Flavio Schramm SchenkelUniversity of Guelph | UOGuelph · Animal Biosciences
Flavio Schramm Schenkel
BBA BSc MSc PhD
Full Professor with research interests ranging from theoretical to applied genetics and genomics in livestock breeding.
About
665
Publications
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Introduction
Dr. Schenkel is a Professor with research interests ranging from theoretical to applied genetics and genomics in livestock breeding. Current research focuses on the use of genomic information to enhance genetic evaluation of livestock species with emphasis on genomic selection and novel traits.
Additional affiliations
July 2014 - present
July 2009 - June 2014
September 2005 - June 2009
Education
September 1994 - September 1998
Publications
Publications (665)
Ruminants have the ability to digest human-inedible plant materials, due to the symbiotic relationship with the rumen microbiota. Rumen microbes supply short chain fatty acids, amino acids, and vitamins to dairy cows that are used for maintenance, growth, and lactation functions. The main goal of this study was to investigate gene-microbiome networ...
Body conformation traits are directly associated with longevity, fertility, health, and workability in dairy cows and have been under direct genetic selection for many decades in various countries worldwide. The main objectives of this study were to perform genome-wide association studies and functional enrichment analyses for fourteen body conform...
Background
Structural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation...
For a more sustainable dairy industry it is crucial to select for feed-efficient cattle. Although feed efficiency research has primarily focused on lactating animals, genetic selection for feed efficiency in calves has continued to gain research interest. Previously estimated genetic parameters for pre-weaned calf feed efficiency suggest residual m...
Given the increasing global demand for animal products, increasing lamb survival is a key breeding objective for sheep. However, high prolificacy can be associated with increases in fetal and lamb mortality. Therefore, the goal of this study was to estimate the variance components and genetic parameters for lamb survival (LS), using a: 1) single-tr...
Gastrointestinal nematodes (GINs) are a major constraint to the sheep industry. Infected animals can develop clinical signs, like anemia, hypoproteinemia, diarrhea, and in extreme cases death. The misuse of anthelmintics to treat infected animals has led to the development of GIN resistance making necessary the integration of different approaches t...
Unique genetic patterns in the genome of individuals who have experienced a selection process are called selection signatures. These signatures can identify genomic regions with phenotypic effects. In the case of dairy cattle, the Holstein breed was intensively selected to maximize productivity in temperate environments. In contrast, zebu cattle ar...
Gastrointestinal nematodes (GINs) parasites are a major problem in the sheep industry. To mitigate their impact, combined approaches need to be applied, which may include the implementation of genomic evaluation for indicator traits of resistance to GIN to increase genetic gain. This study aimed to investigate the impact of including genomic inform...
The goal of infectious disease control is often local eradication, but this is theoretically impossible to achieve based on classical quantitative genetic theory. Current methods focus on the susceptibility of individuals to disease and assume that exposure to a pathogen is 1) constant over time, 2) equal among individuals, and (3) due entirely to...
Cattle methane emissions (ME) account for approximately 6% of global anthropogenic greenhouse gas emissions. Given the challenges in measuring ME directly from individual animals, there is a need for the development of novel indirect methods. Rumination time (RT) and milk mid-infrared spectral data (MIR) show promise for the indirect assessment of...
In sheep meat production, prolificity is one of the main factors influencing economic profitability of a farm. Belclare sheep are used for meat production and have passed through intense selection pressure to high prolificity, leading them to have large litter sizes. This study aimed to identify selection signature regions and carry out functional...
Canada’s goat herd is about 243,000 animals, with national yearly milk production of approximately 62.6 million L. However, the ongoing import of 182,000 kg of goat cheese highlights the potential for further expansion in milk production within the country. The period between two lactations when females are not producing milk is called the “dry per...
Implementing breeding strategies for a more sustainable food system is one of the most pressing topics for livestock industries. Although different species face different challenges, large-scale research projects can pave the way for future opportunities in these key sectors. Herein, we present two examples (dairy and poultry) of how research proje...
Advancements in agricultural data collection and methodologies for data analysis offer opportunities for beef cattle producers to improve herd genetics. Genetic evaluation systems (GES) can benefit from modern programming approaches to keep up with these advancements. Python, a fast-developing programming language with scientific computing librarie...
Traits related to calving have a significant impact on animal welfare and farm profitability in dairy production systems. Identifying genomic regions associated with calving traits could contribute to refining dairy cattle breeding programs and management practices in the dairy industry. Therefore, the primary objectives of this study were to estim...
Background
A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two con...
Our objective was to evaluate the effects of omega-3 fatty acids (n3 FA)
supplementation on circulating metabolites and lactation performance. In a randomized controlled trial, cows (n = 104) were blocked by parity and BCS, and assigned randomly to 1 of 4 dietary treatments from 2 to 90 DIM: (1) UNSUP: unsupplemented control; (2) CaPO: calcium salt...
The rumen microbiome is crucial for converting feed into absorbable nutrients used for milk synthesis, and the efficiency of this process directly impacts the profitability and sustainability of the dairy industry. Recent studies have found that the rumen microbial composition explains part of the variation in feed efficiency traits, including dry...
Background
The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models...
The rumen microbiome of dairy cows is affected by parity and diet, especially dietary changes from pre- to postpartum periods. Despite this understanding, there is limited knowledge regarding the interaction between these factors and changes in the microbiome. Here, we investigated such interactions using a deep shotgun metagenomics approach. The r...
Our objective was to evaluate the effects of complete replacement of supplementary inorganic salts of trace minerals (STM; Co, Cu, Mn, and Zn sulfates and Na selenite) by organic trace minerals (OTM; Co, Cu, Mn, and Zn proteinates and selenized yeast) on the rumen microbiome. Heifers and cows (n = 72) were enrolled at 45 ± 3 d before expected calvi...
Our objective was to evaluate the effects of short- and long-term supplementation of omega-3 fatty acids (n3 FA) on ovarian and uterine biology. Healthy Holstein cows (n = 104) were assigned to 1 of 4 dietary treatments from 2 to 90 DIM: (1) UNSUP: unsupplemented control; (2) CaPO: calcium salts of palm oil (EnerGII; Virtus Nutrition) through 90 DI...
Background
Johne’s disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne’s disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne’s disease, genetic selection and improvements in management practices could...
Ketosis, evidenced by hyperketonemia with elevated blood β-hydroxybutyrate (BHB) levels, is a significant metabolic disorder of dairy cattle, typically diagnosed within the first 6 weeks post-calving when high energy levels are essential to milk production. Our study aimed to identify genetic markers linked to hyperketonemia (HYK) patterns in Holst...
Simple Summary
Cytochrome P450 2E1 (CYP2E1) is a key enzyme involved in the hepatic metabolism of the major boar taint compound, skatole. Here, we identified single-nucleotide polymorphisms (SNPs) in the promoter region of the CYP2E1 gene that were associated with CYP2E1 mRNA expression, but not with CYP2E1 protein expression. This demonstrates the...
Gastrointestinal nematodes (GINs) are a major problem affecting sheep production systems worldwide. The flocks infected with GINs can undergo significant economic losses due to a decrease in productivity, the animals’ deaths, and the costs associated with treatments. The over-reliance on anthelmintics in the past years to eliminate GINs has resulte...
Genetic selection has remarkably helped U.S. dairy farms to decrease their carbon footprint by more than doubling milk production per cow over time. Despite the environmental and economic benefits of improved feed and milk production efficiency, there is a critical need to explore phenotypical variance for feed utilization to advance the long-term...
Stress in farrowing sows is associated with the number of piglets crushed or attacked. Sow’s behaviour is variable and heritable, therefore genetic selection can be a viable approach for improving pig’s welfare. In this report, we used first parity litter records of Yorkshire sows to test a genetic evaluation model for piglet crushing. The data wer...
It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then...
Sheep infected with gastrointestinal nematodes (GIN) can show weight loss, anemia, diarrhea, decrease appetite, and hypoproteinemia, which can sometimes lead to death. These signs of infection decrease productivity and cause economic losses. Economic losses can also be associated with treatment without efficacy due to GIN resistance to most anthelm...
Intensive selection pressure coupled with the use of a limited number of high genetic merit sires has resulted in reduced effective population size and increased levels of inbreeding in dairy cattle populations. The increased rate of inbreeding amplifies the frequency of recessive deleterious alleles, possibly leading to inbreeding depression in ec...
The development of an across-country genomic evaluation scheme is a promising alternative for enlarging reference popula- tions and successfully implementing genomic selection in small ruminant populations. However, the feasibility of such evaluations depends on the genetic similarity among the populations, and therefore, high connectedness and hig...
Hoof diseases is a major welfare and economic issue in the worldwide dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. There...
The objective of the present study was to verify the effect of handling in corrals on the stress of beef cattle of Nelore, Caracu, and Guzerá breeds through the analysis of the relationship between behavioral traits, growth, and blood parameters. A total of 778 records of entry scores, chute scores, exit scores, flight speed, cortisol, glucose, lac...
Residual feed intake is viewed as an important trait in breeding programs that could be used to enhance genetic progress in feed efficiency. In particular, improving feed efficiency could improve both economic and environmental sustainability in the dairy cattle industry. However, data remain sparse, limiting the development of reliable genomic eva...
Genetic factors are known to play a role in Lamb survival (LS) and knowing its heritability and genetic correlations with other economically important traits is required to optimize the inclusion of LS into sheep breeding programs. The goal of this study was to perform a meta-analysis on the genetic parameters for LS. The dataset comprised 24 herit...
Feed efficiency has become an increasingly important research topic in recent years. As feed costs rise and the environmental impacts of agriculture become more apparent, improving the efficiency with which dairy cows convert feed to milk is increasingly important. However, feed intake is expensive to measure accurately on large populations, making...
The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake...
The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in...
The growing concern of consumers with the welfare of production animals searches welfare in a production system extremely important; thus, the study of animal temperament is necessary to select less excitable temperament animals resulting in healthy development and fewer accidents. The objective of this study was to estimate genetic parameters for...
Heat stress is a prominent issue in livestock production, even for intensively housed dairy herds in Canada. Production records and meteorological data can be combined to assess heat tolerance in dairy cattle. The overall aim of this study was to evaluate the possibility of genetic evaluation for heat tolerance in Canadian dairy cattle. The 2 speci...
Spastic syndrome is a chronic, progressive disorder of adult cattle characterized by episodes of sudden involuntary muscle contractions or spasms of the extensor and abductor muscles of one or both hind limbs. In this study, a case-control genome-wide association study (GWAS) was performed on an adult Holstein cattle cohort. Based on the 50 K and h...
Background
Biological mechanisms affecting gametogenesis, embryo development and postnatal viability have the potential to alter Mendelian inheritance expectations resulting in observable transmission ratio distortion (TRD). Although the discovery of TRD cases have been around for a long time, the current widespread and growing use of DNA technolog...
Growing consumer awareness means that the dairy industry needs to continuously review and improve standards of animal health and welfare. Genetic selection is a tool which can contribute to this, however, limited research has been conducted on the genetics of resistance to enzootic bovine leukosis (LEUK) and calf-hood diseases in Canadian dairy cat...
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. Abstract Non-additive genetic effects are well known to play an imp...
The goal of this study was to investigate whether the inclusion of genomic information and epistatic (additive by additive) genetic effects would increase the accuracy of predicting phenotypes adjusted for known environmental effects, reduce prediction bias and minimize the confounding between additive and additive by additive epistatic effects on...
Context Feed is the largest expense on a dairy farm, therefore improving feed efficiency is important. Recording dry-matter intake (DMI) is a prerequisite for calculating feed efficiency. Genetic variation of feed intake and feed efficiency varies across lactation stages and parities. DMI is an expensive and difficult-to-measure trait. This raises...
Genetic selection can be a feasible method to help mitigate enteric methane emissions from dairy cattle, as methane emission-related traits are heritable and genetic gains are persistent and cumulative over time. The objective of this study was to estimate heritability of methane emission phenotypes and the genetic and phenotypic correlations betwe...
Several biological mechanisms affecting the sperm and ova fertility and viability at developmental stages of the reproductive cycle resulted in observable transmission ratio distortion (i.e., deviation from Mendelian expectations). Gene-by-gene interactions (or epistasis) could also potentially cause specific transmission ratio distortion patterns...
Calf diseases remain a challenge for dairy producers from both an economic and welfare perspective. Genetically selecting for disease resistance in calves is a promising approach that could contribute to sustainable dairy farming. Genetic evaluations, however, require well-defined and consistently recorded phenotypes to be successful. Therefore, th...
In the dairy industry, mate allocation is dependent on the producer’s breeding goals and the parents’ breeding values. The probability of pregnancy differs among sire-dam combinations, and the compatibility of a pair may vary due to the combination of gametic haplotypes. Under the hypothesis that incomplete incompatibility would reduce the odds of...
Understanding how cows respond to heat stress has helped to provide effective herd management practices to tackle this environmental challenge. The possibility of selecting animals that are genetically more heat tolerant may provide additional means to maintain or even improve the productivity of the Canadian dairy industry, which is facing a shift...
Transmission ratio distortion (TRD), or significant deviations from Mendelian inheritance, is a well-studied phenomenon on autosomal chromosomes, but has not yet received attention on sex chromosomes. TRD was analyzed on 3832 heterosomal single nucleotide polymorphisms (SNPs) and 400 pseudoautosomal SNPs spanning the length of the X-chromosome usin...
Irregular milking intervals in automated milking systems contribute to additional variation in daily milk yield records in comparison to those derived from systems using regular milking intervals. Various methods have been developed to estimate 24-h adjusted milk yields, though they are not well suited for the evaluation of serial milk yield data,...
Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk...
Weather station data and test-day production records can be combined to quantify the effects of heat stress on production traits in dairy cattle. However, meteorological data sets that are retrieved from ground-based weather stations can be limited by spatial and temporal data gaps. The National Aeronautics and Space Administration Prediction of Wo...
Simple Summary: Global warming and events of heat waves even in temperate climatic zones signify the importance of the genetic makeup of heat stress. Our earlier acute heat stress exposure study (from 30 min to 120 min treatments) in rats led to the designation of aberrant differentially expressed genes (DEGs) and pathways through RNA-sequencing of...
The molecular mechanisms underlying heat stress tolerance in animals to high temperatures remain unclear. This experiment was performed with Sprague-Dawley rats housed at 22 ℃ (control group; CT), and 42 ℃ for 30 min (H30), 60 min (H60), and 120 min (H120). Transcriptomic analysis using RNA-Sequencing (RNA-Seq) from blood (CT and H120), liver (CT,...