Chicken family BC1 1998: transcriptome profiling used for QTL/eQTL detection

The family concerns 44 offspring of the sire BC1 n°1998 (produced from a F1 male obtained by-intercrossing two fat (FL) and lean (LL) meat-type chicken lines that divergently selected on fatness [Leclercq et al 1980] mated with 8 LL females. Hepatic transcriptomic profiles were obtained using a chicken 20K oligochips (ARK-genomics). The 44 chickens were fed ad libitum using a conventional starter diet (0-3 weeks: 12.8 MJ of metabolizable energy) and then a growing broiler diet (4-9 weeks: 13.0 Mj of metabolizable energy). Light/dark periods were 24h light for the first 2 days, then 14h light/10h night up to slaughtering. At 4 weeks of age, blood samples were collected for DNA extraction and genotyping. At 9 weeks of age, the birds were fed ad libitum for 4 hours minimum after overnight fasting and then weighed and sacrificed by electrical stunning in the experimental processing plant (Station de Recherches Avicoles, Inra, Nouzilly, France). Following sacrifice, livers were collected, quickly frozen in liquid nitrogen and stored at −80°C until RNA extraction for transcriptome analyses Five micrograms of total RNA from each sample were labelled with Cy5 and then hybridized to the microarray with a same Cy3-labeled reference probe. The reference RNA pool was made from an equal amount of RNA derived from all liver samples.