title: Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress.
abstract: Circulating extra-cellular microRNAs (miRNAs) have emerged as promising minimally invasive markers in human medicine. We evaluated miRNAs isolated from total plasma as biomarker candidates of a response to an abiotic stress (feed deprivation) in a livestock species. Two chicken lines selected for high (R+) and low (R-) residual feed intake were chosen as an experimental model because of their extreme divergence in feed intake and energy metabolism. Adult R+ and R- cocks were sampled after 16 hours of feed deprivation and again four hours after re-feeding. More than 292 million sequence reads were generated by small RNA-seq of total plasma RNA. A total of 649 mature miRNAs were identified; after quality filtering, 148 miRNAs were retained for further analyses. We identified 23 and 19 differentially abundant miRNAs between feeding conditions and between lines respectively, with only two miRNAs identified in both comparisons. We validated a panel of six differentially abundant miRNAs by RT-qPCR on a larger number of plasma samples and checked their response to feed deprivation in liver. Finally, we evaluated the conservation and tissue distribution of differentially abundant miRNAs in plasma across a variety of red jungle fowl tissues. We show that the chicken plasma miRNome reacts promptly to the alteration of the animal physiological condition driven by a feed deprivation stress. The plasma content of stress-responsive miRNAs is strongly influenced by the genetic background, with differences reflecting the phenotypic divergence acquired through long-term selection, as evidenced by the profiles of conserved miRNAs with a regulatory role in energy metabolism (gga-miR-204, gga-miR-let-7f-5p and gga-miR-122-5p). These results reinforce the emerging view in human medicine that even small genetic differences can have a considerable impact on the resolution of biomarker studies, and provide support for the emerging interest in miRNAs as potential novel and minimally invasive biomarkers for livestock species.
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Jouy-en-Josas, France; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Paris, France.
authors.forename: Marie-Laure Endale
authors.initials: ML
authors.lastname: Ahanda
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Jouy-en-Josas, France; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Paris, France.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Zerjal
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Jouy-en-Josas, France; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Paris, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Dhorne-Pollet
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Paris, France.
authors.forename: Andrea
authors.initials: A
authors.lastname: Rau
authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America; BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America.
authors.forename: Amanda
authors.initials: A
authors.lastname: Cooksey
authors.affiliation: INRA, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France; CEA, DSV, IRCM, SREIT, Laboratoire de Radiobiologie et Etude du Génome, Jouy-en-Josas, France; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Paris, France.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Giuffra
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D016000:Cluster Analysis; D063990:Gene Ontology; D035683:MicroRNAs / Q000097:blood* / Q000235:genetics; D058977:Molecular Sequence Annotation; D034622:RNA Interference; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D035683:MicroRNAs