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The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en UNIVERSITAT AUTÒNOMA DE BARCELONA Departament de Ciència Animal i dels Aliments Facultat de Veterinària CENTRE DE RECERCA EN AGRIGENÒMICA Grup de Recerca de Genòmica Animal GENOMIC ANALYSIS OF FATTY ACID COMPOSITION AND GUT MICROBIOTA IN PIGS Daniel Crespo Piazuelo Doctoral thesis to obtain the PhD degree in Animal Production of the Universitat Autònoma de Barcelona, October 2018 Supervisors Dr. Josep Maria Folch Albareda Dr. Maria Ballester Devis El Dr. Josep Maria Folch Albareda, professor titular del Departament de Ciència Animal i dels Aliments de la Universitat Autònoma de Barcelona (UAB), i la Dra. Maria Ballester Devis, investigadora del Departament de Genètica i Millora Animal del Institut de Recerca i Tecnologia Agroalimentàries (IRTA), fan constar que el treball de recerca i la redacció de la memòria de la tesi doctoral titulada ‘Genomic analysis of fatty acid composition and gut microbiota in pigs’ han estat realitzats sota la seva direcció per DANIEL CRESPO PIAZUELO i certifiquen que aquest treball s’ha dut a terme al Departament de Ciència Animal i dels Aliments de la Facultat de Veterinària de la Universitat Autònoma de Barcelona i a la unitat de Genòmica Animal del Centre de Recerca en Agrigenòmica, considerant que la memòria resultant es apta per optar al grau de Doctor en Producció Animal per la Universitat Autònoma de Barcelona, i perquè quedi constància, signen aquest document a Bellaterra, A 29 de octubre de 2018. Dr. Josep Maria Folch Albareda Dr. Maria Ballester Devis Daniel Crespo Piazuelo Original watercolour painting of the cover by Miguel Ángel Crespo Barberán, 2018. This work was funded by the Ministerio de Economía y Competitividad (MINECO) and the Fondo Europeo de Desarrollo Regional (FEDER) projects AGL2014-56369-C2-2-R and AGL2017-82641-R. We acknowledge the support of the Spanish Ministry of Economy and Competitiveness for the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics and the CERCA Programme / Generalitat de Catalunya. Daniel Crespo Piazuelo was funded by a “Formació i Contractació de Personal Investigador Novell (FI-DGR)” fellowship provided by the “Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR)” from the Generalitat de Catalunya (2015-2018). The predoctoral stay (Short Term Scientific Mission) at the Génétique Animale et Biologie Intégrative (GABI) laboratory of the Institut National de la Recherche Agronomique (INRA) was funded by a COST Action grant of the PiGutNet (www.pigutnet.eu). “For in a minute there are many days” Romeo and Juliet (3.5.25) - William Shakespeare - Content Summary/Resumen .......................................................................................... 11 List of tables ..................................................................................................... 15 List of figures .................................................................................................... 19 List of publications ............................................................................................ 25 Related publications by the author ................................................................... 26 Abbreviations .................................................................................................... 27 1. General introduction .................................................................................. 31 1.1 Evolution of the pork production .......................................................... 33 1.2 Pork meat quality ................................................................................ 35 1.2.1 Fatty acid composition in adipose tissue and muscle ................... 36 1.3 Fatty acid metabolism ......................................................................... 38 1.3.1 De novo fatty acid synthesis ......................................................... 38 1.3.2 Mitochondrial fatty acid β-oxidation .............................................. 40 1.4 Development of NGS and TGS technologies ...................................... 42 1.5 Applications of ‘omics’-based tools ..................................................... 43 1.6 Genomics in animal breeding .............................................................. 47 1.6.1 Genetic variants used as molecular markers ................................ 47 1.6.1.1 Single nucleotide polymorphisms (SNPs) .............................. 49 1.6.1.2 Small insertions and deletions (indels) ................................... 50 1.6.2 QTL mapping and GWAS ............................................................. 51 1.7 Microbiomics ....................................................................................... 54 1.7.1 Microbiota profiling through the 16S rRNA gene sequencing ....... 54 1.7.2 Anatomy and physiology of the pig gut ......................................... 57 1.8 European swine breeds ....................................................................... 58 1.9 The IBMAP Consortium ....................................................................... 60 2. Objectives ................................................................................................. 65 3. Articles and studies ................................................................................... 69 Paper I. Genome-Wide Association Study for backfat and intramuscular fatty acid composition in three different pig crosses based on the Iberian breed .. 71 Paper II. Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs ........................................................................ 113 Paper III. Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions .......................... 145 Paper IV. Association between the pig genome and its gut microbiota composition ................................................................................................. 181 4. General discussion .................................................................................. 215 4.1 Genetic variants and candidate genes associated with fatty acid metabolism in muscle and adipose tissue ................................................... 218 4.2 Characterization of the pig gut microbiota along the digestive tract and associations between host genome and microbiota composition ................ 227 4.3 Future perspectives and challenges .................................................. 235 5. Conclusions ............................................................................................. 241 6. References .............................................................................................. 247 7. Annexes .................................................................................................. 279 7.1 Supplementary material Paper I: ‘Genome-Wide Association Study for backfat and intramuscular fatty acid composition in three different pig crosses based on the Iberian breed’ ........................................................................ 281 7.2 Supplementary material Paper II: ‘Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs’ ................. 296 7.3 Supplementary material Paper III: ‘Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions’ .............................................................................................. 300 7.4 Supplementary material Paper IV: ‘Association between the pig genome and its gut microbiota composition’ ............................................................. 331 Acknowledgements ........................................................................................ 341 Summary Pork is one of the most consumed meats worldwide and it is subjected to consumer’s preferences. Meat quality is affected by fatty acid (FA) composition in muscle and adipose tissues. Gut microbiota composition can also affect meat quality through the production of metabolites such as short-chain fatty acids. However, the relationship between pig genome and gut microbiota is not fully understood. In the current thesis, several studies have been performed to improve our knowledge about the genetic determinism of FA composition. In addition, the composition of the microbiota along the pig gut and its interaction with the host genome has been also analysed. Genome-wide association studies (GWAS) were performed among 38,424 single nucleotide polymorphisms (SNPs) and 60 phenotypic traits related to FA composition in backfat and muscle. This analysis was performed in 441 pigs from three different backcrosses: BC1_LD (25% Iberian and 75% Landrace), BC1_PI (25% Iberian and 75% Pietrain), and BC1_DU (25% Iberian and 75% Duroc) belonging to the IBMAP experimental