2018 91 Elena Flavia Mouresan Evaluation of the efficiency of the procedures of genomic selection in the autochthonous spanish beef cattle populations Departamento Producción Animal y Ciencia de los Alimentos Director/es Varona Aguado, Luis Reconocimiento – NoComercial – © Universidad de Zaragoza SinObraDerivada (by-nc-nd): No se Servicio de Publicaciones permite un uso comercial de la obra original ni la generación de obras derivadas. ISSN 2254-7606 Tesis Doctoral EVALUATION OF THE EFFICIENCY OF THE PROCEDURES OF GENOMIC SELECTION IN THE AUTOCHTHONOUS SPANISH BEEF CATTLE POPULATIONS Autor Elena Flavia Mouresan Director/es Varona Aguado, Luis UNIVERSIDAD DE ZARAGOZA Producción Animal y Ciencia de los Alimentos 2016 Repositorio de la Universidad de Zaragoza – Zaguan http://zaguan.unizar.es FACULTAD DE VETERINARIA Evaluation of the efficiency of the procedures of Genomic Selection in the Autochthonous Spanish Beef Cattle populations Memoria presentada por: Elena – Flavia Mouresan Para optar al Grado de Doctor Mayo 2016 FACULTAD DE VETERINARIA D. LUIS VARONA AGUADO, Catedrático del Departamento de Anatomía, Embriología y Genética Animal de la Facultad de Veterinaria de la Universidad de Zaragoza, CERTIFICA: Que la tesis titulada: “Evaluation of the efficiency of the procedures of Genomic Selection in the Autochthonous Spanish Beef Cattle populations”, con proyecto de tesis aprobado el 5 de MAYO de 2014 por el programa de doctorado en PRODUCCIÓN ANIMAL, y de la que es autor ELENA - FLAVIA MOURESAN, ha sido realizada bajo mi dirección y cumple los requisitos necesarios para optar al grado de Doctor por la Universidad de Zaragoza. Zaragoza, 09 de Mayo de 2016 Fdo: Prof. Dr. Luis Varona Aguado INDEX Index Index. ................................................................................................................ III Figure Index ..................................................................................................... IX Table Index ..................................................................................................... XIX Acknowledgements ..................................................................................... XXV Abstract ....................................................................................................... XXIX Resumen .................................................................................................... XXXV Introduction Spanish beef cattle breeds ................................................................................. 3 Genomic Selection ............................................................................................. 8 Molecular Markers and Genomic Selection ............................................. 8 Genomic Selection methods .................................................................. 10 Gaussian Regularization ............................................................. 11 Non-Gaussian Regularization...................................................... 13 Machine Learning and non-parametric methods ......................... 15 Comparison of Methods .............................................................. 17 Genomic Selection in livestock populations ........................................... 17 Genomic Selection in beef cattle ...................................................................... 21 Across breed Genomic Selection ..................................................................... 24 Objectives ....................................................................................................... 31 Materials .......................................................................................................... 35 III Index Chapter 1: Performance of genomic selection under a single-step approach in Autochthonous Spanish beef cattle populations Introduction ....................................................................................................... 41 Material and Methods ....................................................................................... 42 Simulation .............................................................................................. 42 Single step ............................................................................................. 43 Validation ............................................................................................... 44 Simulation Scenarios ............................................................................ .44 Results and Discussion .................................................................................... 45 Standard BLUP evaluation ..................................................................... 47 Base scenario ........................................................................................ 48 Sensitivity analysis ................................................................................ .52 Conclusions ..................................................................................................... .58 Chapter 2: Evaluation of the potential use of a meta-population for Genomic Selection in Spanish Beef Cattle Populations Introduction ....................................................................................................... 61 Materials ........................................................................................................... 62 Methods............................................................................................................ 63 Simulation .............................................................................................. 63 Genomic evaluation ............................................................................... 65 Validation ............................................................................................... 67 Results and Discussion .................................................................................... 67 Single breed evaluation ......................................................................... 67 Evaluation in admixed ×2 ....................................................................... 71 IV Index Evaluation in admixed ×7 ....................................................................... 74 Admixed vs reduced pure-bred .............................................................. 75 Genetic architecture of traits .................................................................. 77 Conclusions ...................................................................................................... 80 Chapter 3: Genetic architecture of the persistency of linkage disequilibrium across seven Spanish beef cattle populations Introduction ....................................................................................................... 83 Materials ........................................................................................................... 84 Methods............................................................................................................ 85 Persistency of linkage disequilibrium ..................................................... 85 Identification of candidate genes and metabolic pathways .................... 86 Integration into across breed genomic evaluation .................................. 87 Results and Discussion .................................................................................... 88 Architecture of linkage disequilibrium..................................................... 88 Identification of candidate genes and metabolic pathways .................... 94 Integration into across breed genomic evaluation .................................. 98 Conclusions .................................................................................................... 100 Chapter 4: On the haplotype diversity along the genome in Spanish Beef Cattle populations. Introduction ..................................................................................................... 103 Materials ......................................................................................................... 104 Methods.......................................................................................................... 104 V Index Results and Discussion .................................................................................. 104 Conclusions .................................................................................................... 115 General Discussion ...................................................................................... 117 Conclusions .................................................................................................. 131 Conclusiones ................................................................................................ 135 References .................................................................................................... 139 Annexes Annexe 1 .............................................................................................. 163 Annexe 2 .............................................................................................. 165 Annexe 3 .............................................................................................. 168 Annexe 4 .............................................................................................. 188 VI FIGURE INDEX Figure Index Materials Figure 1. Geographic distribution map of the Spanish breeds included in this study ........................................................................................................................