Know more

MOTS-CLES : sequencing, DNA, RNA, polymorphism, bovine, cattle

Genetic variations modulate gene expression on the transcriptionnal or post-transcriptional level and can therefore alter the phentoype of an individual. The measurement of allelic differential expression on the heterozygous loci level in an individual, a phenomenon called allele-specific expression (ASE), can be used to detect variants having a cis-regulating effect on gene expression. With the current massive sequencing methods of DNA and RNA, it is now possible to study this allele expression bias at the whole genome level.

In cattle, this type of study has only been done in the Holstein breed. In our study, we performed an analysis of ASE on the genome scale from 19 muscle samples of the Limousine breed.

We sequenced complete genomes and transcriptomes from 19 Limousine animals and identified 5658 Single Nucleotide Polymorphisms (SNP) showing an allele expression bias in 13% of the genes expressed. What is interesting is that we noticed an allele expression bias in the genes AOX1, PALLD and CAST. We also found 2107 SNP ASE located in the regions associated with traits for meat quality. In order to identify the regulating causal variants that explain ASE, we searched for SNP that modify the transcription factor binding sites or microRNA target sites. We therefore identified SNP in the 3'UTR region of the PRNP gene which could be a causal variation.

In this study we showed that ASE is a frequent phenomenon in muscle tissue.

These results should help us identify cis-regulating variants  that have a direct impact on important agronomic traits (like meat quality). These causal variants could then be used to improve genetic selection methods.