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Analysis of the Genetic Basis of Porcine Meat Quality and Coat Color by Using Genomic and Transcriptomic Tools

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Analysis of the Genetic Basis of Porcine Meat Quality and Coat Color by Using Genomic and Transcriptomic Tools ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. 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 Departament de Genètica Animal Analysis of the genetic basis of porcine meat quality and coat color by using genomic and transcriptomic tools Tainã Figueiredo Cardoso Doctoral thesis to obtain the Ph.D degree in Animal Production of the Universitat Autònoma de Barcelona, April 2018 Supervisors Dr. Marcel Amills Eras Dra. Angela Canovas Tienda El Dr Marcel Amills Eras, professor agregat del Departament de Ciència Animal i dels Aliments de la Universitat Autònoma de Barcelona, i la Dra. Angela Canovas Tienda, professora assistent de la Universitat de Guelph, fan constar que el treball de recerca i la redacció de la memòria de la tesi doctoral titulada “Analysis of the genetic basis of porcine meat and color phenotypes by using genomic and transcriptomic tools” han estat realitzats sota la seva direcció per Tainã Figueiredo Cardoso I certifiquen que aquest treball s’ha dut a terme al Departament de Ciència Animal i del Aliments de la Facultat de Veterinària de la Universitat Autònoma de Barcelona i al Departament de Genètica 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 perqué quedi constància, signen aquest document al març del 2018. Dr. Marcel Amills Eras Dra. Angela Canovas Tienda Tainã Figueiredo Cardoso Cover design by Renata Benites, 2018 This work was funded by the Spanish Ministry of Economy and Competitiveness (grant numbers: AGL2010-22208-C02-02 and AGL2013-48742-C2-1-R). We acknowledge the support of the Spanish Ministry of Economy and Competitiveness for the Centre of Excellence Severo Ochoa 2016–2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics. Tainã Figueiredo Cardoso was funded by the program “Science without Borders” fellowship provided by the “Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)” from Brazilian Federal Government (2014-2018). Aos meus pais, Jorge Tomás e Denize, e a minha irmã Thaís. Porque não importa a distância que nos separa, se há um céu que nos une. Content Summary .......................................................................................................................... 11 Resumen ........................................................................................................................... 13 Resumo ............................................................................................................................. 15 List of Tables .................................................................................................................... 17 List of Figures .................................................................................................................. 19 List of annexes .................................................................................................................. 21 List of publications .......................................................................................................... 23 Other publications from the author ............................................................................... 25 Chaper 1: General introduction .................................................................................... 27 1.1 A brief history of pig breeds .............................................................................. 29 1.2 The search for causal mutations in pigs associated with economical traits ...... 30 1.3 The generation of biological information is essential to identify potencial causal mutations ......................................................................................................... 35 1.4 The landscape of mammalian transcriptomes .................................................... 39 1.4 Methods to characterize the transcriptome ........................................................ 44 1.5 Transcriptomic studies in pigs ........................................................................... 55 Chapter 2: Objectives.................................................................................................... 63 Chapter 3: Papers and Studies ..................................................................................... 67 Paper I: RNA-Seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles ............................................ 69 Paper II: Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. ........................................................... 93 Paper III: Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle. ........................................................................................................ 119 Paper IV: The ingestion of food promotes changes in the expression of genes regulating circadian rhythms in four porcine tissues containing peripheral clocks ........................................................................................................................ 145 Paper IV: The red and blond pigmentation of Mangalitza pigs is strongly associated with the variability of the Solute Carrier Family 45 Member 2 (SLC45A2) gene ....................................................................................................... 167 Chaper 4: General Discussion ..................................................................................... 193 4.1 Differential expression of metabolic genes in the skeletal muscle of Duroc pigs with different fatness profiles ................................................................ 195 4.2 Limited contribution of the non-coding RNA transcriptome to differential expression between HIGH and LOW pigs. .............................................................. 199 4.3 Differential expression of mRNA isoforms in the skeletal muscle of Duroc pigs with different fatness profiles ................................................................ 201 4.4 The ingestion of food influences the expression of multiple transcription factors in the skeletal muscle .................................................................................... 203 4.5 Food intake promotes changes in the expression of genes related to oxidative stress and angiogenesis ............................................................................. 207 4.6 Existence of a close relationship between nutritional status and the expression of genes regulating circadian rhythms. .................................................. 208 4.7 The polymorphism of the SLC45A2 gene is associated with the red and blond pigmentation of Mangalitza pigs.................................................................... 211 Chapter 5: General conclusions .................................................................................. 215 Chapter 6: References .................................................................................................. 221 Chapter 7: Annexes ....................................................................................................... 239 Chapter 8: Acknowledgements .................................................................................... 279 Summary The main objectives of this Thesis were to investigate the genetic basis of fatness in pigs and to identify the genetic factors involved in the establishment of blond vs red pigmentation patterns in Mangalitza pigs by using genomic and transcriptomic tools. In the first study of the Thesis (Chapter 3), we compare the skeletal muscle expression patterns of two groups of Duroc pigs with different growth and fatness profiles (HIGH: high backfat thickness, intramuscular fat, saturated and unsaturated fatty acid content and serum lipids vs LOW: opposite phenotypes). By using a RNA-Seq technology, we identified 96 genes differentially expressed. Several of these genes are related to lipid metabolism (e.g. SLC27A4, SFRP5 and CES1) and the transcription factor PPARG appears to be a key regulator of porcine fatness. We have also observed that very few non-coding RNAs are differentially expressed in these two groups of pigs, suggesting that the non-coding transcriptome has a limited effect on the establishment of the HIGH and LOW phenotypes. In the second study of the Thesis, we demonstrate the differential expression of specific mRNA isoforms of four genes with a known role in obesity (ITGA5, LITAF, TIMP1 and ANXA2) in HIGH vs LOW pigs. The differential expression of these isoforms may have effects on transcript structure as well as on the protein sequence. In the third study, we aimed to investigate the differential expression of mRNA encoding genes in response to food ingestion. This goal has been achieved by comparing
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