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Thesis : genetics of feed efficiency in laying hen

Genetics of feed efficiency in laying hen

Identification of genes responsible for feed efficiency variation in laying hen, by combining different genetic approaches on lines diverging for this trait.

Feed efficiency and adiposity

Our main model of study is composed of two laying hen lines divergently selected for 40 years on residual feed intake, a trait of economic significance in animal production. These animals are therefore strongly differing for feed efficiency, but also for body fat content.
Moreover, as part of the ANR program Chickstress, these lines underwent a heat or a feed stress (under-optimal feed). Since these animals are produced all over the world and have a long production career, they are more likely to underwent one of these stresses.

Hen

Objectives of the Ph.D

  • The study of laying hens’ adaptation to stressing conditions, by collecting phenotypes and transcriptomes using multi-tissues RNA-seq.
  • The study of the genetic markers of feed efficiency and body fat, by combining two approaches. On the one hand, the identification of selective sweeps, the analysis of RNA-seq based transcriptome (RNA markers) in key tissues for both those traits (blood, liver, adipose tissue and hypothalamus) and the analysis of whole genomes (SNPs, INDEL, etc.) using DNA-seq on our lines of interest.
  • The study of the link existing between genotype – tissue – expression, thanks to the accumulation of tissues expression data by RNA-seq, in order to better understand the regulation of expression at the transcripts levels, in line with the work of the GTEX consortium.

Identification of causal genes affected by a polymorphism

Currently, most of the identified causal genes are affected by a polymorphism that alters the structure of the coded protein. In this thesis, the data available will allow to go further, by identifying causal genes that regulates other genes’ expression, but that are not protein coding (long non-coding RNAs), as well as those genes, whether coding or non-coding, bearing a polymorphism that modifies their quantity of transcripts.

Variant

The effects of a variant depend on the region of the gene where it appears (transcribed vs. regulatory) and of the affected gene type (coding vs. non-coding)
A: a variant affecting the transcribed and translated part of a coding gene might alter the coded protein structure.
B: a variant affecting the transcribed part of a non-coding gene might have effects on the regulatory function of the gene.
C: a variant affecting the regulatory region of a coding gene might affect the quantity of mRNA, thus the quantity of translated protein.
D: a variant affecting the regulatory region of a non-coding gene might affect the quantity of non-coding RNA produced, affecting the expression of the genes it regulates

Frédéric Jehl is working on this thesis subject since the 1st November 2017 for a period of 3 years. He is supervised by Sandrine Lagarrigue in the team Genetics and Genomics and co-supervised by Tatiana Zerjal in the team PSGen (UMR Gabi).

Contact

Frédéric Jehl, frederic.jehl[at]inra.fr

Modification date : 07 February 2023 | Publication date : 13 February 2018 | Redactor : Pegase