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Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay

INRA GABI Unit

GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

Detection of a locus for adaptation in cattle using resequencing data

Detection of a locus for adaptation in cattle using resequencing data
By analyzing 90 animals from four different breeds, we looked for regions responsible for adaptation in cattle. Our study showed the interest of resequencing in this context along with the complementarity of the two detection approaches used. In addition, it allowed identifying several new genes responsible for adaptation in the cow while confirming several previously identified candidates.

Context and stakes

The detection of genomic regions having evolved in an adaptive manner in a species is a theoretically important challenge. For agricultural species, identifying adaptive regions improves our understanding of the impact of domestication on ulterior selection practices by man: what traits are concerned? When? With what intensity? What are the regions implicated and what is the proportion of these regions in the genome?

Results

We searched for regions under selection in the cow by analyzing the sequences of 90 animals from four breeds (Angus, Fleckvieh, Holstein and Jersey) produced as part of the 1000 bovine genome consortium. We compared two detection approaches: one approach searches for regions with low intra-population genetic diversity and one searches for regions that are highly differentiated among populations. From a methodological point of view, our study shows that resequencing data allows detecting more adaptive regions than does high-throughput genotyping data. It also enables locating much more finely the adaptive regions and even in some favorable cases determining a very minute number of candidate variants. Our work also illustrates the complementarity of the two approaches used, which tend to detect selection events different in both age and type. In the bovine species, we confirmed the existence of several previously identified adaptive genes such as MC1R, KIT, GHR, PLAG1 or NCAPG/LCORL, and we identified new ones such as ARL15, PRLR, CYP19A1, PPM1L. Our analyses consider the estimated demographic models for the breeds concerned, which allows us to conclude that only selection provides an explanation to the genetic diversity observed in these regions.

Perspectives

DNA sequencing in the domestic cow and/or its wild ancestor the aurochs will allow us in the near future to gain more precise information on the evolving adaptive regions in the detected regions. The comparison of our results with those of association studies should also allow the identification, for some regions, of the exact variants under selection.

Valorization

This study was published in a high impact genetic journal (cf ref figuring below). It was presented in several conferences and will notably be the object of an invited oral presentation during the next Plant and Animal Genome meeting (SanDiego, January 2017).

References

S. Boitard, M. Boussaha, A. Capitan, D. Rocha and B. Servin (2016). Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds. Genetics 203:433-450.