Evaluation of the Efficiency of the Procedures of Genomic Selection in the Autochthonous Spanish Beef Cattle Populations

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 ........................................................................................................................

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