The Buffalo Genome and the Application of Genomics in Animal Management and Improvement

The publication of the human genome sequence in 2001 was a major step forward in knowledge necessary to understand the variations between individuals. For farmed species, genomic sequence information will facilitate the selection of animals optimised to live, and be productive, in particular environments. The availability of cattle genome sequence has allowed the breeding industry to take the first steps towards predicting phenotypes from genotypes by estimating a genomic breeding value (gEBV) for bulls using genome-wide DNA markers. The sequencing of the buffalo genome and creation of a panel of DNA markers has created the opportunity to apply molecular selection approaches for this species.The genomes of several buffalo of different breeds were sequenced and aligned with the bovine genome, which facilitated the identification of millions of sequence variants in the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome compared with the bovine genome, 90,000 putative single nucleotide polymorphisms (SNP) were selected to create an Axiom (R) Buffalo Genotyping Array 90K. This SNP Chip was tested in buffalo populations from Italy and Brazil and found to have at least 75% high quality and polymorphic markers in these populations. The 90K SNP chip was then used to investigate the structure of buffalo populations, and to localise the variations having a major effect on milk production.

Genomic selection and assisted reproduction technologies to foster cattle breeding

Genomics has been propagated as a paradigm shifting innovation in livestock during the last decade. The possibility of predicting breeding values using genomic information has revolutionized the dairy cattle industry and is now being implemented in beef cattle. In this paper we discuss how genomics is changing cattle breeding through genomic selection, and how this change is creating new ways to articulate assisted reproduction technologies with animal breeding. We also debate that the scientific community is still starting the long journey to reveal the functional aspects of the cattle genome, and that knowledge in this field is the frontier to a whole new venue for the development of novel applications in the livestock sector.

Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Quantitative genetic study of age at subsequent rebreeding in Nellore cattle by using survival analysis

The continuous trait age at subsequent rebreeding (ASR) was evaluated using survival analysis in Nellore breed cows that conceived for the first time at approximately 14 months of age. This methodology was chosen because the restricted breeding season produces censored data. The dataset contained 2885 records of ASR (in days). Records of females that did not produce calves in the following year after being exposed to a sire were considered censored (48.3% of the total). The statistical model used was a Weibull mixed survival model, which included fixed effects of contemporary groups (CG) and period and a random effect of individual animal. The effect of contemporary groups on ASR was significant (P < 0.01). Heritabilities obtained for ASR were 0.03 and 0.04 in logarithmic and original scales, respectively. These results indicate that the genetic selection response for subsequent reproduction of 2-year-old Nellore breed females is not expected to be effective based on survival analysis. Furthermore, these results suggest that environmental improvement is fundamental to this important trait. It should be highlighted that an increase in the average date of birth can produce an adverse effect in the future, since this cannot be compensated by genetic improvement.

Genome-Wide Association for Growth Traits in Canchim Beef Cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Cluster and meta-analyses of genetic parameters for feed intake traits in growing beef cattle

A data set based on 50 studies including feed intake and utilization traits was used to perform a meta-analysis to obtain pooled estimates using the variance between studies of genetic parameters for average daily gain (ADG); residual feed intake (RFI); metabolic body weight (MBW); feed conversion ratio (FCR); and daily dry matter intake (DMI) in beef cattle. The total data set included 128 heritability and 122 genetic correlation estimates published in the literature from 1961 to 2012. The meta-analysis was performed using a random effects model where the restricted maximum likelihood estimator was used to evaluate variances among clusters. Also, a meta-analysis using the method of cluster analysis was used to group the heritability estimates. Two clusters were obtained for each trait by different variables. It was observed, for all traits, that the heterogeneity of variance was significant between clusters and studies for genetic correlation estimates. The pooled estimates, adding the variance between clusters, for direct heritability estimates for ADG, DMI, RFI, MBW and FCR were 0.32 +/- 0.04, 0.39 +/- 0.03, 0.31 +/- 0.02, 0.31 +/- 0.03 and 0.26 +/- 0.03, respectively. Pooled genetic correlation estimates ranged from -0.15 to 0.67 among ADG, DMI, RFI, MBW and FCR. These pooled estimates of genetic parameters could be used to solve genetic prediction equations in populations where data is insufficient for variance component estimation. Cluster analysis is recommended as a statistical procedure to combine results from different studies to account for heterogeneity.

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Supplementation based on protein or energy ingredients to beef cattle consuming low-quality cool-season forages: I. Forage disappearance parameters in rumen-fistulated steers and physiological responses in pregnant heifers

Two experiments evaluated the influence of supplement composition on ruminal forage disappearance, performance, and physiological responses of Angus x Hereford cattle consuming a low-quality cool-season forage (8.7% CP and 57% TDN). In Exp. 1, 6 rumen-fistulated steers housed in individual pens were assigned to an incomplete 3 x 2 Latin square design containing 2 periods of 11 d each and the following treatments: 1) supplementation with soybean meal (PROT), 2) supplementation with a mixture of cracked corn, soybean meal, and urea (68:22:10 ratio, DM basis; ENER), or 3) no supplementation (CON). Steers were offered meadow foxtail (Alopecurus pratensis L.) hay for ad libitum consumption. Treatments were provided daily at 0.50 and 0.54% of shrunk BW/steer for PROT and ENER, respectively, to ensure that PROT and ENER intakes were isocaloric and isonitrogenous. No treatment effects were detected on rumen disappearance parameters of forage DM (P >= 0.33) and NDF (P >= 0.66). In Exp. 2, 35 pregnant heifers were ranked by initial BW on d -7 of the study, allocated into 12 feedlot pens (4 pens/treatment), and assigned to the same treatments and forage intake regimen as in Exp. 1 for 19 d. Treatments were fed once daily at 1.77 and 1.92 kg of DM/heifer for PROT and ENER, respectively, to achieve the same treatment intake as percent of initial BW used in Exp. 1 (0.50 and 0.54% for PROT and ENER, respectively). No treatment effects (P = 0.17) were detected on forage DMI. Total DMI was greater (P < 0.01) for PROT and ENER compared with CON and similar between PROT and ENER (P = 0.36). Accordingly, ADG was greater (P = 0.01) for PROT compared with CON, tended to be greater for ENER compared with CON (P = 0.08), and was similar between ENER and PROT (P = 0.28). Heifers receiving PROT and ENER had greater mean concentrations of plasma glucose (P = 0.03), insulin (P <= 0.09), IGF-I (P <= 0.04), and progesterone (P = 0.01) compared to CON, whereas ENER and PROT had similar concentrations of these variables (P >= 0.15). A treatment x hour interaction was detected (P < 0.01) for plasma urea N (PUN), given that PUN concentrations increased after supplementation for ENER and PROT (time effect, P < 0.01) but did not change for CON (time effect, P = 0.62). In conclusion, beef cattle consuming low-quality cool-season forages had similar ruminal forage disappearance and intake, performance, and physiological status if offered supplements based on soybean meal or corn at 0.5% of BW.

Wolf presence in the ranch of origin: Impacts on temperament and physiological responses of beef cattle following a simulated wolf encounter

This experiment evaluated temperament, vaginal temperature, and plasma cortisol in beef cows from wolf-naive and wolf-experienced origins that were subjected to a simulated wolf encounter. Multiparous, pregnant, nonlactating Angus-crossbreed cows from the Eastern Oregon Agricultural Research Center located near Burns, OR (CON; n = 50), and from a commercial operation near Council, ID (WLF; n = 50), were used. To date, grey wolves are not present around Burns, OR, and thus CON were naive to wolves. Conversely, wolves are present around Council, ID, and WLF cows were selected from a herd that had experienced multiple confirmed wolf-predation episodes from 2008 to 2012. Following a 50-d commingling and adaptation period, CON and WLF cows were ranked by temperament, BW, and BCS and allocated to 5 groups (d 0; 10 CON and 10 WLF cows/group). Groups were individually subjected to the experimental procedures on d 2 (n = 3) and d 3 (n = 2). Before the simulated wolf encounter, cow temperament was assessed and blood samples and vaginal temperatures (using intravaginal data loggers) were collected (presimulation assessments). Cows were then sorted by origin, moved to 2 adjacent drylot pens (10 WLF and 10 CON cows/pen), and subjected to a simulated wolf encounter event for 20 min, which consisted of 1) cotton plugs saturated with wolf urine attached to the drylot fence, 2) continuous reproduction of wolf howls, and 3) 3 leashed dogs that were walked along the fence perimeter. Thereafter, WLF and CON cows were commingled and returned to the handling facility for postsimulation assessments, which were conducted immediately after exposure to wolf-urine-saturated cotton plugs, wolf howl reproduction, and 20-s exposure to the 3 dogs while being restrained in a squeeze chute. Chute score, temperament score, and plasma cortisol concentration increased (P <= 0.01) from pre- to postsimulation assessment in WLF but did not change in CON cows (P >= 0.19). Exit velocity decreased (P = 0.01) from pre-to postsimulation assessment in CON but did not change (P = 0.79) in WLF cows. In addition, WLF cows had a greater (P = 0.03) increase in temperature from pre-to postsimulation assessments compared with CON cows. In conclusion, the simulated wolf encounter increased excitability and fear-related physiological stress responses in cows that originated from a wolf-experienced herd but not in cows that originated from a wolf-naive herd.

Comparison of a genetic group and unknown paternity models for growth traits in Nellore cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

History, structure, and genetic diversity of Brazilian Gir cattle

The Gir cattle breed (Bos indicus) is an important genetic resource for milk production throughout the tropics. The small number of Gir animals introduced in Brazil, rapid dissemination of this breed recently, and the intensification of selection practices could contribute to increase of inbreeding level and reduce genetic diversity in this population. The population was analyzed in terms of pedigree completeness level, inbreeding coefficient, coancestry, generation interval, effective population size, effective number of founders and ancestors, among others. Despite the low mean inbreeding (around 2%), minor problems were identified in the population structure of the Brazilian Gir cattle, e.g., trend of narrower bottlenecks in the pedigree in recent years. The effective population sizes based on inbreeding (94) or coancestry (165.9) as well as the effective number of ancestors (76) and founders (143) were relativity high. The major subdivision of the Gir breed was observed between 1993 and 2002 (dairy and dual-purpose herds, wide use of within-herd matings). In this period the level of inbreeding remained at a higher level, there was a small increase in coancestry and the number of equivalent subpopulations was approximately 6. After 2002, there was genetic exchange between subpopulations, reduction in the average inbreeding, pronounced increase in the average coancestry, and the number of equivalent subpopulations was about 2. Furthermore, it was found that the mean generation interval of the population tended to increase in recent years (around 9 years). About 23% of genetic diversity has been lost since the first generation of founders. Based on the effective population size, number of equivalent subpopulations, inbreeding, coancestry, and loss of genetic diversity, the Gir population is still highly structured, but there is ample room for artificial selection. The results regarding the effective number of founders and ancestors in the present population demonstrate the existence of bottlenecks in the pedigree and indicate the need for population structure monitoring. Nevertheless, the Brazilian Gir breed can perfectly face a breeding program with high selection intensity. (C) 2014 Elsevier B.V. All rights reserved.

Polymorphism analysis in genes of the somatotropic axis in Nellore cattle selected for growth

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Effects of flunixin meglumine administration on physiological and performance responses of transported feeder cattle

The objective was to evaluate the effects of flunixin meglumine administration on physiological and performance responses of transported cattle during feedlot receiving. Forty-five Angus x Hereford steers were ranked by BW on d 0 and assigned to 1 of 3 treatments:1) transport for 1,280 km in a commercial livestock trailer and administration of flunixin meglumine (1.1 mg/kg BW; intravenous) at loading (d 0) and unloading (d 1; FM), 2) transport for 1,280 km in a commercial livestock trailer and administration of 0.9% saline (0.022 mL/kg BW; intravenous) at loading (d 0) and unloading (d 1; TRANS), or 3) no transport and administration of 0.9% saline (0.022 mL/kg BW; intravenous) concurrently with loading (d 0) and unloading (d 1) of FM and TRANS cohorts (CON). Upon arrival and processing for treatment administration on d 1, steers within each treatment were ranked by BW and assigned to 15 feedlot pens (5 pens/treatment, 3 steers/pen). Full BW was recorded before (d -1 and 0) treatment application and at the end of experiment (d 28 and 29) for ADG calculation. Total DMI was evaluated daily from d 1 to 28. Blood samples were collected on d 0 (before treatment administration), 1 (after unloading but before treatment administration), 4, 7, 10, 14, 21, and 28. Body weight shrink from d 0 to 1 was less (P < 0.01) in CON vs. FM and TRANS but similar (P = 0.94) between TRANS and FM. Mean ADG was greater (P <= 0.04) in CON vs. FM and TRANS but similar (P = 0.69) between TRANS and FM. No treatment effects were detected on DMI, but CON had greater G:F vs. TRANS (P = 0.08) and FM (P = 0.02), whereas G:F was similar (P = 0.68) between TRANS and FM. Mean plasma cortisol concentrations tended (P <= 0.09) to be greater in TRANS vs. FM and CON but was similar (P = 0.87) between CON and FM. Plasma NEFA concentrations were greater (P <= 0.02) for TRANS and FM vs. CON on d 1 and greater (P <= 0.04) for FM vs. TRANS and CON on d 4. Plasma ceruloplasmin concentrations were greater (P <= 0.03) for TRANS vs. CON on d 1, 4, and 7, greater (P <= 0.05) for TRANS vs. FM on d 4 and 7, and greater (P <= 0.04) for FM vs. CON on d 1 and 4. Plasma haptoglobin concentrations were greater (P < 0.01) for TRANS vs. CON and FM on d 1 and 4 and greater (P <= 0.05) for FM vs. CON on d 1 and 4. In conclusion, flunixin meglumine reduced the cortisol and acute-phase protein responses elicited by road transport but did not improve receiving performance of feeder cattle.

Rest stops during road transport: Impacts on performance and acute-phase protein responses of feeder cattle

Angus x Hereford steers (n = 42) and heifers (n = 21) were ranked by gender and BW on d 0 of the experiment and randomly assigned to 1 of 3 treatments: 1) no transport and full access to feed and water (CON); 2) continuous road transport for 1,290 km (TRANS), or 3) road transport for 1,290 km, with rest stops every 430 km (STOP; total of 2 rest stops). Treatments were applied from d 0 to 1 of the experiment. Cattle from TRANS and STOP treatments were transported in separate commercial livestock trailers, within a single 2.1 x 7.2 m compartment, but through the exact same route. During each rest stop, STOP cattle were unloaded and offered mixed alfalfa-grass hay and water for ad libitum consumption for 2 h. Upon arrival of STOP and TRANS on d 1, cattle were ranked by sex and BW within each treatment and assigned to 21 feedlot pens (7 pens/treatment; 2 steers and 1 heifer/pen). Full BW was recorded before (d -1 and 0) treatment application and at the end of experiment (d 28 and 29). Total DMI was evaluated daily from d 1 to 28. Blood samples were collected on d 0 (before loading of TRANS and STOP cattle), 1 (immediately after unloading of TRANS and STOP cattle), 4, 7, 10, 14, 21, and 28. Body weight shrink from d 0 to d 1 was reduced (P < 0.01) in CON compared to TRANS and STOP, and reduced in STOP compared to TRANS. Mean ADG was greater (P < 0.05) in CON compared to TRANS and STOP, but similar (P = 0.68) between TRANS and STOP. No treatment effects were detected (P >= 0.18) on hay, concentrate, and total DMI. Mean G: F was greater (P = 0.05) in CON compared to STOP, tended to be greater (P = 0.08) in CON compared to TRANS, and similar (P = 0.85) between TRANS and STOP. Plasma cortisol concentrations were greater (P <= 0.04) in TRANS compared to CON and STOP on d 1, and greater (P = 0.04) in TRANS compared to CON on d 4. Serum NEFA concentrations were greater (P < 0.01) in TRANS compared to CON and STOP on d 1, and greater (P <= 0.05) in TRANS compared to CON on d 4 and 7. Mean plasma ceruloplasmin concentrations were similar (P = 0.19) among treatments. Plasma haptoglobin concentrations were greater (P <= 0.04) in TRANS compared to CON and STOP on d 1, and in STOP compared to CON on d 1. In conclusion, inclusion of rest stops during a 1,290-km transport prevented the increase in circulating cortisol and alleviated the NEFA and haptoglobin response elicited by transport, but did not improve feedlot receiving performance of transported cattle.

Genome-Wide Mapping of Loci Explaining Variance in Scrotal Circumference in Nellore Cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)