@2017 by Performance Genetics LLC

  • Byron Rogers

Interesting Papers from ISAG

There were a couple of really interesting abstracts from the ISAG (International Society of Animal Genetics) meeting in Cairns Australia in July this year. Most of these will be at some stage published in Animal Genetics. In light of what is going on in thoroughbred circles right now, these ones caught my eye.

S0107 Genetic architecture of complex traits and prediction of genetic value.

M. Goddard*1,2, 1University of Melbourne, Melbourne, Victoria, Australia, 2Department of Primary Industries, Victoria, Bundoora, Victoria, Australia.

Complex traits are those controlled by many genes and by environmental factors. They are important in human health (e.g., obesity), in agriculture (e.g., yield of wheat) and in natural evolution (e.g., clutch size in birds). Despite their importance, few of the genes and mutations causing variation in these traits have been identified. However, recently, the use of genome-wide genetic markers has greatly increased our knowledge of these traits. It now appears that thousands of genes cause the normal variation in most complex traits. Nearly all these genes have very small effects which explains why they have been difficult to identify. There are many situations in which it would be useful to be able to predict the genetic value of individuals for complex traits. In agriculture, we use prediction of genetic value to select parents of future generations. In human medicine, we use genetic information to predict an individual’s risk of a given disease. It is now possible to predict individual’s genetic value from a complex trait from genome-wide genetic markers. The most accurate method for predicting genetic value from markers is a Bayesian method that uses knowledge of the genetic architecture of the trait. The accuracy of the prediction is limited by the proportion of the genetic variance that is tracked by the markers and the accuracy with which marker effects are estimated. In cattle, the markers track about 80% of the genetic variance but in humans only about 50%.

Key Words: quantitative genetics, genomic selection

P1034 Application of non-linear modeled heritability estimates for GWAS.

Tozaki Tozaki*1, Takeshi Miyake2, Hironaga Kakoi1, Hitoshi Gawahara1, Kei-ichi Hirota1, and Masahiko Kurosawa1, 1Laboratory of Racing Chemistry, Utsunomiya, Japan, 2Comparative Agricultural Sciences, Kyoto University, Kyoto, Japan.

A categorical trait analysis for non-linear models is known to be useful for estimating the heritability of non-normally distributed traits. This study estimated heritability by performing linear and non-linear model analyses concerning lifetime earnings or ranking of Japan Racing Association to investigate the variation in heritability within the various categorizations of the phenotypes. The heritability (0.25) obtained from a non-linear model concerning formal ranking was much higher than that obtained from a linear model (0.11). In particular, the heritability (0.34) for binary categorizations with non-winning and winning horses was much higher than those for the other categorizations. These results may reflect possible presences of genetic discriminations between the binary categorizations. The binary categorizations were consistent with the case/ control classification in the GWAS that only identified the MSTN gene variant (g.66493737C/T, OR = 2.31). It was also demonstrated by a large-scale cohort study that the allele frequency distribution of the non-winning category (C: 39%) was particularly different from those of the winning categories (C: 44–49%). Those findings suggested that the non-linear modeled heritability estimates from several categorizations of phenotypes are useful for the determination of thresholds for QTL phenotypes and the selection of case/control populations in GWAS.

Key Words: heritability, horse

P2054 Metabolomic and lipidomic analysis of equine serum in acute laminitis.

S. Steelman*1, P. Johnson2, and B. Chowdhary1, 1Texas A&M University, College Station, TX, USA, 2University of Missouri, Columbia, MO, USA.

Equine laminitis often occurs secondary to gastrointestinal (GI) disorders, although it is unclear how the GI system affects the laminae of the foot. Many authors have postulated that proteins, lipids, or other metabolites are transported via the bloodstream from the GI tract to the foot, where they trigger laminar inflammation. To test this hypothesis, we performed metabolomic and lipidomic analyses on serum collected from horses (n = 6) before (CON) and after induction of carbohydrate overload induced laminitis (LMN). Using mass spectrometry, we identified 256 metabolites and 922 lipids in equine serum. In CON samples, the serum metabolome was similar to that described in humans, although the presence of microbial-derived metabolite in horses suggests a link between the gut microflora and the serum metabolome. Laminitis altered serum levels of 32 lipids and 18 metabolites, many of which were involved in lactic acid metabolism. Some of the upregulated metabolites were of microbial origin, including a bacterial quorum-sensing signal that has been shown to have pro-inflammatory effects on epithelial cells. Our results support the hypothesis that bacterial metabolites escape from the GI tract during carbohydrate-induced laminitis and could initiate laminar inflammation. Further analyses are required to determine the specific effects of these metabolites on laminar tissue.

Key Words: metabolomics

P3025 Identifying equine MHC haplotypes with microsatellites.

K. T. Graves*1, P. J. Henney1, B. Mealy2, E. Bailey1, L. B. Daugherty1, K. L. Davies1, and R. Leach1, 1University of Kentucky, 2Washington State University.

The major histocompatibility complex (MHC) plays an important role in regulation of the immune response and identification of MHC genes is important for many types of research, from infectious disease to cancer Equine MHC haplotypes were originally defined serologically but a system was recently devised to assess the MHC using haplotypes based on 5 linked microsatellite markers. This study examined the MHC microsatellite genotypes among serotyped and non-serotyped horses, including Arabian horses. A large number of new haplotypes were identified. The haplotypes previously identified for Arabian horses were not found in this study. There was good correspondence of ELA serotype with the COR110 microsatellite.

Key Words: MHC, haplotype, equine

P3045 The aggrecan (ACAN) gene polymorphisms in horses of different morphological types.

M. Mackowski,* A. Klimowska, G. Cholewinski, and J. Cieslak, Poznan University of Life Sciences. Department of Horse Breeding. Horse Genetic Markers Laboratory, Poznan, Poland.

Aggrecan is a major proteoglycan found in the extracellular matrix of cartilage. Dwarfism in Dexter cattle is caused by mutations in the ACAN gene. Therefore, this gene is considered as strong candidate for dwarfism in horses. It is well known that horse breeds present a variety of morphological phenotypes, but the genetic background of this variability remains unclear. The aim of this study was an analysis of the ACAN gene, including screening for polymorphism in selected gene fragments and an evaluation of genotypes interbreed distribution. Searching for polymorphism was performed by sequencing in a panel of 96 unrelated horses from 12 breeds: Thoroughbred, Arabian, Wielkopolski, Silesian, Percheron, Polish Heavy Horse, Haflinger, Norwegian Fjord, Hucul, Polish Primitive Horse, Welsh and Shetland Pony. Altogether 5 polymorphisms were identified. Two of them (g.94349700T>C and g.94376486G>C) were already described in EquCab 2.0 database, whereas remaining 3 SNPs (g.2406G>A, g.5379C>T and g.5775C>T) turned out previously unknown. Initial results showed uneven distribution of identified SNPs among horse breeds representing different morphological types. Further analyses will be focused on their putative association with selected phenotypic traits of horses. Study was funded by the Polish Ministry of Science and Higher Education. Grant: N311 241438.

Key Words: horse, polymorphism, morphological traits

P3059 Mitochondrial genome haplogroups associated with Thoroughbred racing performance.

Aladaer Qi*1, Li Wen3, Shi Zhou2, Bin Liu1, Yong Zhang3, and Allan Davie2, 1Center of Systematic Genomics, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China, 2School of Health and Human Sciences, Southern Cross University, Lismore, Australia, 3Tianjin Key Lab of Exercise Physiology and Sports Medicine and Department of Health and Exercise Science, Tianjin University of Sports, Tianjin, China.

Mitochondria are the powerhouse in cellular energy metabolism and breeding evidence suggested matrilineal inheritance has strong influence on aerobic endurance of racing horses. The aim of this study is to examine the association between the mitochondrial genomes and the elite racing performance of Thoroughbred horses. Blood samples were collected and the mitochondrial genome sequences were obtained to determine the haplogroup structures. Case and control groups were set up among 160 thoroughbred horses. The racing performance is ranked by the value of lifetime earnings divided by life time wins: horses with zero life time wins were selected as poor performance group and top ranking 30 horses were selected as elite performance group. Eight mitochondrial genome haplogroups A, B, G, H, I, L, M, N were identified, in which haplogroups I (25%), L (47%) and N (8%) were among the main genotypes. The haplogroup distribution of the elite group differed significantly from the poor (P < 0.05), with the elite showing a greater proportion of haplogroup I (elite = 37%, poor = 16%) and lesser proportion of haplogroup L (elite = 30%, poor = 43%) and haplogroup N (elite = 3%, poor = 16%). In the entire sample set, the distribution of haplogroup I is positively correlated to the elite racing performance with r = 0.99 (P = 0.05) while haplogroup N and L showed negative correlation with r = −0.93 and −0.54, although not statistically significant. Our results suggested a genetic connection between mitochondrial haplogroups and elite racing performance of Thoroughbred horses. These findings may have practical implications in the training, selection and breeding of racing horses.

Key Words: Thoroughbred, mitochondria, elite performance

P4036 Genomic signatures of selection in the horse.

Jessica L. Petersen, James R. Mickelson,* Stephanie J. Valberg, and Molly E. McCue, University of Minnesota, St Paul MN USA.

We have used genome-wide SNP data from more than 20 horses from 33 breeds to identify putative genomic regions under selection in the horse. Such loci were identified using the FST-based statistic (di) calculated in sliding 500 kb windows. This statistic detects locus specific deviation in allele frequencies for each breed relative to the genome-wide average of pair-wise FST summed across breeds. Numerous potential targets of selection were identified, and analysis of breeds fixed for the chestnut coat color mutation demonstrated the utility of this method. One striking feature of these genome scans was a 6 Mb region on ECA18 with a highly significant di value in the Quarter Horse. Further analysis of the region revealed a ~1 Mb conserved haplotype surrounding the MSTN gene that is present in 92.8% of QH and 50% of Thoroughbreds, but rare (<1%) in all other breeds. MSTN variants including a promoter SINE insertion and an intronic SNP are significantly associated with the conserved haplotype. Histological data from 79 horses shows a significant association of muscle fiber type proportions with the MSTN polymorphisms. Another striking result was that the gaited breeds, including the Standardbred, Icelandic, Peruvian Paso, and others, share a highly conserved haplotype on ECA23 under a strong signal of selection that contains a polymorphism demonstrated to be important in the ability to gait. Further, conserved haplotypes underlying signals of selection on ECA11 in the Belgian, Percheron, Shire, Clydesdale, and Miniature horse suggest the presence of a locus or loci important in the determination of size. Numerous other loci await a detailed evaluation. Mapping signatures of selection in the modern horse is the first step in the identification of genes important in the domestication and specialization of modern horse breeds.

Key Words: selection, equine, breeds

P4048 First results on genomic selection in French show-jumping horses.

A. Ricard*1, S. Danvy2,

and A. Legarra3, 1Institut National de la Recherche Agronomique, UMR1313, Jouy-En-Josas, France, 2Institut Français du cheval et de l’Equitation, Exmes, France, 3Institut National de la Recherche Agronomique, UR 631, Castanet-Tolosan, France.

Genomic selection could be highly interesting for horse breeding because it would reduce the currently high generation interval, at a low cost compared with the value of an animal. The aim of this study was to estimate the observed accuracies of genomic estimated breeding values. A sample of 908 stallions specialized in show jumping (71% Selle français (SF), 17% Foreign sport horses (FH), 13% Anglo Arab(AA)) were genotyped. Genotyping was performed using Illumina Equine SNP50 BeadChip and after quality tests, 44444 SNP were retained. From whole population BLUP-based estimated breeding values and their reliability, a specific procedure was developed to obtain de-regressed proofs combining own performances and performances of relatives outside the genotyped sample. Two methods were used for genomic evaluation: GBLUP and Bayes CΠ, and 6 validation data sets were compared, chosen according to breeds SF+FH+AA or SF+FH, family structure (more than 3 half sibs), reliability of sires (>0.97) or sons (>0.72). Results showed low advantage of genomic evaluation. On the validation sample SF+FH+AA, the correlation between deregressed proofs and GBLUP or BayesCΠ predictions was: 0.39, 0.37, 0.51 according to the different validation data sets compared with 0.36, 0.33, 0.53 obtained with BLUP predictions. GWAS analysis would be performed on the same data.

Key Words: horse, genomic selection, jumping

P4065 Genetic selection for racing durability in Thoroughbreds.

B. D. Velie,* N. A. Hamilton, and C. M. Wade, The University of Sydney, Sydney, NSW, Australia.

Concern for racehorse welfare is receiving increasing global attention. Racehorse attrition, or wastage has become a contentious topic, with many believing the amount of wastage in horseracing is unacceptably high. Genetic influences on the racing durability of thoroughbreds are yet to be fully explored. Our objective is to help improve the welfare of racing thoroughbreds through the creation of a selection index that emphasizes racing durability. Complete pedigrees and performance records were acquired for all thoroughbreds racing in Australia and Hong Kong between August 1, 2000 and February 22, 2011. The sample includes 2,882,773 individual records and 169,049 horses. Ten thousand randomly selected horses were used for preliminary analyses. A model including sex and color as fixed effects yielded heritabilities for career length (0.19 ± 0.03), career starts (0.17 ± 0.03), career earnings (0.10 ± 0.02), spells per 10 starts (0.09 ± 0.02), and spells per year (0.14 ± 0.03). Starts per month does not appear to be heritable (0.02 ± 0.02). Estimation of heritabilities and other genetic parameters using the entire sample based on an expanded model are currently underway. The assessment of genetic parameters for these traits is the first step in the construction of a selection index emphasizing racing durability and will aid in identifying horses suited to genetic mapping studies for specific issues relating to durability.

Key Words: horse, welfare, wastage

P5018 Molecular mechanisms involved in equine osteochondrosis.

C. Desjardin*1, A. Vaiman1, T. Balliau1, J. Rivière1, R. Legendre1, X. Mata1, M. Zivy2, E-P. Cribiu1, and L. Schibler1, 1INRA, Jouy-en-Josas, France, 2CNRS.

Equine osteochondrosis (OC) is a juvenile osteoarticular pathology characterized by a local failure of cartilage maturation, leading to dissection of an articular flap or to subchondral cysts development in joints. With an incidence of 10 to 30%, OC is a major concern in terms of animal health care and economy. Many factors have been suggested including nutrition, trauma and genetics. The aim of our study is to bring new insight into molecular mechanisms and biological process involved in OC susceptibility. We performed a comparative study focused on histology, proteome and microtranscriptome of normal cartilage and subchondral bone from healthy and OC affected foals. Proteomic analyses of cartilage have long been impaired because of technical challenges related to their biochemical properties. We have developed an efficient method to characterize the proteome of cartilage and bone and compare healthy and OC foals. Our study highlighted several modulated proteins involved in extracellular matrix structure and dynamics, chondrocyte metabolism as well as bone mineralization. In addition, a SOLIDTM RNA-Seq strategy was followed to establish the cartilage and bone miRNA catalogs and define a set of modulated miRNAs. Taken together, our findings point out the heterogeneous nature of OC and suggest that both cartilage and bone defects may be involved in the physiopathology.

Key Words: equine osteochondrosis, proteomic, microtranscriptome

P5022 Whole genome association study of Type 2 polysaccharide storage myopathy (PSSM) in Quarter Horses.

K. L. Fritz*1, S. J. Valberg2, A. K. Rendahl2,3, M. A. Lucio2, J. R. Mickelson1, and M. E. McCue2, 1Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA, 2Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA, 3School of Statistics, University of Minnesota, Minneapolis, MN, USA.

We previously identified a mutation within the GYS1 gene in horses with Type 1 polysaccharide storage myopathy (PSSM), which results in an accumulation of glycogen and amylase-resistant abnormal polysaccharide in skeletal muscle fibers; however, a proportion of horses diagnosed with PSSM do not have the GYS1 mutation. The high prevalence of this form of PSSM, termed Type 2 PSSM, in breeds such as the Quarter Horse, suggests that Type 2 PSSM may have a genetic basis. The purpose of this study was to utilize a genome wide association mapping strategy to identify positional candidate genes for Type 2 PSSM in Quarter Horses. The genotypes of 50,856 SNPs were analyzed among 124 Quarter Horse controls and 104 Quarter Horse PSSM Type 2 cases in a logistic regression test with 10,000 case/control label-swapping permutations. The results revealed suggestive associations of a single SNP on ECA3 and 6 SNPs within a haplotype on ECA18 (most significant P-value = 2.0 Å~ 10−6). The strength of the association on ECA18 persisted when the data was analyzed to account for population stratification and cryptic relatedness, suggesting that the association was real and not spurious. In the future, a functional mutation for Type 2 PSSM may be revealed by sequencing genes in this region of ECA18.

Key Words: GWAS, equine SNP chip, tying up

P5025 Heritability of epistaxis associated with exercise-induced pulmonary haemorrhage in Australian racehorses.

N. A. Hamilton*1, G. Chaudhuri1, P. T. Thomson1, and P. K. Knight2, 1Faculty of Veterinary Science, The University of Sydney, Sydney, NSW, Australia, 2Discipline of Biomedical Science, Sydney Medical School, Lidcombe, NSW, Australia.

The pathogenesis of exercise induced pulmonary hemorrhage (EIPH) is highly disputed, with inconclusive results suggesting the onset of the disease is multifactorial. Previous research into the South African Thoroughbred racing population demonstrated that EIPH-related epistaxis has a strong genetic basis. We aimed to estimate the heritability of EIPH-related epistaxis in Australian racehorses to investigate whether genetics plays a significant role in the occurrence of this disease. Pedigree information was supplied by the Australian Studbook, and records of all horses banned from racing due to epistaxis between 1999 and 2009 were supplied by Racing Industry Services Australia. Using a sire model, heritability for incurring one episode of epistaxis associated with EIPH was estimated at 0.51 ± 0.01; and at 0.14 ± 0.03 for a recurrent episode. This was similar to the heritability reported in the previous study. Sex and age were also significant predictors of the disease; which was positively associated with geldings and older horses. Estimated breeding values for sires ranged from –1.12 to 2.10, indicating a 25–fold difference in the odds of the disease. The heritability using an animal model is currently being calculated. These results suggest there is a genetic basis to the disease in Australian Thoroughbreds.

Key Words: horse, epistaxis, heritability