New approaches of phenotyping for animal breeding

Abstract

Phenotyping requires measuring traits chosen for their socio-economic importance or their cognitive value. Needs for phenotyping dependon the trend in breeding methods and production systems, and also on technological developments allowing for high throughput standardisedapproaches at a reasonable cost. Considering animal breeding, implementation of genomic selection introduces the concept ofreference population, where specific phenotypes not routinely available can be obtained to associate genetic markers with performance.Association between markers and phenotypes also open the way towards individual diagnostic to support herd management. Robotics andindividual electronic identification require important investments but offer quite new prospects for phenotyping traits such as feed efficiencyor behaviour. Complementary tools are provided by technological developments in functional genomics and by spectral analysis ofproteins, which can unravel underlying mechanisms and refine the definition of phenotypes at the molecular scale. The concept of biomarkerhas emerged in human medicine in order to predict phenotype and is expected to be applied also to farm animals. The closer thephenotyping is from the biological mode of action, the more accurate will be the detection of genes determining phenotypic variation. Moreparticularly, the search for genome regions controlling gene expression (eQTL) makes possible to explore the mechanisms responsible forthe variability of complex traits. Great progress can thus be expected for the identification of genes underlying QTL thanks to simultaneousimprovements in phenotyping and genome sequencing..