Congratulations to the Winners!
1. Hematological Characteristics of Disease Resilient Pigs in a Natural Challenge Model
J.Lim1,2, T.Yang1,2, Z.Yang1,2, M.Newell2, S.Goruk2, J.Harding3, F.Fortin4, M.K.Dyck1,2, PigGen Canada5, J.C.M.Dekkers6, Z.Wang1,2, C.J.Field2 and G.S.Plastow1, 2
The high health status in nucleus and multiplication farms at the top of swine breeding pyramid is a barrier to genetic selection of disease resilient pigs that perform better in the lower health commercial level. At this time, practical tools to select for such pigs do not exist. Our objective is to identify resilient pigs by adapting a relatively cost-effective hematological test using blood samples from a novel natural challenge model. A total of 397 high health crossbred (Landrace x Yorkshire) barrows from multiplication farms were introduced in batches, and exposed naturally to multiple diseases simultaneously in a test station established using seeder pigs to simulate high disease pressure in a commercial situation. Whole blood samples were collected before and after challenge. Growth rate and treatment number were used to classify pigs into resilient and susceptible groups. Hemoglobin, mean corpuscular volume, lymphocytes and monocytes were found to be significantly different between groups before challenge. These measures are therefore potential predictors of resilience at the commercial level in high health farms (nucleus and multiplication farms). Significant differences between groups were also observed in several erythrocyte & platelet traits after challenge. Pigs with neutrophil-lymphocyte ratio (NLR) > 0.9 before challenge had higher slaughter weight and growth rate, fewer days to market and lower treatment number. Initial results showed that hematological differences before challenge can potentially be applied in the selection of resilient pigs in high health farms. NLR may offer insights into differences of immune response between resilient and susceptible pigs.
2. The effect of energy intake on NPY and POMC gene expression at the onset of lay in broiler breeder pullets
S.H. Hadinia1, G.Y. Bédécarrats2, C. Fitzsimmons1, and M.J. Zuidhof1
1Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, CANADA.; 2Department of Animal Biosciences, University of Guelph, Guelph, ON, CANADA.
Current understanding of the molecular mechanisms impacted by metabolizable energy intake (MEI) in poultry is limited. In the present study, the effect of MEI on gene expression of neuropeptide Y (NPY) and proopiomelanocortin (POMC) was evaluated in the hypothalamus of Ross 308 broiler breeder pullets at the onset of lay. It has been proposed that stimulation of NPY neurons mediates increased feed intake whereas stimulation of the POMC neurons causes energy intake to decrease. The current experiment consisted of 2 treatments: 1. broiler breeder pullets fed a high energy diet with no feed restriction (High MEI); 2. broiler breeder pullets fed a low energy diet with feed restriction to the breeder-recommended body weight profile (Low MEI). Pullets were allocated to the 2 treatments and fed using precision feeding (PF) stations from 22 to 26 week of age. Total RNA was extracted from hypothalamus samples and was used for qRT-PCR assays. Pullets with High MEI had a 30% increase in POMC mRNA levels compared to pullets with Low MEI (P = 0.04). However, MEI did not affect the expression of NPY gene between both treatments (P > 0.05). In response to lowered energy status in chickens adenosine monophosphate kinase (AMPK) pathway is activated which inhibits energy-consuming (anabolic) pathways while stimulates energy producing (catabolic) pathways [1,2]. The mechanism for down-regulation of POMC expression by Low MEI has not been assessed but it may have occurred via AMPK. It seems that control of energy expenditure in birds is similar to mammalian species.
 Proszkowiec-Weglarz, M., Richards, M. P., Ramachandran, R., and McMurtry, J. P. (2006) Characterization of the AMP-activated protein kinase pathway in chickens. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 143: 92– 106.
 Richards, M. P., Rosebrough, R. W., Coon, C. N., and McMurtry, J. P. (2010) Feed intake regulation for the female broiler breeder: In theory and in practice. J. Appl. Poult. Res. 19: 182–193.
3.Quantifying the yet unknown: Individual phenotypic data for feed efficiency in broiler breeders
van der Klein, S.A.S., Zuidhof, M.J.
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB
Increasing interest in feed efficiency in the poultry sector stresses the need for innovation in poultry breeding. Quantifying phenotypes for feed efficiency in individual pure line broiler breeding stock, which are bred in group housed settings, has been particularly challenging. The competition for feed also creates a major challenge in controlling body weight (BW) of the birds. At the University of Alberta, a novel automated feeding system has been developed that can overcome these challenges. The precision feeding (PF) system can control and measure BW and feed intake in group housed poultry and gathers phenotypic information of individual birds. Each time a bird visits the PF system, its unique radio frequency identification tag is recognized and the BW is recorded, after which a feed allocation decision is made. Preliminary results show that in an experiment rearing 155 Ross 708 broiler breeder pullets in 6 environmentally controlled rooms to 21 weeks of age, feed conversion ratio phenotypes averaged 3.95 ± 0.165. Using a model allocating metabolizable energy (ME) intake towards maintenance and gain, we found that the standard deviation of residual ME intake was 19.88 kcal/d, the minimum was -122.91 kcal/d, and the maximum 200.81 kcal/d. Average daily ME allocated towards maintenance was 101.61 ± 4.773 kcal/kgb. With a PF system, increased frequency and precision of phenotypic data collection on individual feed restricted free run birds will allow more informed selection decisions to be made based on efficiency parameters, which will move the broiler industry towards a sustainable future.
4. Can we use residual ruminal volatile fatty acid concentration and microbial populations as a proxy for feed efficiency in beef steers?
P.B. Anusha I.K. Bulumulla1, Meng M Li2, Yanhong Chen1, Fuyong Li1, Robin R. White3, Mark D. Hanigan2, Graham Plastow1 and Le Luo Guan1
1Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB, Canada, 2Department of Dairy Science, Virginia Tech, Blacksburg, VA, 3 Department of Animal & Poultry Sciences, Virginia Tech, Blacksburg, VA
Breeding and management of animals to achieve improved feed efficiency are a significant priority for the beef industry. Residual feed intake (RFI) is a popular measurement for feed efficiency, though it has limitations and practical challenges. The identification of additional, cost-effective indicators of feed efficiency are needed to improve breeding programs. We hypothesised that volatile fatty acids (VFA), the end products of rumen microbial fermentation and the primary energy source for ruminants, could potentially dictate feed utilisation for growth and production. Rumen content was collected from a total of 204 beef (Angus, Charolais and Kinsella composite) steers raised under the Growsafe® system, and VFA concentrations (mol/L) were analysed. Microbial populations were estimated along with phenotypic measures related to feed efficiency and feed nutrient content was analysed. VFA concentrations were predicted using the Molly mathematical model and residual VFA concentrations were calculated. Statistical analysis carried out with regression models. Residual acetate (ResAc), propionate (ResPro) and total VFA concentrations were significantly correlated with body weight, dry matter intake (DMI), and breed. Residual butyrate (ResBu) was affected only with DMI. Total bacterial copy number was negatively correlated with eating frequency (p<0.05) and ResAc (p<0.01), and positively associated with ResPro (p<0.01) concentrations. Total archeal copy number was inversely related to ResPro. RFI was significantly affected by DMI (p<0.01), ResAc, and showed a significant negative relationship with ResPr and ResBu (p< 0.05). Although the work needs to be independently evaluated, our preliminary results identified the potential of using VFA concentrations to predict feed efficiency traits.
5. Repeatability of maternal productivity of cows selected for post-weaning residual feed intake using molecular breeding values
Akanno, E. C.1, Ekine-Dzivenu, C.1, Abo-Ismail, M. K.1,2, McKeown, L.1,3, Irving, B.1, Baker, L.4, Vinsky M.4, Wang Z1, Crowley J.1, MacNeil, M. D.5, Plastow, G1, Basarab J. A.1,3, Li, C.1,4, Fitzsimmons C.1,4
1Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5; 2Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt; 3Alberta Agriculture and Forestry, Lacombe Research Centre, 6000 C&E Trail Lacombe, AB, Canada, T4L 1W; 4Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB, Canada T4L 1W1; 5Delta G 145 Ice Cave Rd, Miles City, Montana 59301
A general concern in the beef industry is that genetic improvement of production traits can compromise the maternal productivity of cows subjected to intense selection. The objective of this study was to evaluate repeatability of maternal productivity of cows selected for post-weaning residual feed intake (RFI) using molecular breeding values. A total of 1,763 cows bred between 2012 and 2016 were collated from three experimental herds namely Angus (AN; 468), Charolais (CH; 303) and Kinsella Composite (KC; 992). The KC population was randomly split into feed-efficient and control herds contributing 503 and 489 cows, respectively. In total, there were 1,096 cows with 2 or more parities. All breeding stock for AN, CH and KC-Efficient herds were selected for multi-trait maternal and feedlot profitability indexes which included RFI. Breeding and management for the KC control herd was subjected to standard industry practices. Estimation of repeatability and most probable producing ability (MPPA) of weight of calf born (BWT) or weaned (WWT) per cow exposed to bulls, pre-weaning daily gain (PDG) and calving dates (CD) coded as the number of days from January 1 to a cow’s calving date within year were assessed via mixed model analyses using ASReml software. Estimates of repeatability were moderate to high for BWT (0.21–0.39), WWT (0.22-0.46) and PDG (0.22-0.51) across the studied populations but low for CD (0.04-0.16). Within a calving year, mature cows ranked differently in MPPA with older cows having higher values. Prediction of future performance showed a slightly downward trend in productivity as younger cows replace older ones. The performance of KC–Efficient cows was better than the KC–control cows for BWT and CD but not for WWT and PDG reflecting positive impact of selection. This study indicates that cows selected for low RFI are likely to repeat their maternal performance in the future as selection continues.
6. One Hays Converter genome, one unique improvement in Canadian beef industry
Khorshidi, R.1, MacNeil, M. D.2,3, Hays, D. P.4, Akanno, E.1, Fleming, A.5, Crowley, J. J.1,6, Abo-Ismail M. K.1,7 and Plastow, G.1
1Livestock Gentec, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada; 2Delta G, Miles City, MT 59301, USA; 3Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein 9301, South Africa; 4Red Bow Ranching Ltd., Calgary, AB, Canada; 5Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; 6Canadian Beef Breeds Council, 6815 8th Street N.E., Calgary, AB T2E 7H7, Canada; 7Department of Animal and Poultry Production, Damanhour University, Damanhour, Egypt
The Hays Converter (HC) was the first registered pure beef breed developed in Canada by the late Canadian Senator Harry Hays in the 1950’s. As a synthetic, it combines genetics from Holstein, Hereford and Brown Swiss. It benefits from having leaner meat with excellent grading, efficient conversion of feed to gain to reach the preferred market weight at the earliest age and is well adapted to harsh Canadian climate conditions. Its unique origin makes it an intriguing model for genomic investigation. For example, how have each of the foundation breeds contributed to today’s breed? As a first step, we investigated the genetic improvement in weaning and yearling weights during recent years using a multiple-trait model. The results demonstrate the challenge of maintaining a small population. For example, a decrease in the nucleus herd size in 2000, resulted in a corresponding drop in the genetic trends between 2004-2008. Subsequently, the trends have gradually improved to the present day. Preliminary analysis of genomic breed composition indicates a reduced contribution of Hereford with increased percentages of Holstein and Brown Swiss over time. In the same period Angus was also introduced into the breed to help with heifer calving ease. Future analysis will include further genomic dissection of the breed contributions and their association with measures of performance. The HC nucleus herd will be moved to the Kinsella Research Ranch to provide opportunities to explore how genomics can help develop the breed and test its potential to contribute to the productivity and competitiveness of the Canadian beef sector.
7. Genomic tool for breed composition and hybrid vigor in crossbred beef cattle
M. K. Abo-Ismail1,2, J. Crowley1,3, E. C. Akanno1, G. Manafiazar1, C. Li1,4, M. MacNeil5, M. Miller6, D. Berry7, P. Stothard1, G. Plastow1, J. A. Basarab1,8
1Livestock Gentec at University of Alberta, 1400 College Plaza, 8215 112st Edmonton, AB; 2Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt; 3Canadian Beef Breeds Council, 165-6815 8 St NE, Calgary, AB; 4Rangeland Research Institute, 410 Agriculture/Forestry Center, University of Alberta, Edmonton, AB; 5Delta G, Miles City, MT, USA and Department of Animal, Wildlife and Grassland Sciences, 17 University Free State, Bloemfontein, South Africa; 6Delta Genomics, Edmonton, AB; 7Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork, Ireland; 8Alberta Agriculture and Forestry, Lacombe Research Centre, Lacombe, AB; * Presenting author
Hybrid vigour is the most cost effective way to improve the performance of hard to measure but economically relevant traits such as fertility. The objective of this study was to develop a genomic tool for beef producers named “EnVigour HXTM” by assessing the effectiveness of different methods of single nucleotide polymorphism (SNP) marker selection to predict genomic breed composition (gBC) for crossbred beef cattle and subsequently evaluate the use of those breed fractions to calculate retained heterozygosity (RH), also known as hybrid vigour. This study looked at 8,792 individual genotypes from six breeds (Gelbvieh, Charolais, Angus, Simmental, Limousin, and Hereford), three commercial crossbred herds and two crossbred research herds as well as a crossbred validation group (n=102). The gBC was predicted for all individuals using different approaches in terms of number of SNPs, methods of SNP selection and breed information. The results indicated that the largest number of SNPs in this study (7,616 SNPs) gave genomic breed composition accuracies (R2) of 97% versus an R2 of 80% with the ISAG core parentage panel, suggesting that EnVigour HXTM should continue to use the larger SNP panel for accurate analysis until SNP selection methods can be refined. The gBC from the current work was used by Basarab et al (2017) to demonstrate the benefits for the cow calf and feedyard producers. The demonstrated benefit was shown to be $161 per heifer per year based on 5 calvings. In feeder steers, increasing hybrid vigour from 30% to 60% would result in feed savings of $18/head over 250 days of feeding. Predicting genomic breed composition was achieved with high accuracy of calculation of hybrid vigour making this exciting option available to producers.
8. Transcriptome analysis of skeletal muscle tissue in Canadian beef cattle with divergent residual feed intake phenotypes
Mukiibi, R.1, Vinsky, M.2, Keogh, K.3, Fitzsimmmons, C1,2, Waters, S. M.3, Stothard, P.1 and C. Li1,2
1Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada,2 Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada,3 Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland.
The molecular mechanisms underpinning variation in residual feed intake (RFI) in beef cattle are largely unknown. In this study, we aimed to identify genes associated with RFI based on skeletal muscle whole transcriptome analyses in Canadian beef cattle. Gluteus medias muscle was collected at slaughter from each of Angus, Charolais and Kinsella Composite (KC) steers of high (n=6) and low (n=6) RFI phenotypes. RNA was extracted from the muscle samples and used to prepare cDNA libraries, which were single-end sequenced via the Illumina 2500 HiSeq sequencing system. Quality assessment was performed on the mRNAseq data using FastQC and reads with lengths less than 90bp in each sample were excluded from further analyses. Differential gene expression analyses were performed on the read count data using a generalized linear mixed model under a negative binomial distribution as implemented in edgeR. On average, sequencing generated 29 million reads per sample with an average quality score of 36, and 97.5% of the reads were of desired length (>90bp). Of the retained reads, 92% were uniquely aligned to the bovine reference genome (UMD3.1). At a false discovery rate < 0.05 and fold change > 2, 103 differentially expressed genes (DE genes) were identified in Angus (81 down and 22 upregulated in low-RFI steers), 17 in Charolais (10 down and 7 upregulated), and 271 in KC (238 down and 33 upregulated). None of the DE genes were shared by all the three breeds. However, 39 DE genes were common between Angus and KC, three genes were shared between Angus and Charolais, and one DE gene was shared between KC and Charolais. Biological functional enrichment analysis revealed that the DE genes identified are mainly involved in cell death and survival, cellular development, cellular growth and proliferation, gene expression, carbohydrate metabolism, cell morphology and cellular assembly and organization. Our results contribute towards a better understanding of the molecular control of RFI in different beef cattle breeds/populations.
9. Performance evaluation for feed efficiency and growth in progeny of parents selected for low residual feed intake The “Kinsella Breeding Project”, results following two years of selection
Ekine-Dzivenu.C.1, E. C. Akanno1, L. Chen1, L. McKeown1,2, B. Irving1, L. Baker3, M. Vinsky3, S. Miller4, Z. Wang1, J. Crowley1, M. Colazo5, D. Ambrose5, M. Juarez3, H. Bruce1, M. D. MacNeil6, G. Plastow1, J. Basarab1,2, C. Li1,3, C. Fitzsimmons1,3
1 Livestock Gentec,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5; 2 Alberta Agriculture and Rural Development, Lacombe Research Centre, 6000 C&E Trail Lacombe, AB, Canada, T4L 1W; 3 Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB, Canada T4L 1W1;4Angus Genetics Inc. (AGI), St. Joseph, Missouri;5Alberta Agriculture and Forestry, 7000 - 113 Street, Edmonton, AB, Canada T6H 5T6; 6Delta G 145 Ice Cave Rd, Miles City, Montana 59301
The aim of the breeding project at the University of Alberta Roy Berg Kinsella Research Ranch, is to breed for feed efficient herds (low residual feed intake (RFI)) using molecular breeding values in a multiple trait selection index. The project began in 2013 and uses three beef cattle populations maintained at the ranch namely, the Kinsella beef composite (KC - split into efficient and control lines), purebred Angus (AN), and purebred Charolais (CH). After two years of selection, preliminary evaluation of progeny (born between 2013 and 2015) of parents selected for low RFI in all three populations, showed favorable progress. Means of phenotypic values adjusted for systematic effects including gender and contemporary group showed that the efficient line (n=165) had a lower RFI value (-0.11±0.10 vs -0.09±0.10), birth weight (BW - 85.09±0.98 vs 85.41±1.02), weaning weight (WWT - 529.83±3.35 vs 532.56±3.44) and a higher average daily gain (ADG - 1.38±0.03 vs 1.36±0.03) compared to the control line (n=165). Dry matter intake (DMI) did not differ between lines (10.14±0.12 vs 10.14±0.13). In the Charolais (n=289) population, RFI values decreased from 0.17±0.11 to -0.30±0.10 and was accompanied with a reduction in DMI (10.27±0.15 to 9.66±0.14), ADG (1.49±0.04 to 1.21±0.03) and BW (108.79±1.87 to 100.44±1.32) with a fluctuating response in WWT. RFI also decreased, from 0.02±0.05 to -0.05±0.06 in the Angus population (n=536), and was accompanied with an increase in DMI (9.59±0.08 to 10.27±0.09) and fluctuating responses for ADG, BWT and WWT.
With the accumulation of more phenotypic data as the project progresses, it is expected that responses to selection will be better demonstrated.
10. Genome-wide association study for feeding behaviour traits in crossbred beef cattle
Valente, T.S.1, Abo-Ismail, M.K.1,2, Crowley. J.1,3, Basarab, J.A.1,4, Plastow, G. 1
1University of Alberta, Livestock Gentec, Edmonton, AB; 2Damanhour University, Department of Animal and Poultry Production, Damanhour, Egypt; 3Canadian Beef Breeds Council, Calgary, AB; 4Alberta Agriculture and Forestry, Lacombe, AB.
The aim of this study was to identify genomic regions and candidate genes associated with feeding behaviour related traits including feeding event frequency (FREQ), feeding duration (DUR) and feeding head down time (HD) in crossbred beef cattle. The phenotypes were collected using the GrowSafe system during performance tests carried out between 2003 and 2013. The average of FREQ, DUR and HD were calculated for 3,509, 3,511 and 3,511 animals, respectively. These animals were genotyped for BovineSNP50. Quality control was performed and 37,298 SNPs remained for the analyses. The genome-wide association analyses were executed using the weighted single-step GBLUP (WssGBLUP) method, combining pedigree and genomic information to estimate the genomic breeding values and SNP effects (Wang et al., 2012). The results were reported as proportion of additive genetic variance explained by each window of 20 consecutive SNPs. The top 10 SNP-windows with the major effects for each trait were located on Bos taurus chromosomes (BTA) 1, 2, 6, 7, 9, 12, 13, 14 and 16 for FREQ, BTA 1, 3, 4, 5, 8, 13, 20, 23 and 28 for DUR and BTA 1, 4, 5, 7, 11, 16, 22, 24, 25 and 27 for HD. These regions explained 12.96%, 10.29% and 11.24% of the additive genetic variance and contain 17, 163 and 81 positional candidate genes for FREQ, DUR and HD, respectively. Potential genomic regions and candidate genes were identified and may help explain the biology behind feeding behavior related traits in feedlot beef cattle.
Wang H., I. Misztal, I. Aguillar, A. Legarra & W.M. Muir, 2012. Genome-wide association mapping including phenotypes from relatives without genotypes. Genet Res. 94:73-83.
11. Does the adoption of genomics technology in the forestry sector benefit society?
1Department of Resource Economics & Environmental Sociology, University of Alberta, Edmonton, AB
In response to threats from climate change, such as an increased likelihood of droughts and insect outbreaks, scientists have proposed the use of genomics-assisted tree breeding (GATB) in the forestry sector. The main advantage of GATB is that it greatly reduces the amount of R&D time to come up with a new product, and it is much more precise than traditional breeding techniques. While GATB offers numerous improvements upon traditional methods, it does come with higher upfront R&D costs and it is unclear exactly how much it can improve upon traditional methods regarding quantity and quality attributes. To help quantify the economic effects and inform investment decisions, we assess the welfare effects of adopting GATB in the province of Alberta. Specifically, we estimate a timber supply model and a spatial equilibrium model to compare social surpluses under scenarios with and without the use of GATB. Our results show that there is significant social surplus gain when GATB is adopted. We also find that the main driving factor behind the increase in social surplus is the time saved during the breeding process. This suggests that the use of genomics technology during the breeding process is beneficial and will result in a positive return to R&D even in the absence of quantity and quality improvements. Our results not only provide a justification for adopting GATB but also provides evidence to support genomics-enhanced reforestation policies.
12. Genome wide association studies for feed efficiency traits based on imputed 7.8 million whole genome sequence SNPs in multi-breed populations of Canadian beef cattle.
Zhang, F.1,2,3, Wang, Y.1,2, Chen, L1, Vinsky M.2, Crowley, J. J.1,5, Plastow, G.1, Basarab, J.A.4, Stothard, P.1 and Li, C. 1, 2
1Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada;2Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; 3Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, China; 4Lacombe Research Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada; 5Canadian Beef Breeds Council, Calgary, AB, Canada.
Feed provision represents the largest variable cost in beef production. Identification of DNA markers for feed efficiency will not only enhance our understanding of genetic influence on feed efficiency but also help improve the accuracy of genomic prediction for the trait. In this study, we consolidated data of 7,573 animals from multiple breeds/populations including Angus (N=1,162), Charolais (N=717), Kinsella (UofAlberta, N=1,506), Elora (UofGuelph, N=775), commercial animals PG1 (N=1,911) and TX (Beefbooster, N=1,502). These animals were originally genotyped with various Bovine SNP50 Beadchips (i.e. 50K single nucleotide polymorphisms (SNP) chips), and their feed efficiency related data including residual feed intake (RFI, N=7,410), average daily gain (ADG, N=7,534), and daily dry matter intake (DMI, N=7,479) were collected under multiple research projects. The 50K SNPs were first imputed up to Affymetrix high density (HD) SNPs, and then to whole genome sequence SNPs using FImpute 2.2, resulting in approximately 38 million SNP genotypes for each animal. After removal of SNPs that were of low imputation accuracy (< 95%), low minor allele frequency (MAF < 0.5%), or deviated from the Hardy Weinberg equilibrium (p-value threshold 10-5) within any breed/population, 7,852,046 SNPs were kept and were employed for genome wide association studies (GWAS). The GWAS was conducted on a single SNP basis using a mixed linear model with a genomic relationship matrix (GRM) to account for the background genetic effects. For RFI, the majority of SNPs had low or close to zero effects. However, 165 SNPs showed effects beyond the mean ± 8 standard deviation (SD), ranging from -0.2030 to 0.1958 kg DMI/d with the corresponding p-values from 5.2138×10-6 to 0.0060. Similarly,the majority of SNPs had low or close to zero effects on ADG and DMI, For ADG, only 106 SNPs showed effects beyond mean ± 8 SD from -0.0751 to 0.0664 kg/day with the corresponding p-values from 1.2709×10-6 to 0.0056. For DMI, 111 SNPs had effects beyond mean ± 8 SD from -0.3413 to 0.2751 kg/day with corresponding p-values from 4.4496×10-6 to 0.0066. Moreover, three and two SNPs were found to have effects on ADG and DMI, respectively, with extremely low p-values from 1.7695×10-17 to 8.2563×10-08. On-going studies are undertaken to pinpoint the causative SNPs for the feed efficiency related traits and to utilize the GWAS results to improve their genomic prediction accuracies in Canadian beef cattle.
Key Words: beef cattle, genome wide association studies, whole genome sequence imputed SNPs, feed efficiency