Publication: Aplicación de métodos de secuenciación paralela masiva y genómica al estudio de variantes génicas que regulan: crecimiento, conformación y calidad de carne en cerdo
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2018-09-17
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Universidad Complutense de Madrid
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Abstract
Las estrategias de análisis llevadas a cabo hasta ahora para la identificación de labase genética de caracteres complejos no han resultado del todo eficientes, en partedebido a la sobreestimación de los efectos y la aparición de falsos negativos y de falta devalidación en fondos genéticos distintos. Es por ello, que la aparición de nuevasmetodologías de análisis masivo del genoma, que se encuentran en pleno desarrollo,pueden aumentar la potencia de este tipo de análisis, proveyendo nueva información aprecios relativamente asequibles que permiten superar estas limitaciones.El presente trabajo de tesis doctoral se basa en la gran cantidad recursos, datos yresultados de detección de QTL, genes candidato y expresión génica diferencial llevadosa cabo a partir de la población experimental Ibérico x Landrace (IBMAP) y posterioresgeneraciones. El objetivo del presente trabajo ha sido explorar diferentes aproximacionesbasadas en el estudio masivo del genoma porcino para profundizar en el conocimiento dela base genética de caracteres productivos, específicamente los relacionados concrecimiento, deposición grasa y rendimiento de piezas nobles en tres retrocrucesexperimentales F1 (Ibérico x Landrace) x Landrace, F1 (Ibérico x Duroc) x Duroc y F1(Ibérico x Pietrain) x Pietrain. Para abordar este objetivo se han planteado tresaproximaciones que han dado lugar a tres estudios...
The analysis strategies carried out for the identification of the genetic basis ofcomplex traits have not been completely efficient so far, in part due to the overestimationof the effects and the occurrence of false negatives and lack of validation in differentgenetic backgrounds. For this reason, the emergence of new methodologies of massiveanalysis of the genome, which are in full development, can increase the power of this typeof analysis, providing new information at relatively affordable prices that overcome theselimitations.The current thesis is based on the great amount of resources, data and results ofdetection of QTL, candidate genes and differential gene expression studies carried out inthe experimental population Iberian x Landrace (IBMAP) and later generations. Theobjective of the present thesis was to explore different approaches based on massiveanalysis of the porcine genome to deepen the knowledge of the genetic basis of productivetraits, specifically those related to growth, fat deposition and premier cut yields in threeexperimental backcross F1 (Iberian x Landrace) x Landrace, F1 (Iberian x Duroc) x Durocand F1 (Iberian x Pietrain) x Pietrain. Three approaches have been proposed to addressthis objective and have led to three studies.The objective of the first study was the identification of SNPs from RNAsequencing, RNA-Seq, data from liver and hypothalamus of Iberian x Landracebackcrossed pigs. The experimental design based on the comparison of extreme groupsfor growth and fat deposition, allowed us to identify more than 90,000 SNPs, 4,396 SNPsidentified in the hypothalamus and 1,862 in the liver that would be potentially related tothe trait variability, providing a relevant database of candidate mutations. In addition,RNA editing phenomena were identified, showing that this is not a negligiblephenomenon and may be responsible of trait variability. In addition, it could be affectingthe false negative rate when validating polymorphisms...
The analysis strategies carried out for the identification of the genetic basis ofcomplex traits have not been completely efficient so far, in part due to the overestimationof the effects and the occurrence of false negatives and lack of validation in differentgenetic backgrounds. For this reason, the emergence of new methodologies of massiveanalysis of the genome, which are in full development, can increase the power of this typeof analysis, providing new information at relatively affordable prices that overcome theselimitations.The current thesis is based on the great amount of resources, data and results ofdetection of QTL, candidate genes and differential gene expression studies carried out inthe experimental population Iberian x Landrace (IBMAP) and later generations. Theobjective of the present thesis was to explore different approaches based on massiveanalysis of the porcine genome to deepen the knowledge of the genetic basis of productivetraits, specifically those related to growth, fat deposition and premier cut yields in threeexperimental backcross F1 (Iberian x Landrace) x Landrace, F1 (Iberian x Duroc) x Durocand F1 (Iberian x Pietrain) x Pietrain. Three approaches have been proposed to addressthis objective and have led to three studies.The objective of the first study was the identification of SNPs from RNAsequencing, RNA-Seq, data from liver and hypothalamus of Iberian x Landracebackcrossed pigs. The experimental design based on the comparison of extreme groupsfor growth and fat deposition, allowed us to identify more than 90,000 SNPs, 4,396 SNPsidentified in the hypothalamus and 1,862 in the liver that would be potentially related tothe trait variability, providing a relevant database of candidate mutations. In addition,RNA editing phenomena were identified, showing that this is not a negligiblephenomenon and may be responsible of trait variability. In addition, it could be affectingthe false negative rate when validating polymorphisms...
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Tesis inédita de la Universidad Complutense de Madrid, Facultad de Ciencias Biológicas, leída el 22-06-2017