeds: Beefmaster, Brangus, Bonsmara, and Romosinuano, as well as Hereford and Angus. Treatment records for BRD, infectious keratoconjunctivitis, and infectious pododermatitis were available for these populations. Incidence of BRD was treated as an independent effect. Incidences of the 3 microbial pathogenic diseases were pooled into a single trait to represent overall pathogenic disease incidence. Traits evaluated were HCW; KPH; LM area; marbling score; fat thickness; dressing percentage; yield grade; retail, fat, and bone yields; and meat tenderness. Both BRD and IPD were associated with differences in yield grade in GPE7 and GPE8 steers. Animals treated for BRD had decreased yield grades (P = 0.003 and P = 0.02, in GPE7 and GPE8, respectively) compared with untreated animals. Animals treated for IPD had decreased yield grades (P = 0.0006 and P = 0.004, in GPE7 and GPE8, respectively) compared with untreated animals. Incidence of BRD and IPD were associated with a reduction in fat thickness in GPE7 and GPE8 steers. Animals treated for BRD had reduced adjusted fat measurements (P = 0.0007 and P = 0.01, in GPE7 and GPE8) compared with untreated animals. Animals treated for IPD also had reduced adjusted fat measurements (P = 0.0003 and P = 0.002, in GPE7 and GPE8) compared with untreated animals. Animals treated for BRD (P < 0.007) or IPD (P < 0.02) in the GPE7 population also had decreased estimated KPH measurements compared with unaffected animals. Animals affected with BRD in GPE8 had greater (P < 0.05) shear force measurements than unaffected animals. Animals affected with IPD in GPE8 had greater HCW (P < 0.03) and fat yield (P < 0.01) measurements but lesser bone yield (P < 0.03) and retail product yield (P < 0.01) measurements than unaffected animals. The relationship between disease and carcass traits should be given consideration by future studies that aim to develop selection strategies based on specific traits.

Birth and weaning traits in crossbred cattle from Hereford, Angus, Brahman, Boran, Tuli, and Belgian Blue sires

The objective of this study was to characterize breeds representing diverse biological types for birth and weaning traits in crossbred cattle. Gestation length, calving difficulty, percentage of unassisted calving, percentage of perinatal survival, percentage of survival from birth to weaning, birth weight, BW at 200 d, and ADG were measured in 2,500 calves born and 2,395 calves weaned. Calves were obtained by mating Hereford, Angus, and MARC III (one-fourth Hereford, one-fourth Angus, one-fourth Pinzgauer, and one-fourth Red Poll) mature cows to Hereford or Angus (British breed), Brahman, Tuli, Boran, and Belgian Blue sires. Calves were born during the spring seasons of 1992, 1993, and 1994. Sire breed was significant for all traits (P < 0.002). Offspring from British breeds and the Belgian Blue breed had the shortest gestation length (285 d) when compared with progeny from other sire breeds (average of 291 d). Calving difficulty was greater in offspring from Brahman sires (1.24), whereas the offspring of Tuli sires had the least amount of calving difficulty (1.00). Offspring from all sire breeds had similar perinatal survival and survival from birth to weaning (average of 97.2 and 96.2%, respectively), with the exception of offspring from Brahman sires, which had less (92.8 and 90.4%, respectively). Progeny of Brahman sires were heaviest at birth (45.7 kg), followed by offspring from British breed, Boran, and Belgian Blue sires (average of 42.4 kg). The lightest offspring at birth were from Tuli sires (38.6 kg). Progeny derived from Brahman sires were the heaviest at 200 d (246 kg), and they grew faster (1.00 kg/d) than offspring from any other group. The progeny of British breeds and the Belgian Blue breed had an intermediate BW at 200 d (238 kg) and an intermediate ADG (average of 0.98 kg/d). The progeny of Boran and Tuli sires were the lightest at 200 d (227 kg) and had the least ADG (0.93 kg/d). Male calves had a longer gestation length, had a greater incidence of calving difficulty, had greater mortality to weaning, were heavier, and grew faster than female calves. Sire breed effects can be optimized by selection and use of appropriate crossbreeding systems.

Loci on Bos taurus chromosome 2 and Bos taurus chromosome 26 are linked with bovine respiratory disease and associated with persistent infection of bovine viral diarrhea virus 1

The objective of this study was to identify loci linked with bovine respiratory disease (BRD) and subsequently to determine if these same loci were associated with bovine viral diarrhea virus persistent infection (BVD-PI) in affected calves or their dams. A genome-wide linkage study using 312 microsatellites was conducted to identify loci linked with BRD in a Brahman × Hereford sire half-sib family. Disease incidence was recorded from birth to slaughter by daily monitoring. Linkage was suggestive for a QTL on BTA2 (F = 7.31, P = 0.007) and BTA26 (F = 10.46, P = 0.001). Six and 7 markers were added and genotyped between 110 and 126 cM on BTA2 and between 42 and 72 cM on BTA26, respectively, in the intervals where linkage was found. These markers were used to reevaluate the Brahman × Hereford family and to evaluate 3 additional crossbred half-sib families. Linkage was found with BRD on BTA2 (F = 4.94, P < 0.01), with a peak at 110 cM, and on BTA26 (F = 4.03, P < 0.05), with peaks at 42 and 52 cM. The same markers were then tested for an association with BVD-PI in 1) BVD-PI calves compared with age-matched unaffected calves from the same herd or 2) dams with BVD-PI compared with age-matched unaffected calves. Sixty commercial beef cow-calf herds were tested for BVD-PI, and 79 calves from 8 ranches had BVD-PI. Four of 6 markers were associated (P = 4.8 × 10(-9) to P = 0.01) with BVD-PI on BTA2, and 4 of 7 markers were associated (P = 0.008 to P = 0.04) with BVD-PI on BTA26 when BVD-PI calves were compared with unaffected calves. The comparison of BVD-PI dams with unaffected calves detected associations with BVD-PI for all markers tested on BTA2 (P = 3 × 10(-9) to P = 0.005) and for 3 of 7 markers on BTA26 (P = 1.4 × 10(-6) to P = 0.006).

Evaluation of Dorset, Finnsheep, Romanov, Texel, and Montadale breeds of sheep: II. Reproduction of F 1 ewes in fall mating seasons

Objectives were to estimate effects of sire breed (Dorset, Finnsheep, Romanov, Texel, and Montadale), dam breed (Composite III and northwestern whiteface), mating season (August, October, and December), ewe age (1, 2, and 3 yr), and their interactions on reproductive traits of F1 ewes. A total of 1,799 F1 ewes produced 3,849 litters from 4,804 exposures to Suffolk rams during 35-d mating seasons over 3 yr. Ewes were weighed at breeding. Conception rate and ewe longevity (present or absent at 42 mo of age) were determined. Number born and litter birth weight were recorded, and number and weight at weaning and 20 wk of age were analyzed separately for dam- and nursery-reared litter mates. Total productivity through 3 yr of age for each ewe entering the breeding flock was calculated as the sum of 20-wk weights for dam- or nursery-reared lambs. Interactions of sire breed x mating season, sire breed x ewe age, and mating season x ewe age were generally significant, whereas interactions of sire breed, mating season, and ewe age x dam breed were seldom detected. Interactions of sire breed x mating season were often due to changes in rank as well as magnitude, indicating the importance of matching sire breed to a specific mating season. The number born to Dorset-, Texel-, and Montadale-sired ewes was not affected by dam breed; however, Finnsheep-sired ewes out of northwestern whiteface dams were more prolific than Finnsheep-sired ewes out of Composite III dams, and the opposite situation existed for Romanov-sired ewes. Least squares means of sire breeds (P < 0.001) for total productivity of dam-reared lambs were 98.5, 103.5, 106.9, 124.6, and 154.9 kg/ewe entering the breeding flock for Texel, Dorset, Montadale, Finnsheep, and Romanov, respectively. Superior reproduction of Romanov-sired ewes was due to greater conception rate and prolificacy for each mating season and ewe age, as well as greater ewe longevity. Total productivity of F1 ewes by Composite III dams (125.6 kg) was greater (P < 0.001) than for ewes born to northwestern whiteface dams (109.7 kg), and the effect of mating season increased (P < 0.001) from August to October to December. Litter weight at 20 wk of age of 2- and 3-yr-old ewes was similar but greater (P < 0.001) than for 1-yr-old ewes. Experimental results provide comprehensive information about the appropriate use of these breeds in crossbreeding systems to meet specific production-marketing objectives.

µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies,,

Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an increase in mean and an increase in variation. This work confirms the importance of CAPN1 and CAST for tenderness in beef, provides a new effect of CAST on beef tenderness, and questions the utility of GHR as a selection marker for beef quality.