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Multiple Approaches of Animal Breeding and Genetics to Improve Livestock Production, Conservation and Food Security

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Multiple Approaches of Animal Breeding and Genetics to Improve Livestock Production, Conservation and Food Security Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2021 A well-rounded toolbox: Multiple approaches of animal breeding and genetics to improve livestock production, conservation and food security. Josue Chinchilla Vargas Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Chinchilla Vargas, Josue, "A well-rounded toolbox: Multiple approaches of animal breeding and genetics to improve livestock production, conservation and food security." (2021). Graduate Theses and Dissertations. 18476. https://lib.dr.iastate.edu/etd/18476 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A well-rounded toolbox: Multiple approaches of animal breeding and genetics to improve livestock production, conservation, and food security. by Josué Chinchilla-Vargas A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Animal Science Program of Study Committee: Max F. Rothschild, Co-major Professor Kenneth J. Stalder, Co-major Professor Laura L. Greiner James E. Koltes Alejandro Ramirez The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2021 Copyright © Josué Chinchilla-Vargas, 2021. All rights reserved. ii DEDICATION This work and all the effort behind it is dedicated to my wife, my family, friends and mentors that supported me and pushed me to achieve my goals. It is also dedicated to those that left us during this time. In memoriam: Digna Vindas Vindas Josefa Adelia Claudina “Cuya” Quesada Calderon Lilliam “Lili” Vargas Vindas iii TABLE OF CONTENTS Page LIST OF FIGURES ....................................................................................................................... vi LIST OF TABLES ....................................................................................................................... viii ACKNOWLEDGMENTS ...............................................................................................................x ABSTRACT ................................................................................................................................... xi CHAPTER 1. GENERAL INTRODUCTION ................................................................................1 Dissertation organization ........................................................................................................... 3 Literature cited ........................................................................................................................... 3 CHAPTER 2. REVIEW OF LITERATURE ...................................................................................5 Livestock and food security ....................................................................................................... 5 Indicator traits in animal breeding ............................................................................................. 7 A historical overview of animal breeding and the role of genomics in genetic selection. ........ 8 SNP genotyping and genome sequencing ............................................................................... 13 Genome-wide association studies (GWAS) ............................................................................ 17 Signatures of selection ............................................................................................................. 21 The era of precision livestock farming and big data ............................................................... 26 Literature cited ......................................................................................................................... 28 CHAPTER 3. MARKER DISCOVERY AND ASSOCIATIONS WITH BETA-CAROTENE CONTENT IN INDIAN DAIRY CATTLE AND BUFFALO BREEDS .....................................41 Abstract .................................................................................................................................... 41 Introduction ............................................................................................................................. 43 Materials and methods ............................................................................................................. 44 Animal care ........................................................................................................................ 44 High throughput SNP discovery and building of the Sequenom custom panel ................. 44 Beta-carotene measurement and SNP genotyping ............................................................. 46 Statistical association analyses ........................................................................................... 46 Results and discussion ............................................................................................................. 49 SNP discovery and panel performance .............................................................................. 49 Genotyping of the beta-carotene samples and association analyses .................................. 51 Conclusions ............................................................................................................................. 57 Acknowledgements ................................................................................................................. 57 Literature cited ......................................................................................................................... 58 Tables and figures .................................................................................................................... 62 CHAPTER 4. GENETIC BASIS OF BLOOD-BASED TRAITS AND THEIR RELATIONSHIP WITH PERFORMANCE AND ENVIRONMENT IN BEEF CATTLE AT WEANING ............83 Abstract .................................................................................................................................... 83 Introduction ............................................................................................................................. 84 iv Materials and methods ............................................................................................................. 87 Data description .................................................................................................................. 87 Imputation .......................................................................................................................... 88 Population structure ............................................................................................................ 88 Statistical analyses .............................................................................................................. 88 Gene ontology and identification of candidate genes ........................................................ 90 Results ..................................................................................................................................... 91 Population structure ............................................................................................................ 91 Phenotypic correlations ...................................................................................................... 91 Genetic correlations ............................................................................................................ 92 Estimation of narrow sense heritability (h2) ....................................................................... 93 Genome-wide association study (GWAS) ......................................................................... 93 Gene ontology enrichment analysis ................................................................................... 95 Discussion ................................................................................................................................ 96 Most blood-based traits and growth traits are weakly correlated ....................................... 96 Blood-based traits tend to have moderate to high heritability ............................................ 97 Maternal genetic effects do not impact genetic and genomic correlations or heritability .......................................................................................................................... 98 Genome wide association study results identify few genomic regions with large effects ................................................................................................................................. 99 Several candidate genes were identified for windows associated with blood-based traits and overlapping with growth traits ............................................................................ 99 Conclusions ........................................................................................................................... 101 Availability of data and materials .........................................................................................
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