PhD student, University of Alberta


Identify biomarker genes and metabolites associated with fertility, health and muscle development

The beef industry strives to produce enough, healthy, and high quality meat products for human consumption as efficiently as possible. Maximizing efficiency and growth potential of beef cattle requires not only genetic selection (i.e. residual feed intake (RFI)) but also adequate nutrition throughout all stages of growth and development. This study aims to investigate the impact of selection for divergent genetic potential for RFI (low-RFI [efficient] animals eat less and produce less greenhouse gases per unit weight gain, yet produce the same quantity/quality carcass) and maternal nutrition during early- to mid-gestation, on bull calf traits such as fertility, muscle development, and health using combination of new ”omics” sciences including genomics, metabolomics, transcriptomics, epigenetics and bioinformatics. To the best of our knowledge, this project is the first to apply a combination of high throughput "omics" technologies to investigate the effect of both RFI and maternal nutrition (at the same time) on the progeny bull traits. Once the biological pathways affected by RFI and/or maternal nutrition are identified, it is expected that candidate biomarker genes and metabolites associated with feed efficiency, fertility, muscle development and/or health will be identified and selected. Using these biomarkers in breeding programs increase the ability to select for superior animals which are efficient in fertility, meat production and/or resistant to specific diseases without slaughter. It is also expected that this work will lead to the development of an online tool that could be used to predict future traits of interest in an animal given its measurable “omics” traits.


Metatranscriptomic profiling reveals linkages between the active rumen microbiome and feed efficiency in beef cattle.

Abstract: Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n=10; inefficient, n=10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic datasets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalki, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. Through comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed efficiency animals (P < 0.10) and one archaeal taxa (Methanomassiliicoccale) tended to more abundant in efficient cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score > 2 with P < 0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZymes were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle may have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.Importance This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome with feed efficiency (residual feed intake) in beef cattle. The data generated from current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in feed efficiency. The findings on the active rumen microbiome that may contribute to variations in feed efficiency of beef cattle highlight the possibility to enhance nutrient utilization and improve cattle feed efficiency through altering rumen microbial functions.

Pub.: 27 Feb '17, Pinned: 31 Aug '17

Residual feed intake and reproductive traits of growing Purunã bulls.

Abstract: Residual feed intake (RFI) and its relationship with reproductive traits was evaluated in growing bulls. Fifty-two growing Purunã bulls (11 mo initial age) were fed ad libitum in individual feedlot pens for 112 d. The animals were ranked for RFI and assigned to 3 feed efficiency groups: efficient (low RFI), intermediate (medium RFI), and inefficient (high RFI). Initial and final BW and ADG did not differ ( > 0.10) among the efficiency groups and were mean values of 254.6 (SD 44), 373.0 (SD 62), and 1.06 kg (SD 0.25), respectively. Mean values of 7.12 ± 0.28, 7.78 ± 0.28, and 8.04 ± 0.28 kg/d for DMI and -0.38 ± 0.04, -0.02 ± 0.04, and 0.51 ± 0.04 kg of DM/d for RFI were observed in the efficient, intermediate, and inefficient groups, respectively. Crude protein and ME intake were strongly correlated ( = 0.74, < 0.001 for both variables) with RFI and were lower ( < 0.10) in the efficient group (13.6 ± 0.2 g DM/kg BW∙d and 0.252 ± 0.003 Mcal/kg BW∙d, respectively) and greater ( < 0.10) in the inefficient group (15.3 ± 0.2 g DM/kg BW∙d and 0.282 ± 0.003 Mcal/kg BW∙d, respectively). Testicular measures (width, length, volume, ultrasonogram pixel intensity, and scrotum perimeter) and serum testosterone were not correlated with RFI ( > 0.10) but showed moderate to strong correlations with initial BW ( ranged from 0.36 to 0.51, ≤ 0.01), final BW ( ranged from 0.36 to 0.64, ≤ 0.01), and ADG ( ranged from 0.29 to 0.53, < 0.05). All the reproductive traits (testicular measurements and concentrations of serum testosterone) showed similar values among the efficiency groups. During the growth phase, feed intake and protein and energy requirements were decreased in more efficient bulls in terms of RFI. However, both groups maintained similar BW and ADG. Regardless of their RFI classification, Purunã bulls had the same reproductive traits during the growth phase.

Pub.: 06 Apr '17, Pinned: 31 Aug '17

Genome-wide methylation analysis reveals differentially methylated loci that are associated with an age-dependent increase in bovine fibroblast response to LPS.

Abstract: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS). Age-dependent differences in IL-8 production are abolished by treatment with 5-aza-2-deoxycytidine and Trichostatin A (AZA-TSA), suggesting epigenetic regulation of the innate response to LPS. In the current study, we performed reduced representation bisulfite sequencing (RRBS) on fibroblast cultures isolated from the same animals at 5- and 16-months of age to identify genes that exhibit variable methylation with age. To validate the role of methylation in gene expression, six innate response genes that were hyper-methylated in young animals were assessed by RT-qPCR in fibroblasts from animals at different ages and from different breeds.We identified 14,094 differentially methylated CpGs (DMCs) that differed between fibroblast cultures at 5- versus 16-months of age. Of the 5065 DMCs that fell within gene regions, 1117 were located within promoters, 1057 were within gene exons and 2891 were within gene introns and 67% were more methylated in young cultures. Transcription factor enrichment of the promoter regions hyper-methylated in young cultures revealed significant regulation by the key pro-inflammatory regulator, NF-κB. Additionally, five out of six chosen genes (PIK3R1, FES, NFATC1, TNFSF13 and RORA) that were more methylated in young cultures showed a significant reduction in expression post-LPS treatment in comparison with older cultures. Two of these genes, FES and NFATC1, were similarly down-regulated in Angus cultures that also exhibit a low LPS response phenotype.Our study has identified immune-related loci regulated by DNA methylation in cattle that may contribute to differential cellular response to LPS, two of which exhibit an identical expression profile in both low-responding age and breed phenotypes. Methylation biomarkers of differential immunity may prove useful in developing selection strategies for replacement cows that are less susceptible to severe infections, such as coliform mastitis.

Pub.: 27 May '17, Pinned: 31 Aug '17