The Experts below are selected from a list of 159 Experts worldwide ranked by ideXlab platform
Samantha A Brooks - One of the best experts on this subject based on the ideXlab platform.
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Whole genome detection of sequence and structural polymorphism in six diverse Horses.
PloS one, 2020Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per Horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all Horses), ZFAT in the Arabian, American Miniature and Percheron Horses and ANKRD1 in the Native Mongolian Chakouyi Horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse.
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Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses
2019Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:Abstract The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 8,128,658 Single Nucleotide Polymorphisms (SNPs), and 830,370 Insertions/Deletions (INDELs), as well as novel Copy Number Variations (CNVs) and Structural Variations (SVs). Our results revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature Horse. We detected a copy number gain in the Latherin gene that may be the result of evolutionary selection for thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse. Author Summary The domesticated Horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the Horse reference genome yielded the discovery of many genetic variants, the remarkable diversity across breeds of Horse calls for additional effort in quantification of the breadth of genetic polymorphism within this unique species. Here, we present genome re-sequencing and variant detection analysis for six Horses belonging to geographically and physiologically diverse breeds. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also large insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number gain in the Latherin gene that could be the result of an evolutionary selection for thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.
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Genetic Selection for Gaits in the Horse
EDIS, 2017Co-Authors: Laura Patterson Rosa, Carissa Wickens, Samantha A BrooksAbstract:Quality and cadence of various locomotion patterns are extremely valuable traits in Horses. Breeds like the Tennessee Walking Horse, Florida Cracker Horse, Mangalarga Marchador, and Icelandic Pony are prized and selected for unique intermediate-speed locomotion patterns. What if genetics could help us unravel and better select for the locomotion patterns of our Horses? This 4-page fact sheet discusses the connection between locomotion patterns and genetics, DMRT3 and locomotion in the Horse, improvement of understanding of the gene function of DMRT3, and current as well as future applications.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
E A Staiger - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
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Loci impacting polymorphic gait in the Tennessee Walking Horse.
Journal of animal science, 2016Co-Authors: E A Staiger, Mohammed Al Abri, C. A. S. Silva, Samantha A BrooksAbstract:Following domestication, man selected the Horse primarily for the purpose of transportation rather than consumption; this selective strategy created divergent traits for locomotion. At intermediate speeds, beyond the flat walk, the Horse can perform a range of diagonal and lateral 2-beat or 4-beat gait patterns. The Tennessee Walking Horse (TWH) is the only U.S. breed able to perform an even-timed 4-beat gait (the "running-walk") at intermediate speeds; however, within the breed, there is remaining variation in gait type. To investigate the contribution of genetics to this unique trait, blood or hair samples for DNA and gait information were collected from 129 TWH and genotyping was performed at approximately 60,000 loci using the Illumina Equine SNP70 beadchip at GeneSeek Inc. (Lincoln, NE). Case-control association tests identified suggestive regions for gait type on equine chromosome (ECA) 19 (-value of 1.50 × 10 after 1 million permutations; PLINK version 1.07). Haplotype analysis identified 2 significant haplotypes on ECA19 and ECA11 (-values of 3.7 × 10 and 3.92 × 10, respectively). Genes within these suggestive regions play roles in developmental processes and biological regulation, indicating there may be variant differences in the neurobiology and regulation of Horses with a polymorphic gait.
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Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
Physiological genomics, 2016Co-Authors: E A Staiger, M. Al Abri, K. M. Pflug, Sara E. Kalla, Dorothy M. Ainsworth, Donald Miller, Terje Raudsepp, Nathan B. Sutter, Samantha A BrooksAbstract:Conformation has long been a driving force in Horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure Horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 Horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in Horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in Horses.
Julia D. Albright - One of the best experts on this subject based on the ideXlab platform.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
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Genome-wide association mapping of heritable temperament variation in the Tennessee Walking Horse.
Genes Brain and Behavior, 2016Co-Authors: E A Staiger, Julia D. Albright, Samantha A BrooksAbstract:: Temperament is a key criterion in the selection of Horses for both leisure and competitive riding to ensure optimal performance and safety. The Tennessee Walking Horse (TWH) is described as a calm, docile breed and is often used as a trail, show and pleasure Horse. However, among Horse owners and caretakers, there are anecdotes supporting familial and disciplinal typical behaviors and personalities. To investigate the contribution of genetics to temperament, we collected a behavior questionnaire, brief training history and identifying information for 276 TWH, as well as blood or hair samples for DNA. Factor analysis was conducted on the 20-item questionnaire for the set of 216 Horses that met inclusion thresholds. Factor analysis identified four temperament factors in TWH: 'anxious', 'tractable', 'agonistic' and 'gregarious'. These four factors account for 64% of the total trait variance. DNA from 113 TWHs were selected and genotyped using the Equine SNP70 bead chip for three separate genome-wide association studies (GWAs) using the factor 1-anxious, factor 2-tractable and factor 3-agonistic scores as the phenotype. Quantitative association analysis identified significant candidate loci for each factor that warrant further investigation.
Sara E. Kalla - One of the best experts on this subject based on the ideXlab platform.
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Whole genome detection of sequence and structural polymorphism in six diverse Horses.
PloS one, 2020Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per Horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all Horses), ZFAT in the Arabian, American Miniature and Percheron Horses and ANKRD1 in the Native Mongolian Chakouyi Horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse.
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Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses
2019Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:Abstract The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 8,128,658 Single Nucleotide Polymorphisms (SNPs), and 830,370 Insertions/Deletions (INDELs), as well as novel Copy Number Variations (CNVs) and Structural Variations (SVs). Our results revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature Horse. We detected a copy number gain in the Latherin gene that may be the result of evolutionary selection for thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse. Author Summary The domesticated Horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the Horse reference genome yielded the discovery of many genetic variants, the remarkable diversity across breeds of Horse calls for additional effort in quantification of the breadth of genetic polymorphism within this unique species. Here, we present genome re-sequencing and variant detection analysis for six Horses belonging to geographically and physiologically diverse breeds. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also large insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number gain in the Latherin gene that could be the result of an evolutionary selection for thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.
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Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
Physiological genomics, 2016Co-Authors: E A Staiger, M. Al Abri, K. M. Pflug, Sara E. Kalla, Dorothy M. Ainsworth, Donald Miller, Terje Raudsepp, Nathan B. Sutter, Samantha A BrooksAbstract:Conformation has long been a driving force in Horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure Horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 Horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in Horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in Horses.
Nathan B. Sutter - One of the best experts on this subject based on the ideXlab platform.
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Whole genome detection of sequence and structural polymorphism in six diverse Horses.
PloS one, 2020Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse, and mapped them to EquCab3.0 genome. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 17,514,723 Single Nucleotide Polymorphisms (SNPs), and 1,923,693 Insertions/Deletions (INDELs), as well as an average of 1,540 Copy Number Variations (CNVs) and 3,321 Structural Variations (SVs) per Horse. Our results revealed putative functional variants including genes associated with size variation like LCORL gene (found in all Horses), ZFAT in the Arabian, American Miniature and Percheron Horses and ANKRD1 in the Native Mongolian Chakouyi Horse. We detected a copy number variation in the Latherin gene that may be the result of evolutionary selection impacting thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse.
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Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses
2019Co-Authors: Mohammed Al Abri, Sara E. Kalla, Nathan B. Sutter, Heather M. Holl, Samantha A BrooksAbstract:Abstract The domesticated Horse has played a unique role in human history, serving not just as a source of animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Completed in 2009, the first domesticated Horse reference genome assembly (EquCab 2.0) produced most of the publicly available genetic variations annotations in this species. Yet, there are around 400 geographically and physiologically diverse breeds of Horse. To enrich the current collection of genetic variants in the Horse, we sequenced whole genomes from six Horses of six different breeds: an American Miniature, a Percheron, an Arabian, a Mangalarga Marchador, a Native Mongolian Chakouyi, and a Tennessee Walking Horse. Aside from extreme contrasts in body size, these breeds originate from diverse global locations and each possess unique adaptive physiology. A total of 1.3 billion reads were generated for the six Horses with coverage between 15x to 24x per Horse. After applying rigorous filtration, we identified and functionally annotated 8,128,658 Single Nucleotide Polymorphisms (SNPs), and 830,370 Insertions/Deletions (INDELs), as well as novel Copy Number Variations (CNVs) and Structural Variations (SVs). Our results revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature Horse. We detected a copy number gain in the Latherin gene that may be the result of evolutionary selection for thermoregulation by sweating, an important component of athleticism and heat tolerance. The newly discovered variants were formatted into user-friendly browser tracks and will provide a foundational database for future studies of the genetic underpinnings of diverse phenotypes within the Horse. Author Summary The domesticated Horse played a unique role in human history, serving not just as a source of dietary animal protein, but also as a catalyst for long-distance migration and military conquest. As a result, the Horse developed unique physiological adaptations to meet the demands of both their climatic environment and their relationship with man. Although the completion of the Horse reference genome yielded the discovery of many genetic variants, the remarkable diversity across breeds of Horse calls for additional effort in quantification of the breadth of genetic polymorphism within this unique species. Here, we present genome re-sequencing and variant detection analysis for six Horses belonging to geographically and physiologically diverse breeds. We identified and annotated not just single nucleotide polymorphisms (SNPs), but also large insertions and deletions (INDELs), copy number variations (CNVs) and structural variations (SVs). Our results illustrate novel sources of polymorphism and highlight potentially impactful variations for phenotypes of body size and conformation. We also detected a copy number gain in the Latherin gene that could be the result of an evolutionary selection for thermoregulation through sweating. Our newly discovered variants were formatted into easy-to-use tracks that can be easily accessed by researchers around the globe.
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Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.
Physiological genomics, 2016Co-Authors: E A Staiger, M. Al Abri, K. M. Pflug, Sara E. Kalla, Dorothy M. Ainsworth, Donald Miller, Terje Raudsepp, Nathan B. Sutter, Samantha A BrooksAbstract:Conformation has long been a driving force in Horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure Horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 Horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in Horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in Horses.
