Universidad Autónoma de Chiapas 26 de octubre de 2022
A Quasi-Exclusive European Ancestry in the Senepol
Tropical Cattle Breed Highlights the Importance of the
slick Locus in Tropical Adaptation
Laurence Flori1,2*, Mary Isabel Gonzatti3
, Sophie Thevenon2
, Isabelle Chantal2
, Joar Pinto3
,
David Berthier2
, Pedro M. Aso3
, Mathieu Gautier4
1 INRA, UMR 1313 GABI, F-78350 Jouy-en-Josas, France, 2 CIRAD, UMR INTERTRYP, Montpellier, France, 3Departamento de Biologi´a Celular, Universidad Simo´n Boli´var,
Caracas, Venezuela, 4 INRA, UMR CBGP, Montferrier-sur-Lez, France
Abstract
Background: The Senepol cattle breed (SEN) was created in the early XXth century from a presumed cross between a
European (EUT) breed (Red Poll) and a West African taurine (AFT) breed (N’Dama). Well adapted to tropical conditions, it is
also believed trypanotolerant according to its putative AFT ancestry. However, such origins needed to be verified to define
relevant husbandry practices and the genetic background underlying such adaptation needed to be characterized.
Methodology/Principal Findings: We genotyped 153 SEN individuals on 47,365 SNPs and combined the resulting data with
those available on 18 other populations representative of EUT, AFT and Zebu (ZEB) cattle. We found on average 89% EUT,
10.4% ZEB and 0.6% AFT ancestries in the SEN genome. We further looked for footprints of recent selection using standard
tests based on the extent of haplotype homozygosity. We underlined i) three footprints on chromosome (BTA) 01, two of
which are within or close to the polled locus underlying the absence of horns and ii) one footprint on BTA20 within the slick
hair coat locus, involved in thermotolerance. Annotation of these regions allowed us to propose three candidate genes to
explain the observed signals (TIAM1, GRIK1 and RAI14).
Conclusions/Significance: Our results do not support the accepted concept about the AFT origin of SEN breed. Initial AFT
ancestry (if any) might have been counter-selected in early generations due to breeding objectives oriented in particular
toward meat production and hornless phenotype. Therefore, SEN animals are likely susceptible to African trypanosomes
which questions the importation of SEN within the West African tsetse belt, as promoted by some breeding societies.
Besides, our results revealed that SEN breed is predominantly a EUT breed well adapted to tropical conditions and
confirmed the importance in thermotolerance of the slick locus.
Citation: Flori L, Gonzatti MI, Thevenon S, Chantal I, Pinto J, et al. (2012) A Quasi-Exclusive European Ancestry in the Senepol Tropical Cattle Breed Highlights the
Importance of the slick Locus in Tropical Adaptation. PLoS ONE 7(5): e36133. doi:10.1371/journal.pone.0036133
Editor: David Caramelli, University of Florence, Italy
Received January 22, 2012; Accepted March 26, 2012; Published May 9, 2012
Copyright: -
2012 Flori et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by an INRA (Institut National de la Recherche Agronomique)-Animal Genetics Department Grant (TROPSENEPOL project), an
ECOS (E´valuation-orientation de la COope´ration Scientifique) Nord No. PI-2008002104 grant and by FONACIT (FOnds NAtional pour les Sciences, les Technologies
et l’Innovation) projects G98-3462 and 2007-1425. MG acknowledges partial funding by the Agence Nationale de la Recherche programme BLANC EMILE 09-
BLAN-0145-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: laurence.flori@jouy.inra.fr
Introduction
Over the past decades, population genetic approaches associ-
ated with archeological evidence have provided better insights into
the origin of modern livestock breeds including domestication
processes, migration routes and their relationships [1–5]. The
recent release of complete genome sequences and the development
of high density SNP genotyping assays (e.g. [6]) in most livestock
species have greatly increased available genomic information to
refine characterization of breed origins and to efficiently detect
footprints of selection in animal genomes. As a result, assembling
large genetic datasets from livestock breeds, it is now possible to
evaluate the accuracy of the reports on the origin of breeds which
are widespread in the scientific literature. For instance, several
publications referred to the Italian Piemontese cattle breed as a
hybrid between the extinct aurochs and Indo-Pakistani Zebu. This
myth was only recently refuted by genetic fingerprinting which
showed that Italian Piemontese (as might have been expected) is a
mixture of several European taurine (EUT) breeds [7]. Less
fanciful, among the tropical cattle, the Kuri cattle breed has long
been reported as an African taurine (AFT) breed in particular
because these animals are humpless [8], characterized by a
submetacentric Y chromosome from a taurine origin and devoid
of Zebu allele on the Y chromosome [9]. However, nuclear
markers such as microsatellites and SNPs showed that Kuri is
actually a hybrid between AFT and Zebu (ZEB) breeds [10–15].
Apart from being of historical interest, such clarification of beliefs
could be essential in the management and diffusion of some cattle
breeds.
In addition, high density SNP dataset has highlighted chromo-
somal regions and genes targeted by artificial selection in dairy
and/or beef cattle and by natural selection in West African cattle
PLoS ONE | www.plosone.org 1 May 2012 | Volume 7 | Issue 5 | e36133