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Using the unique breeding history of Coldblooded trotters to identify genes that influence athletic performance
Journal of Equine Veterinary Science 52 (2017) 73e75
Contents lists available at ScienceDirect
Journal of Equine Veterinary Science journal homepage: www.j-evs.com
Genetics Graduate Student Competition 75 Understanding genetic variation in the equine population S.A. Durward-Akhurst*, R.J. Schaefer, J.R. Mickelson, M.E. McCue University of Minnesota, St Paul, MN, USA In humans, large-scale whole genome sequencing (WGS) projects have enabled improved understanding of genetic diversity by evaluating all genetic variation within and between individuals. Combining all observed sequence variation into a catalog of genetic variants gives us tremendous information about the genetic variation across a population; and can allow for characterization of genetic variation between populations. The success of human population-scale WGS projects has led to interest in similar projects for domestic animals; and initial efforts in cattle demonstrated that WGS from 200 to 300 individuals can accomplish similar objectives to human projects due to less genetic diversity in domestic animals. Our large-scale WGS project aims to evaluate genetic variation within and across breeds. We have obtained or are performing WGS on 430 horses from >30 different breeds. These sequences will be mapped to the equine reference genome and single nucleotide polymorphisms (SNPs), structural variants and inversions will be identified using publically available computer software. The number of genetic variants predicted to have a detrimental effect based on stop-codon introducing or splicesite disrupting SNPs, insertion/deletion variants predicted to disrupt a reading frame, and large deletions removing the first exon or >50% of the coding sequence will be summed to give us the genetic burden for each horse, breed and the population. Initial results from 20 Thoroughbreds and Standardbreds identified 13,341,150 and 16,113,859 variants respectively, with approximately 33% of variants within genes and 0.5% having a predicted functional effect. This study is the first large-scale WGS project of the equine population.
76 Using the unique breeding history of Coldblooded trotters to identify genes that influence athletic performance K.J. Fegraeus*1, B.D. Velie 1, J.R.S. Meadows 2, G. Lindgren 1 1 Swedish University of Agricultural Sciences, Uppsala, Sweden; 2 Uppsala University, Uppsala, Sweden The origin of the Coldblooded trotter (CBT) provides a unique opportunity to identify genes influencing racing performance. 0737-0806/$ e see front matter
The CBT originates from the North Swedish draft horse (NSH) and these 2 breeds retain high levels of genetic similarity (Fst ¼ 0.08). However, before the introduction of paternity testing in 1969, crossbreeding with Standardbreds (SB) was used to improve CBT performance. We hypothesize that the gains in CBT performance over the last 50 years may in part be explained by the maintenance of favorable genetic variants originating from the SB. As such, the aim of the current study was to compare the genetic makeup of these 3 breeds and to identify genetic footprints of athletic performance. A sliding window Delta Fst analysis was performed across all breeds using data generated from the equine SNP50K array (CBT, n ¼ 11; NSH, n ¼ 19; SB, n ¼ 12). The average Delta Fst was calculated for windows of 5 SNPs, by using DFST ¼ FST[Set A] - FST[Set B], where set A included CBTs vs SB and set B included CBT vs NSH. The 5 top regions, where the Fst in set A was low, and the Fst in set B was high (i.e., where the CBT and SB were genetically similar, but together differed from the NSH) were chosen for further investigation. All selected regions had a Ztransformed Delta Fst value above 4. These regions included the tsukushi (TSKU) and F-box and leucine rich repeat protein 4 (FBXL4) genes. Based on the relationship between the CBT and the NSH as well as the intensive selection for racing performance in CBT, we believe that these genes are important for harness racing performance. The candidate genomic regions are currently being genotyped in 400 randomly selected CBTs, and the association with harness racing performance will be investigated. The results for these genes and any other potential candidate genes will be presented at the meeting. The results from this study will provide important information to the horse industry and assist in the selection of better racehorses. Key Words: delta-Fst, Standardbred, introgression
77 Identification of a genetic locus associated with height and metabolic traits in Welsh ponies E.M. Norton*, F. Avila, N.S. Schultz, J.R. Mickelson, M.M. McCue University of Minnesota, St Paul, MN, USA Pony breeds are thought to be more susceptible to equine metabolic syndrome (EMS), a clustering of metabolic derangements that includes hyperinsulinemia, insulin resistance and adiposity. In particular, ponies are reported to have higher fasting insulin concentrations and are more insulin resistant than horses. In humans and mice, genetic alleles resulting in small skeletal size
Contents lists available at ScienceDirect
Journal of Equine Veterinary Science journal homepage: www.j-evs.com
Genetics Graduate Student Competition 75 Understanding genetic variation in the equine population S.A. Durward-Akhurst*, R.J. Schaefer, J.R. Mickelson, M.E. McCue University of Minnesota, St Paul, MN, USA In humans, large-scale whole genome sequencing (WGS) projects have enabled improved understanding of genetic diversity by evaluating all genetic variation within and between individuals. Combining all observed sequence variation into a catalog of genetic variants gives us tremendous information about the genetic variation across a population; and can allow for characterization of genetic variation between populations. The success of human population-scale WGS projects has led to interest in similar projects for domestic animals; and initial efforts in cattle demonstrated that WGS from 200 to 300 individuals can accomplish similar objectives to human projects due to less genetic diversity in domestic animals. Our large-scale WGS project aims to evaluate genetic variation within and across breeds. We have obtained or are performing WGS on 430 horses from >30 different breeds. These sequences will be mapped to the equine reference genome and single nucleotide polymorphisms (SNPs), structural variants and inversions will be identified using publically available computer software. The number of genetic variants predicted to have a detrimental effect based on stop-codon introducing or splicesite disrupting SNPs, insertion/deletion variants predicted to disrupt a reading frame, and large deletions removing the first exon or >50% of the coding sequence will be summed to give us the genetic burden for each horse, breed and the population. Initial results from 20 Thoroughbreds and Standardbreds identified 13,341,150 and 16,113,859 variants respectively, with approximately 33% of variants within genes and 0.5% having a predicted functional effect. This study is the first large-scale WGS project of the equine population.
76 Using the unique breeding history of Coldblooded trotters to identify genes that influence athletic performance K.J. Fegraeus*1, B.D. Velie 1, J.R.S. Meadows 2, G. Lindgren 1 1 Swedish University of Agricultural Sciences, Uppsala, Sweden; 2 Uppsala University, Uppsala, Sweden The origin of the Coldblooded trotter (CBT) provides a unique opportunity to identify genes influencing racing performance. 0737-0806/$ e see front matter
The CBT originates from the North Swedish draft horse (NSH) and these 2 breeds retain high levels of genetic similarity (Fst ¼ 0.08). However, before the introduction of paternity testing in 1969, crossbreeding with Standardbreds (SB) was used to improve CBT performance. We hypothesize that the gains in CBT performance over the last 50 years may in part be explained by the maintenance of favorable genetic variants originating from the SB. As such, the aim of the current study was to compare the genetic makeup of these 3 breeds and to identify genetic footprints of athletic performance. A sliding window Delta Fst analysis was performed across all breeds using data generated from the equine SNP50K array (CBT, n ¼ 11; NSH, n ¼ 19; SB, n ¼ 12). The average Delta Fst was calculated for windows of 5 SNPs, by using DFST ¼ FST[Set A] - FST[Set B], where set A included CBTs vs SB and set B included CBT vs NSH. The 5 top regions, where the Fst in set A was low, and the Fst in set B was high (i.e., where the CBT and SB were genetically similar, but together differed from the NSH) were chosen for further investigation. All selected regions had a Ztransformed Delta Fst value above 4. These regions included the tsukushi (TSKU) and F-box and leucine rich repeat protein 4 (FBXL4) genes. Based on the relationship between the CBT and the NSH as well as the intensive selection for racing performance in CBT, we believe that these genes are important for harness racing performance. The candidate genomic regions are currently being genotyped in 400 randomly selected CBTs, and the association with harness racing performance will be investigated. The results for these genes and any other potential candidate genes will be presented at the meeting. The results from this study will provide important information to the horse industry and assist in the selection of better racehorses. Key Words: delta-Fst, Standardbred, introgression
77 Identification of a genetic locus associated with height and metabolic traits in Welsh ponies E.M. Norton*, F. Avila, N.S. Schultz, J.R. Mickelson, M.M. McCue University of Minnesota, St Paul, MN, USA Pony breeds are thought to be more susceptible to equine metabolic syndrome (EMS), a clustering of metabolic derangements that includes hyperinsulinemia, insulin resistance and adiposity. In particular, ponies are reported to have higher fasting insulin concentrations and are more insulin resistant than horses. In humans and mice, genetic alleles resulting in small skeletal size