MOLECULAR GENETICS OF CATTLE MUSCULARITY By Irida Novianti A thesis submitted to the University of Adelaide in fulfilment of the requirement of the degree of Master of Agricultural Science The University of Adelaide School of Animal and Veterinary Science December 2010 DECLARATION I declare that this thesis is a record of original work and contains no material that has been accepted for the award of any other degree or diploma in any university or other tertiary institution to Irida Novianti. To the best of my knowledge and belief, this thesis contains no material previously published or written by any other person, except where due reference is made in the text. I give consent to this copy of my thesis, when deposited in the University Library, being made available for loan and photocopying, subject to the provisions of the Copyright Act 1968. I also give permission for the digital version of my thesis to be made available on the web, via the University’s digital research repository, the Library catalogue, the Australasian Digital Theses Program (ADTP) and also through web search engines, unless permission has been granted by the University to restrict access for a period of time. Irida Novianti December, 2010 ii TABLE OF CONTENTS Declaration ........................................................................................................... ii Index of Figures ................................................................................................... vi Index of Tables ..................................................................................................... viii Index of Appendix ............................................................................................... x Dedication ............................................................................................................. xi Acknowledgements .............................................................................................. xii Abstract ................................................................................................................ xiii Chapter 1: Literature Review ............................................................................ 1 1.1 Introduction............................................................................................... 2 1.2 Literature review ...................................................................................... 4 1.2.1 Muscle development in cattle ........................................................... 4 1.2.2 Genetic parameter for growth traits .................................................. 5 1.2.3 Genetic parameter for body dimension related to muscularity ......... 7 1.2.3.1 Heritability for body dimension related to muscularity ....... 8 1.2.3.2 Genetic correlation between body dimension related to muscularity, growth and carcass traits ................ 10 1.2.4 Genetic parameters of carcass traits ................................................. 12 1.2.5 Molecular genetics of muscularity traits .......................................... 13 1.2.5.1 QTL for growth and carcass traits ........................................ 13 1.2.5.2 Genes involved in muscle development and carcass traits .. 16 1.2.5.2a Insulin-like growth factor 1 (IGF1) ............................... 17 1.2.5.2b Myostatin ....................................................................... 17 1.2.6 Summary ........................................................................................... 23 1.3 Research objectives ................................................................................... 24 iii Chapter 2: Materials and Methods .................................................................... 25 2.1 J.S Davies cattle mapping project .................................................... 26 2.2 Mapping quantitative trait loci (QTL) ............................................ 31 2.3 Identification of candidate genes ...................................................... 33 2.4 Optimization of PCR condition ........................................................ 34 2.5 DNA purification from PCR reaction .............................................. 35 2.6 Sequencing reaction of PCR product ............................................... 35 2.7 Genotyping using high resolution melts .......................................... 36 2.8 Statistical analysis .............................................................................. 38 Chapter 3: QTL Mapping and Candidate Gene Selection .............................. 43 3.1 Introduction ....................................................................................... 44 3.2 Results ................................................................................................. 44 3.2.1 QTL for muscularity related traits ............................................. 44 3.2.2 Effects of Myostatin F94L genotype on QTL ........................... 48 3.2.3 Candidate gene selection ........................................................... 52 3.3 Discussion ........................................................................................... 58 3.4 Summary ............................................................................................ 64 Chapter 4: SNP Association Studies .................................................................. 65 4.1 Introduction ....................................................................................... 66 4.2 Results and discussion ....................................................................... 67 4.2.1 Candidate gene polymorphisms identification .......................... 67 4.2.2 SNP association analysis ........................................................... 69 4.2.2.1 Effects of FSTL SNP5 ................................................... 72 4.2.2.2 Effects of FSTL SNP8 ................................................... 74 4.2.2.3 Effect of IGF1 SNP1 ..................................................... 76 iv 4.2.2.4 Effects of FST SNP7 ..................................................... 78 4.2.3 SNP interactions with the myostatin F94L variant .................... 83 4.2.3.1 Interactions between myostatin F94L and SNIP1 SNP3, TGFBR3 SNP6 and IGF1 SNP1 ............. 85 4.2.3.2 Interaction between myostatin F94L and IGF1 SNP2 and FST SNP7 ........................................... 88 4.2.4 Interaction between candidate gene SNP genotype ................... 92 4.2.4.1 ACVR1 haplotype effect on meat to bone ratio ............. 95 4.2.4.2 FSTL5 haplotype effect on hot standard carcass weight ............................................................... 96 4.2.5 QTL mapping ............................................................................ 97 4.3 Summary ............................................................................................ 99 Chapter 5: General Discussion ........................................................................... 101 5.1 Introduction ....................................................................................... 102 5.2 Interactions between SNIP1 and myostatin ..................................... 107 5.3 Interactions between TGFBR3 (betaglycan) and myostatin ........... 109 5.4 IGF1 role in muscularity and its interactions with myostatin ....... 110 5.5 Follistatin role in muscularity and its interaction with myostatin .................................................................................... 112 5.6 Future experiments ............................................................................ 114 5.7 Conclusions ......................................................................................... 116 References ............................................................................................................ 158 v INDEX OF FIGURES Figure 1 : Structure of myostatin protein .......................................................... 18 Figure 2.1 : JS Davies cattle mapping herd ......................................................... 27 Figure 2.2 : Stifle width and hip width measurements ........................................ 28 Figure 3.1 : QTL for meat weight (with HSCW as covariate) on BTA 2 ............ 52 Figure 3.2 : QTL for meat percentage on BTA 2................................................. 53 Figure 3.3 : QTL for muscularity on BTA 2 ........................................................ 53 Figure 3.4 : QTL for meat weight (with HSCW as covariate) on BTA 17 .......... 54 Figure 3.5 : QTL for meat percentage on BTA 17............................................... 54 Figure 3.6 : QTL for meat weight (with HSCW as covariate) on BTA 3 ............ 55 Figure 3.7 : QTL for meat percentage on BTA 3................................................. 55 Figure 4.1 : Effect of FSTL5 SNP5 genotype on meat weight (with bone weight as covariate) ..................................................... 73 Figure 4.2 : Effect of FSTL5 SNP5 genotype on meat-to-bone ratio .................. 74 Figure 4.3 : Effect of FSTL5 SNP8 genotype on meat percentage ...................... 75 Figure 4.4 : Effect of FSTL5 SNP8 genotype on eye muscle area....................... 76 Figure 4.5 : Effect of IGF1 SNP1 genotype on HSCW ....................................... 77 Figure 4.6 : Effect of FST SNP7 genotype on meat weight (with HSCW as covariate) ................................................................. 78 Figure 4.7 : Effect of FST SNP7 genotype on meat percentage .......................... 79 Figure 4.8 : Effect of FST SNP7 genotype