Flavio Schramm Schenkel

Flavio Schramm Schenkel
University of Guelph | UOGuelph · Animal Biosciences

BBA BSc MSc PhD
Full Professor with research interests ranging from theoretical to applied genetics and genomics in livestock breeding.

About

546
Publications
88,448
Reads
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8,570
Citations
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.
Additional affiliations
July 2014 - present
University of Guelph
Position
  • Professor (Full)
Description
  • CGIL is a research group affiliated with Department of Animal Biosciences (formerly Department of Animal and Poultry Science) at University of Guelph. Research is done on numerous species of animals including aquaculture, beef, dairy, poultry and swine.
July 2009 - June 2014
University of Guelph
Position
  • Professor (Associate)
Description
  • CGIL is a research group affiliated with Department of Animal and Poultry Science, part of Ontario Agricultural College, at University of Guelph. Research is done on numerous species of animals including aquaculture, beef, dairy, poultry and swine.
September 2005 - June 2009
University of Guelph
Position
  • Professor (Assistant)
Education
September 1994 - September 1998
University of Guelph
Field of study
  • Animal breeding and genomics of livestock

Publications

Publications (546)
Article
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,...
Article
Full-text available
Genomic prediction of breeding values is routinely performed in several livestock breeding programs around the world, but the size of the training populations and the genetic structure of populations evaluated have, in many instances, limited the increase in the accuracy of genomic estimated breeding values. Combining phenotypic, pedigree, and geno...
Article
Pro$ is a Canadian economic selection index aimed to maximize profit by increasing production yields, while maintaining conformation and functional traits. Currently, there is an interest in understanding the individual contributions of conformation traits recorded in Canada to the overall economic value of a cow and whether they are equally import...
Article
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Conformation traits are functional traits known to affect longevity, production efficiency, and profitability of dairy goats. However, genetic progress for these traits is expected to be slower than for milk production traits due to the limited number of herds participating in type classification programs, and often lower heritability estimates. Ge...
Article
This study aimed to integrate GWAS and structural variants to propose possible molecular biomarkers related to gastrointestinal nematode resistance traits in Santa Inês sheep. The phenotypic records FAMACHA, haematocrit, white blood cell count, red blood cell count, haemoglobin, platelets and egg counts per gram of faeces were collected from 700 na...
Article
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Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleot...
Article
Methane emission is not included in the current breeding goals for dairy cattle mainly due to the expense and difficulty in obtaining sufficient data to generate accurate estimates of the relevant traits. While several models have been developed to predict methane emission from milk spectra using reference methane data obtained by the respiration c...
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Full-text available
Although selection for increased milk production traits has led to a genetic increase in body weight (BW), the genetic gain in milk production has exceeded the gain in BW, so gross feed efficiency has improved. Nonetheless, greater gains may be possible by directly selecting for a measure of feed efficiency. Australia first introduced Feed Saved (F...
Conference Paper
Feed efficiency (FE) has become a trait of major focus for breeding organizations worldwide. An increasing number of countries are now recording dry matter intake (mostly in research herds) to bolster the estimation of FE-related genomic breeding values. Selection for FE based on data recorded in early lactation may be unfavourable, as cows are in...
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Genomic evaluations are routine in most plant and livestock breeding programs but are used infrequently in dairy goat breeding schemes. In this context, the purpose of this study was to investigate the use of the single-step genomic BLUP method for predicting ge-nomic breeding values for milk production traits (milk, protein, and fat yields; protei...
Conference Paper
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The aims of this study were to: 1) update the Australian (dairy) breeding value (ABV) for lifetime residual feed intake (RFIlife, covering RFI at the growth and lactation stages) using 3,711 Holstein female records (584 Australian cows, 824 Australian heifers and 2,440 foreign cows) using a multivariate model and 2) re-evaluate the Feed Saved ABV i...
Article
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Reduced fertility is one of the main causes of economic losses on dairy farms, resulting in economic losses estimated at $938 per stillbirth case in Holstein herds. The identification of genomic regions associated with stillbirth could help to develop better management and breeding strategies aimed to reduce the frequency of undesirable gestation o...
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Background The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic measures, effects of genomic inbreeding on production and fertility traits have been observed. However, there have been limited stu...
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Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percenta...
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Fecal egg count (FEC) is an indicative measurement for parasite infection in sheep. Different FEC methods may show inconsistent results. Not accounting for inconsistencies can be problematic when integrating measurements from different FEC methods for genetic evaluation. The objectives of this study were to evaluate the difference in means and vari...
Conference Paper
Stillbirth is an ethically and economically important trait in several production systems. Copy number variants (CNV) may contribute to reduce the frequency of stillbirths in dairy cattle. Therefore, association analyses of high-confidence CNV regions with stillbirth traits were carried out in this study. Four stillbirth traits were evaluated: stil...
Article
Recent issues in the dairy industry related to both animal and public health concerns are leading farmers away from the use of drugs, while placing more focus on animal health and welfare. Public demands are also shifting towards ensuring socially acceptable production practices in terms of good animal health and welfare. Such challenges are moving...
Article
In the dairy industry, mate allocation is mainly based on the parents’ breeding values and inbreeding coefficients aiming to achieve the producer’s breeding goal. With artificial insemination, the portfolio of sires to choose from is large and the quality of the semen doses is standardized. However, not all sire-dam matings are equally likely to pr...
Article
Genetically selecting animals that are heat tolerant can help to maintain production efficiency of the dairy industry under thermal challenges. During the summer months in Canada, dairy cows could be under thermal stress. For instance, in Ontario, cows are expected to be 105 days under thermal stress. The objective of this study was to estimate gen...
Article
Full-text available
Including immune response traits in breeding programs has been suggested as a solution to improve overall animal health and enhance disease resistance but is not yet available for Angus cattle in North America. One way to measure immune response is to use the High Immune Response (HIR™) technology, which identifies animals with superior heritable i...
Article
Genetic improvement of health, welfare, efficiency, and fertility traits is challenging due to expensive and fuzzy phenotypes, the polygenic nature of traits, antagonistic genetic correlations to production traits and low heritabilities. Nevertheless, many organizations have introduced large-scale genetic evaluations for such traits in routine sele...
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Selection based on scrapie genotypes could improve the genetic resistance for scrapie in sheep. However, in practice, few animals are genotyped. The objectives were to define numerical values of scrapie resistance genotypes and adjust for their non-additive genetic effect; evaluate prediction accuracy of ungenotyped animals using linear animal mode...
Article
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The level of genetic diversity in a population is inversely proportional to the linkage disequilibrium (LD) between individual single nucleotide polymorphisms (SNP) and quantitative trait loci (QTL), leading to lower predictive ability of genomic breeding values (GEBV) in high genetically diverse populations. Haplotype-based predictions could outpe...
Article
Heat stress imposes a challenge to the dairy industry, even in northern latitudes. In this study, publicly available weather station data was combined with test-day records for milk, fat, and protein yields to identify the temperature-humidity index (THI) thresholds at which heat load starts affecting milk production traits in Canadian Holstein cow...
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Johne’s disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and...
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Estrus detection has become more difficult over the years due to decreases in the estrus expression of high-producing dairy cows, and increased herd sizes and animal density. Through the use of hormonal synchronization protocols, also known as timed artificial insemination (TAI) protocols, it is possible to alleviate some of the challenges associat...
Conference Paper
Longevity is of great economic importance for the beef cattle industry. Various statistical models are currently used to genetically evaluate this trait, including random regression models (RRM). Due to the binary nature of the expression of longevity (0 = culled, 1 = alive), it is still unclear if threshold RRM would be more adequate than traditio...
Article
Full-text available
Identifying genes or genomic regions influencing carcass-quality traits such as fatness (FTN) is essential to optimize the genetic selection processes in beef cattle. The aim of this study was to identify genomic regions associated with FTN in Nellore cattle as well as to elucidate the metabolic pathways related to the phenotypic expression. Ultras...
Conference Paper
The goals of this study were to develop a genetic evaluation system for a novel trait called functional heifer longevity (FHL), and determine if this novel trait is heritable. The FHL trait was defined as binary, in which the heifers received the code 1 if they had calved by the end of their third year (N = 377,938), or 0 if they were culled/sold d...
Conference Paper
A recent study showed that longevity based on different culling reasons should be considered as different traits in genetic evaluations. However, it is still necessary to create a pipeline that avoid including/excluding animals culled for different reasons in every genetic evaluation run. This study aimed to: 1) perform a genetic evaluation of the...
Conference Paper
Genomic breeding values (GEBVs) predicted based solely on single-nucleotide polymorphism (SNP) markers may represent only a part of the true breeding values (TBVs) of animals. To increase the correlation between GEBVs and TBVs, copy number variations (CNVs) might be useful, as they can capture part of the genetic variation not accounted for by SNPs...
Article
The use of multiple-breed models can increase the accuracy of estimated breeding values (EBV) when few phenotypes are available for a trait. However, pooling breeds is not always beneficial for genomic evaluations due to the low consistency of gametic phase between individual breeds. The objective of this study was to compare the expected gain in a...
Conference Paper
Full-text available
Feed efficiency is an important aspect of dairy cattle productivity. Animals that consume less feed while producing the same amount of milk have the potential to reduce costs without reducing production. The physiology of lactation must be taken into account when selecting for improved feed efficiency. Peak lactation occurs 6 to 8 weeks after calvi...
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Ketosis is one of the most frequent metabolic diseases in high-yielding dairy cows and is characterized by high concentrations of ketone bodies in blood, urine, and milk, causing high economic losses. The search for polymorphic genes, whose alleles have different effects on resistance to developing the disease, is of extreme importance to help sele...
Article
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Selecting for lower methane (CH4) emitting animals is one of the best approaches to reduce CH4 given that genetic progress is permanent and cumulative over generations. As genetic selection requires a large number of animals with records and few countries actively record CH4, combining data from different countries could help to expedite accurate g...
Article
Full-text available
Genome-wide association studies based on SNP have been completed for multiple traits in dairy cattle; however, copy number variants (CNV) could add genomic information that has yet to be harnessed. The objectives of this study were to identify CNV in genotyped Holstein animals and assess their association with hoof health traits using deregressed e...
Article
Full-text available
The inclusion of feed efficiency in the breeding goal for dairy cattle has been discussed for many years. The effects of incorporating feed efficiency into a selection index were assessed by indirect selection (dry matter intake) and direct selection (residual feed intake) using deterministic modeling. Both traits were investigated in three ways: (...
Article
Full-text available
Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; C...
Article
Full-text available
The objective of the present study was to evaluate the effects of different selection practices on the environmental sensitivity of reproductive and growth traits in males and females of three Nellore selection lines [control (NeC), selection (NeS), and traditional (NeT) lines]. Moreover, genetic trends for the intercept and slope were estimated fo...
Article
Full-text available
Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 6...
Article
Full-text available
Genetic selection for improved feed efficiency in dairy cattle has received renewed attention over the last decade to address the needs of a growing global population. As milk yield is a critical component of feed efficiency metrics in dairy animals, our objective was to evaluate the associations between feed efficiency in primiparous Holstein catt...
Article
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This study aimed to evaluate the impact of different proportions (i.e., 20%, 40%, 60% and 80%) of censored (CEN) or penalized (PEN) data in the prediction of breeding values (EBVs), genetic parameters, and computational efficiency for two longevity indicators (i.e., traditional and functional longevity; TL and FL, respectively). In addition, three...
Article
Full-text available
About 30% of producers use hormone protocols to synchronize ovulation and perform timed artificial insemination (AI) in Canada. Days from calving to first service (CTFS) and first service to conception (FSTC) become masked phenotypes leading to biased genetic evaluations of cows for these fertility traits. The objectives of this study were to (1) d...
Article
Full-text available
Background: Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. Long-non-coding RNAs (lncRNAs) play an important role in many biological processes by transcriptional regulation. However, no research has been reported on the characterization and functionality of lncRNAs in heat-stres...
Article
The goals of this study were to develop a genetic evaluation system for a novel trait called functional heifer longevity (FHL), and determine if this novel trait is heritable. The FHL trait was defined as binary, in which the heifers received the code 1 if they had calved by the end of their third year (n = 377,938), or 0 if they were culled/sold d...
Article
Full-text available
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle br...
Article
The objective of this study was to identify genomic regions associated with beef fatty acid (FA) profile in Nellore cattle finished in feedlot, using haplotype based analyzes. Also, the metabolic pathway enrichment analysis was performed to seek for genes with known functions, close to the haplotype blocks, associated with the evaluated traits, pro...
Conference Paper
Genetic evaluation of longevity in beef cattle usually relies on culling records reported by the farmers. However, only a small proportion of cows in the American Angus Association pedigree file have culling records available. Defining a longevity indicator that does not rely on culling information might optimize the use of data in the genetic anal...
Article
A recent study showed that longevity based on different culling reasons should be considered as different traits in genetic evaluations. However, it is still necessary to create a pipeline that avoid including/excluding animals culled for different reasons in every genetic evaluation run. This study aimed to: 1) perform a genetic evaluation of the...
Article
The successful implementation of genomic selection in more genetically diverse populations (e.g., sheep and goats) require larger training populations. Haplotype-based genomic predictions are hypothesized to perform better in comparison to single-SNP methods mainly due to the possibility of better capturing QTL effects in linkage disequilibrium (LD...
Article
Full-text available
The identification of functional genetic variants and associated candidate genes linked to feed efficiency may help improve selection for feed efficiency in dairy cattle, providing economic and environmental benefits for the dairy industry. This study used RNA-sequencing data obtained from liver tissue from 9 Holstein cows [n = 5 low residual feed...