Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses

References

• Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, et al. 2012. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci USA. 109:2449–2454.
   PubMed Web of Science ®Google Scholar
• Andronescu MS, Pop C, Condon AE. 2010. Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA. 16:26–42.
   PubMed Web of Science ®Google Scholar
• Ballard JWO, Whitlock MC. 2004. The incomplete natural history of mitochondria. Mol Ecol. 13:729–744.
   PubMed Web of Science ®Google Scholar
• Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37–48.
   PubMed Web of Science ®Google Scholar
• Binns MM, Boehler DA, Lambert DH. 2010. Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in the Thoroughbred horse in the USA. Anim Genet. 41 (Suppl 2):154–158.
   PubMedGoogle Scholar
• Boles RG, Zaki EA, Lavenbarg T, Hejazi R, Foran P, Freeborn J, Trilokekar S, McCallum R. 2009. Are pediatric and adult-onset cyclic vomiting syndrome (CVS) biologically different conditions? Relationship of adult-onset CVS with the migraine and pediatric CVS-associated common mtDNA polymorphisms 16519T and 3010A. Neurogastroenterol Motil. 21:936–e972.
   PubMed Web of Science ®Google Scholar
• Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RE, Hill EW, Howe CJ, Binns M. 2011. The cosmopolitan maternal heritage of the Thoroughbred racehorse breed shows a significant contribution from British and Irish native mares. Biol Lett. 7:316–320.
   PubMed Web of Science ®Google Scholar
• Bower MA, Whitten M, Nisbet RER, Spencer M, Dominy KM, Murphy AM, Cassidy R, Barrett E, Hill EW, Binns M. 2013. Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. J Anim Breed Genet. 130:227–235.
   PubMed Web of Science ®Google Scholar
• Bowling AT, Del Valle A, Bowling M. 2000. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses. Anim Genet. 31:1–7.
   PubMed Web of Science ®Google Scholar
• Brown WM, George M, Jr., Wilson AC. 1979. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 76:1967–1971.
   PubMed Web of Science ®Google Scholar
• Cardaioli E, Dotti MT, Hayek G, Zappella M, Federico A. 1999. Studies on mitochondrial pathogenesis of Rett syndrome: ultrastructural data from skin and muscle biopsies and mutational analysis at mtDNA nucleotides 10463 and 2835. J Submicrosc Cytol Pathol. 31:301–304.
   PubMedGoogle Scholar
• Coulbault L, Deslandes B, Herlicoviez D, Read MH, Leporrier N, Schaeffer S, Mouadil A, Lombès A, Chapon F, Jauzac P, Allouche S. 2007. A novel mutation 3090 G > A of the mitochondrial 16S ribosomal RNA associated with myopathy . Biochem Biophys Res Commun. 362:601–605.
   PubMed Web of Science ®Google Scholar
• Das J. 2006. The role of mitochondrial respiration in physiological and evolutionary adaptation. Bioessays. 28:890–901.
   PubMed Web of Science ®Google Scholar
• Erdfelder E, Faul F, Buchner A. 1996. GPOWER: a general power analysis program. Behav Res Methods Instruments Comput. 28:1–11.
   Google Scholar
• Essen-Gustavsson B, Lindholm A. 1985. Muscle fibre characteristics of active and inactive standardbred horses. Equine Vet J. 17:434–438.
   PubMed Web of Science ®Google Scholar
• Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186–194.
   PubMed Web of Science ®Google Scholar
• Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185.
   PubMed Web of Science ®Google Scholar
• Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202.
   PubMed Web of Science ®Google Scholar
• Gu J, MacHugh DE, McGivney BA, Park SD, Katz LM, Hill EW. 2010. Association of sequence variants in CKM (creatine kinase, muscle) and COX4I2 (cytochrome c oxidase, subunit 4, isoform 2) genes with racing performance in Thoroughbred horses. Equine Vet J. 42:569–575.
   Web of Science ®Google Scholar
• Gu J, Orr N, Park SD, Katz LM, Sulimova G, MacHugh DE, Hill EW. 2009. A genome scan for positive selection in thoroughbred horses. PLoS One. 4:e5767.
   PubMed Web of Science ®Google Scholar
• Harrison SP, Turrion-Gomez JL. 2006. Mitochondrial DNA: an important female contribution to thoroughbred racehorse performance. Mitochondrion. 6:53–63.
   PubMed Web of Science ®Google Scholar
• Hill EW, Bradley DG, Al-Barody M, Ertugrul O, Splan RK, Zakharov I, Cunningham EP. 2002. History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Anim Genet. 33:287–294.
   PubMed Web of Science ®Google Scholar
• Hill EW, McGivney BA, Gu J, Whiston R, Machugh DE. 2010. A genome-wide SNP-association study confirms a sequence variant (g.66493737C > T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genom. 11:552.
   PubMed Web of Science ®Google Scholar
• Hsieh RH, Li JY, Pang CY, Wei YH. 2001. A novel mutation in the mitochondrial 16S rRNA gene in a patient with MELAS syndrome, diabetes mellitus, hyperthyroidism and cardiomyopathy. J Biomed Sci. 8:328–335.
   PubMed Web of Science ®Google Scholar
• Khanshour AM, Cothran EG. 2013. Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing. BMC Genet. 14:83.
   PubMed Web of Science ®Google Scholar
• Koc EC, Burkhart W, Blackburn K, Moyer MB, Schlatzer DM, Moseley A, Spremulli LL. 2001. The large subunit of the mammalian mitochondrial ribosome. Analysis of the complement of ribosomal proteins present. J Biol Chem. 276:43958–43969.
   PubMed Web of Science ®Google Scholar
• Li JY, Hsieh RH, Peng NJ, Lai PH, Lee CF, Lo YK, Wei YH. 2007. A follow-up study in a Taiwanese family with mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes syndrome. J Formos Med Assoc. 106:528–536.
   PubMed Web of Science ®Google Scholar
• Lin X, Zhou S, Wen L, Davie A, Yao X, Liu W, Zhang Y. 2015. Potential role of maternal lineage in the thoroughbred breeding strategy. Reprod Fertil Dev. 28:1704–1711.
   Web of Science ®Google Scholar
• Lippold S, Matzke NJ, Reissmann M, Hofreiter M. 2011. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol. 11:328.
   PubMed Web of Science ®Google Scholar
• Lorenz R, Bernhart SH, Honer Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL. 2011. ViennaRNA Package 2.0. Algorithms Mol Biol. 6:26.
   PubMed Web of Science ®Google Scholar
• Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA. 101:7287–7292.
   PubMed Web of Science ®Google Scholar
• McBane S. 1997. The illustrated encyclopedia of horse breeds. New York: Wellfleet Press.
   Google Scholar
• McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, et al. 2012. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet. 8:e1002451.
   PubMed Web of Science ®Google Scholar
• McGivney BA, Browne JA, Fonseca RG, Katz LM, Machugh DE, Whiston R, Hill EW. 2012. MSTN genotypes in Thoroughbred horses influence skeletal muscle gene expression and racetrack performance. Anim Genet. 43:810–812.
   PubMed Web of Science ®Google Scholar
• Mishra P, Chan DC. 2014. Mitochondrial dynamics and inheritance during cell division, development and disease. Nat Rev Mol Cell Biol. 15:634–646.
   PubMed Web of Science ®Google Scholar
• Parker R. 2007. Equine Science. Delmar: Cengage Learning.
   Google Scholar
• Poso AR, Essen-Gustavsson B, Persson SG. 1993. Metabolic response to standardised exercise test in standardbred trotters with red cell hypervolaemia. Equine Vet J. 25:527–531.
   PubMedGoogle Scholar
• Roneus M, Lindholm A, Asheim A. 1991. Muscle characteristics in thoroughbreds of different ages and sexes. Equine Vet J. 23:207–210.
   PubMed Web of Science ®Google Scholar
• Roneus N, Essen-Gustavsson B, Lindholm A, Eriksson Y. 1994. Plasma lactate response to submaximal and maximal exercise tests with training, and its relationship to performance and muscle characteristics in standardbred trotters. Equine Vet J. 26:117–121.
   PubMed Web of Science ®Google Scholar
• Shen YY, Liang L, Zhu ZH, Zhou WP, Irwin DM, Zhang YP. 2010. Adaptive evolution of energy metabolism genes and the origin of flight in bats. Proc Natl Acad Sci USA. 107:8666–8671.
   PubMed Web of Science ®Google Scholar
• Shen YY, Shi P, Sun YB, Zhang YP. 2009. Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 19:1760–1765.
   PubMed Web of Science ®Google Scholar
• Shin DH, Lee JW, Park JE, Choi IY, Oh HS, Kim HJ, Kim H. 2015. Multiple genes related to muscle identified through a joint analysis of a two-stage genome-wide association study for racing performance of 1,156 thoroughbreds. Asian-Australas J Anim Sci. 28:771–781.
   PubMed Web of Science ®Google Scholar
• Shoffner JM, Brown MD, Torroni A, Lott MT, Cabell MF, Mirra SS, Beal MF, Yang CC, Gearing M, Salvo R, et al. 1993. Mitochondrial DNA variants observed in Alzheimer disease and Parkinson disease patients. Genomics. 17:171–184.
   PubMed Web of Science ®Google Scholar
• Tanaka N, Goto Y, Akanuma J, Kato M, Kinoshita T, Yamashita F, Tanaka M, Asada T. 2010. Mitochondrial DNA variants in a Japanese population of patients with Alzheimer's disease. Mitochondrion. 10:32–37.
   PubMed Web of Science ®Google Scholar
• Tang J, Qi Y, Bao XH, Wu XR. 1997. Mutational analysis of mitochondrial DNA of children with Rett syndrome. Pediatr Neurol. 17:327–330.
   PubMed Web of Science ®Google Scholar
• Tang S, Batra A, Zhang Y, Ebenroth ES, Huang T. 2010. Left ventricular noncompaction is associated with mutations in the mitochondrial genome. Mitochondrion. 10:350–357.
   PubMed Web of Science ®Google Scholar
• Tozaki T, Miyake T, Kakoi H, Gawahara H, Sugita S, Hasegawa T, Ishida N, Hirota K, Nakano Y. 2010. A genome-wide association study for racing performances in Thoroughbreds clarifies a candidate region near the MSTN gene. Anim Genet. 41 (Suppl 2):28–35.
   PubMedGoogle Scholar
• Turner DH, Mathews DH. 2010. NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Res. 38:D280–D282.
   PubMed Web of Science ®Google Scholar
• Wallace DC. 2005. A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet. 39:359–407.
   PubMed Web of Science ®Google Scholar
• Wilson AJ, Rambaut A. 2008. Breeding racehorses: what price good genes? Biol Lett. 4:173–175.
   PubMed Web of Science ®Google Scholar
• Zaki EA, Freilinger T, Klopstock T, Baldwin EE, Heisner KR, Adams K, Dichgans M, Wagler S, Boles RG. 2009. Two common mitochondrial DNA polymorphisms are highly associated with migraine headache and cyclic vomiting syndrome. Cephalalgia. 29:719–728.
   PubMedGoogle Scholar