A global analysis of CNVs in swine using whole genome sequence data and association analysis with fatty acid composition and growth traits
Visualitza/Obre
Autor/a
Revilla, Manuel
Puig-Oliveras, Anna
Castelló, Anna
Paludo, Ediane
Fernández, Ana I.
Ballester, Maria
Folch, Josep M.
Data de publicació
2017-05-04ISSN
1932-6203
Resum
Copy number variations (CNVs) are important genetic variants complementary to SNPs, and can be considered as biomarkers for some economically important traits in domestic animals. In the present study, a genomic analysis of porcine CNVs based on next-generation sequencing data was carried out to identify CNVs segregating in an Iberian x Landrace backcross population and study their association with fatty acid composition and growthrelated traits. A total of 1,279 CNVs, including duplications and deletions, were detected, ranging from 106 to 235 CNVs across samples, with an average of 183 CNVs per sample. Moreover, we detected 540 CNV regions (CNVRs) containing 245 genes. Functional annotation suggested that these genes possess a great variety of molecular functions and may play a role in production traits in commercial breeds. Some of the identified CNVRs contained relevant functional genes (e.g., CLCA4, CYP4X1, GPAT2, MOGAT2, PLA2G2A and PRKG1, among others). The variation in copy number of four of them (CLCA4, GPAT2, MOGAT2 and PRKG1) was validated in 150 BC1_LD (25% Iberian and 75% Landrace) animals by qPCR. Additionally, their contribution regarding backfat and intramuscular fatty acid composition and growth–related traits was analyzed. Statistically significant associations were obtained for CNVR112 (GPAT2) for the C18:2(n-6)/C18:3(n-3) ratio in backfat and carcass length, among others. Notably, GPATs are enzymes that catalyze the first step in the
biosynthesis of both triglycerides and glycerophospholipids, suggesting that this CNVR may contribute to genetic variation in fatty acid composition and growth traits. These findings provide useful genomic information to facilitate the further identification of trait-related CNVRs affecting economically important traits in pigs.
Tipus de document
Article
Versió del document
Versió publicada
Llengua
English
Matèries (CDU)
619 - Veterinària
637 - Productes dels animals domèstics, de la caça i de la pesca
Pàgines
17
Publicat per
Public Library of Science
Publicat a
PLoS ONE
Citació
Revilla, Manuel, Anna Puig-Oliveras, Anna Castelló, Daniel Crespo-Piazuelo, Ediane Paludo, Ana I. Fernández, Maria Ballester, and Josep M. Folch. 2017. "A Global Analysis Of Cnvs In Swine Using Whole Genome Sequence Data And Association Analysis With Fatty Acid Composition And Growth Traits". PLOS ONE 12 (5): e0177014. doi:10.1371/journal.pone.0177014.
Número de l'acord de la subvenció
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2011-29821-C02/ES/APLICACION DE METODOS DE SECUENCIACION PARALELA MASIVA Y GENOMICA AL ESTUDIO DE VARIANTES GENICAS QUE REGULAN:CRECIMIENTO,CONFORMACION Y CALIDAD DE CARNE EN CERDO.SUBPROYECTO2/
MINECO/Programa Estatal de I+D+I orientada a los retos de la sociedad/AGL2014-56369-C2/ES/VALIDACION GENETICA Y FUNCIONAL DE QTLS, GENES Y REDES GENICAS Y ESTUDIO DEL EFECTO DEL MICROBIOMA SOBRE CRECIMIENTO, DEPOSICION DE GRASA Y CALIDAD DE CARNE EN PORCINO/
MINECO/Programa Estatal de promoción del talento y su empleabilidad en I+D+I/RYC 2013 12573/ES/ /
Programa
Genètica i Millora Animal
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