InterBOC
Tool for Estimating Breeding Values (EBV) for the Border Collie Breed
Ing. Bc. Jana Grešová
MCs in Biotechlogy and animal breeding ..
Project Title:
Development of an Algorithm for Estimating Breeding Values (EBV) for the Border Collie Breed
Goals:
The goal of this project is to develop an algorithm for estimating EBV, aimed at identifying and reducing the incidence of essential health problems such as hip and elbow dysplasia, OCD, and epilepsy within the border collie breed. Apart of UK and Finnish Kennel club, there are no EBVs calculated for this breed - and those are only for hips, so no available EBVs for OCD or epilepsy worldwide. The project also aspires to future expansions of the tool to evaluate character traits, working attributes, conformation attributes, and inclusion of genomic data.
Methodology:
The project will utilize quantitative genetics to estimate EBV, implementing cutting-edge statistical models and algorithms. Key phases will include:
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Collection and integration of data from various sources and countries.
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Development of an algorithm for calculating EBV.
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Creation of a Graphical User Interface (GUI) for ease of access and use by breeders and kennel clubs.
Expected Outcomes:
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Improvement of the overall health and quality of life of border collies and therefore their owners through targeted breeding.
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Development of a robust online tool for EBV estimation, accessible to breeders worldwide.
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Potential for extending the tool to other breeds and attributes, representing a breakthrough in dog breeding.
Significance and Innovation:
This project represents the first comprehensive attempt to unify dispersed data and research efforts in the field of canine genetics. Its innovation lies in connecting quantitative genetics, advanced statistical methods, and industrial user interface design. This approach will address existing challenges in dog breeding and set a new standard for future research and practice.
c. Expansion to Other Traits and Breeds:
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Character and Working Traits, Exterior: A long-term goal is to expand the tool to also evaluate the character, working, and exterior traits of the breed.
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Application to Other Breeds: Developing a tool that would be flexible enough to be applied to other breeds in the future.
More about Goals and Expectations:
a. Reduction of Health Problems Incidence:
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Improving Dog Health: Developing a tool that would help reduce the occurrence of serious health problems, such as hip dysplasia, elbow dysplasia, OCD, and epilepsy, among border collie breeds.
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Increasing Quality and Lifespan: The aim is to enhance the overall quality of life for dogs and their lifespan by reducing the costs of treating affected animals.
b. Research on Canine Epilepsy as a Benefit to Human Health:
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Studying the Dog Genome for Identifying Relevant Areas: Future use of EBV for canine epilepsy may work together with genomic data to identify specific areas of the genome responsible for this disease.
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Benefits to Human Research: Studying the genetics of epilepsy in dogs may bring understanding that would be beneficial for the research of genetic diseases in humans, as dogs live with people in a very similar environment.
c. Expansion to Other Traits and Breeds:
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Character and Working Traits, Exterior: A long-term goal is to expand the tool to also evaluate the character, working, and exterior traits of the breed.
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Application to Other Breeds: Developing a tool that would be flexible enough to be applied to other breeds in the future.
More about Hypotheses and Literature:
a. Reduction of Health Problems Incidence:
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Improving Dog Health: Developing a tool that would help reduce the occurrence of serious health problems, such as hip dysplasia, elbow dysplasia, OCD, and epilepsy, among border collie breeds.
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Increasing Quality and Lifespan: The aim is to enhance the overall quality of life for dogs and their lifespan by reducing the costs of treating affected animals.
b. Research on Canine Epilepsy as a Benefit to Human Health:
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Studying the Dog Genome for Identifying Relevant Areas: Future use of EBV for canine epilepsy may work together with genomic data to identify specific areas of the genome responsible for this disease.
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Benefits to Human Research: Studying the genetics of epilepsy in dogs may bring understanding that would be beneficial for the research of genetic diseases in humans, as dogs live with people in a very similar environment.
c. Quantitative Genetics:
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Bayesian Methods: Applying Bayesian probability to incorporate prior information and uncertainties in the data, enhancing the predictive accuracy.
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REML Technique: Using Restricted Maximum Likelihood (REML) for the fitting of mixed linear models that consider both fixed and random effects, providing unbiased estimates of variance components.
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EBV Estimation: Utilizing BLUP to estimate Estimated Breeding Values (EBV) for various traits such as health problems, character traits, etc.
d. User Interface Development (GUI):
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Interface Design: Creating a user-friendly interface for data input, storage, and visualization.
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Output Accessibility: Ensuring that EBV outputs will be easily accessible and understandable to breeders and clubs worldwide.
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Compatibility and Expandability: Designing the system to be compatible with various data formats and capable of being expanded to other breeds or traits in the future.
More about Development of Methodology
a. Database Integration:
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Data Collection: Gathering data from various countries and databases, including data manipulation and cleaning, format adjustments, and merging the obtained data files. Working in SAS.
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Statistical Analysis: Applying statistical methods for the analysis of integrated data, identifying trends and patterns relevant to research.
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Data Standardization: Developing standardized formats for storing data suitable for EBV calculation.
b. Algorithm Creation:
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Algorithm Design for EBV Calculation: Developing an algorithm that will utilize available data for the calculation of EBV, taking into account the latest scientific knowledge and practical experience with breeding.
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Simulation and Testing: Conducting simulations and testing the equitation and its fixed effects and random effect to ensure its functionality and efficiency.
c. Cross-Species Contribution to Human Health Research:
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Uniqueness: The proposed study of canine epilepsy's genetics and its correlation with human epilepsy is groundbreaking.
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Impact: This novel approach may not only contribute to theoretical debates in genetic research but also have practical implications for human health research and medical practices.
d. Comprehensive Tool with User-Friendly Interface:
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Uniqueness: Developing an all-encompassing, user-friendly tool for breeders and clubs worldwide stands out in its ambition and user-centered design.
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Impact: By making genetic tools more accessible, we aim to democratize scientific advancements and influence the way breeding practices are conducted globally.
e. Flexibility and Scalability for Other Breeds:
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Uniqueness: Our project’s design, which anticipates future applications to other breeds, represents forward-thinking innovation.
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Impact: This scalability ensures that our tool's impact is not confined to border collies, potentially setting a new trend for breed-specific tools.
f. Ethical Considerations:
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Uniqueness: Emphasizing ethical considerations, transparency, and responsible conduct aligns our project with modern societal values.
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Impact: This stance may influence the broader scientific community, promoting ethical practices in genetic research.
In summary, our project's innovation lies in its multifaceted approach, combining advanced methodologies, targeted focus on health, user accessibility, cross-species implications, and ethical considerations. Its significance extends beyond academic contributions, promising to shape current practices, influence policies, and contribute to broader debates in genetics, animal breeding, and human health.
More about Innovation and Significance:
a. Innovative Methodology in Quantitative Genetics:
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Uniqueness: By integrating statistical models such as Bayesian probability and REML with cutting-edge algorithm design and data integration techniques, we are pushing the envelope of current practices in EBV estimation.
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Impact: Our methodology provides a more precise and robust estimation of various traits, promising to set a new standard in quantitative genetics for canine breeding.
b. Focus on Canine Health and Life Quality:
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Uniqueness: Our explicit aim to reduce severe health problems like hip dysplasia, elbow dysplasia, OCD, and epilepsy among border collies through genetic analysis is a distinctive feature.
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Impact: This focus has the potential to revolutionize breeding practices, leading to a healthier canine population and subsequently influencing pet care policies and regulations.
c. Algorithm Development and Validation:
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Challenge: Designing an efficient algorithm that takes into account the latest scientific findings and practical breeding experiences.
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Mitigation: Continual testing, simulation, and refinement of the algorithm, seeking expert insights where necessary, to ensure functionality and efficiency.
d. User Interface Design and Accessibility:
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Challenge: Creating a user-friendly interface that is both accessible to breeders and clubs worldwide and capable of handling various data formats.
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Mitigation: Involve end-users in the design and testing phases, ensure cross-platform compatibility, and provide clear documentation and support.
e. Ethical Considerations in Genetic Research:
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Challenge: Handling genetic data and the implications of EBV estimation in breeding might raise ethical concerns.
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Mitigation: Adhere to ethical guidelines, seek necessary permissions, and ensure transparent communication with stakeholders to maintain trust and compliance.
f. Potential Impact on Different Breeds and Traits:
g. Understanding Human Genetic Diseases through Canine Genetics:
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Challenge: Translating the understanding of canine epilepsy genetics into insights for human genetic diseases.
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Mitigation: Collaborate with human genetic researchers and ensure the methodological alignment of the studies to make meaningful connections between the two fields.
More about Potential Challenges and Mitigation Strategies:
a. Complexity of Genetic Data:
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Challenge: The diverse and complex nature of genetic data can lead to difficulties in accurately estimating EBVs for various traits.
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Mitigation: Utilize advanced statistical models, including Bayesian probability and REML methods, combined with rigorous validation procedures to ensure robust analysis.
b. Data Integration from Various Sources:
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Challenge: Integrating data from different countries and databases might result in inconsistencies and quality issues.
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Mitigation: Implement thorough data cleaning, standardization, and validation processes to ensure compatibility and maintain data integrity.
Research Questions or Hypotheses:
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How can quantitative genetics be effectively utilized to estimate Estimated Breeding Values (EBV) for various traits in border collie breeds, such as health problems (including dysplasia, OCD and epilepsy), character traits, and exterior qualities?
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What statistical models, including Bayesian probability and REML methods, can be developed and validated to ensure accurate and reliable calculation of EBV, considering both genetic and environmental diversity?
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How can an algorithm be designed and tested that utilizes available data for EBV calculation, reflecting the latest scientific insights and practical long-term breeding experiences?
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What methods can be implemented for integrating data from various countries and databases, including data cleaning, format adjustment, and merging of acquired data files, to facilitate statistical analysis and standardization for EBV calculation?
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How can a user-friendly interface be developed that provides accessible and comprehensible outputs of EBVs for individual traits and animals for breeders and clubs worldwide?
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In what ways can the developed tool be expanded to evaluate character and working traits and applied to other breeds, ensuring compatibility and scalability?
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How can the study of canine epilepsy's genetics contribute to the understanding of similar genetic diseases in humans, given the shared environment?
The estimation of Estimated Breeding Values (EBV) is a critical concern in quantitative genetics and has received considerable attention in scientific literature. Here, I summarize the current state of research in this field and how our project builds on and diverges from existing work:
a. Quantitative Genetics and EBV in dogs:
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Current State: Quantitative genetics has been extensively applied to animal breeding to predict the genetic merit of individuals for various traits (Falconer and Mackay, 1996). Calculation of EBVs in dog breeding and dog health show mild heritabilities (Lewis, 2013; Wilson, 2013; Zhiwu Zhang, 2009; Shizhi Wang, 2020).
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Project Contribution: By applying these models to specific traits such as health problems, character traits, and more in border collies, I aim to create a comprehensive and breed-specific tool.
b. Genetic Algorithms and Data Integration:
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Current State: Algorithm development for EBV calculation has evolved with advancements in computational biology. Simultaneously, data integration across diverse sources has been a recurring challenge (Vandenplas, 2012; Hamadani, 2020).
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Project Contribution: We propose to develop a novel algorithm, integrating data from various countries and databases, ensuring a more robust and applicable tool across different breeds.
c. Canine Health and Genetic Studies:
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Current State: Canine genetic research has provided insights into various health conditions, including hip dysplasia, OCD and epilepsy (Sallander, 2006; Santifort, 2022). It has also led to understanding the correlation between canine and human diseases (Ostrander et al., 2017).
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Our Contribution: We focus on improving the health of border collies and exploring the potential benefits of this research on human health, a novel application of canine genetics.
d. User Interface in Genetic Tools:
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Current State: User-friendly interfaces for genetic data processing are emerging but remain limited in scope and flexibility (Cobb et al., 2019).
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Our Contribution: By developing a user-friendly interface tailored to breeders and clubs, we innovate in making genetic tools more accessible and applicable.
e. Ethical Considerations in Genetic Research:
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Current State: Ethical considerations in animal genetic research have been a point of debate and regulation (Thompson, 2012).
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Our Contribution: Our project puts an emphasis on adhering to ethical guidelines, setting a precedent for transparency and responsible conduct in the field.
In conclusion, our project builds upon key theories, models, and studies in quantitative genetics, data integration, canine health research, user interface design, and ethical considerations. It aims to innovate by applying these principles specifically to border collies, with potential wider implications for other breeds and human health. The approach diverges from existing work by combining these elements into a comprehensive, breed-specific tool designed with both scientific rigor and practical usability in mind.
Literature Review:
