Molecular, genealogical and morphometric characterisation of the Pallaresa, a Pyrenean relic cattle breed: Insights for conservation

doi:10.1016/j.livsci.2010.05.004

Livestock Science

Volume 132, Issues 1–3, August 2010, Pages 65-72

https://doi.org/10.1016/j.livsci.2010.05.004 Get rights and content

Abstract

The Pallaresa cattle breed is a native population of beef cattle found in the western regions of the Catalan Pyrenees (Spain). Since the second half of the twentieth century, population size decreased dramatically in favour of the Bruna dels Pirineus breed. At the present time, it is classified as a relic breed on the brink of extinction by the FAO, as only 22 breeding animals remain alive (2 bulls and 20 cows). Its importance as genetic and cultural heritage and its contribution in maintaining the landscape and ecosystem, as well as its unquestionable interest as a tourist attraction, make it an irreplaceable element in this area.

In this paper, we present the breed characterisation of the population at the molecular, genealogical and morphological levels, and the comparison and phylogenetic relationships with other local breeds, in order to contribute to the characterisation of this prominent genetic resource.

Genealogical analyses showed that the Pallaresa population is highly inbred. The mean inbreeding for both the whole pedigree and the living population was 18.93% and 25.71%, respectively. A set of 15 microsatellites were typed on the available Pallaresa individuals to ascertain the genetic variability of the breed at the molecular level and to allow a direct comparison with a set of previously studied 19 local cattle breeds from Spain, Portugal and France. The average number of alleles per locus for the Pallaresa breed (4.3) was the lowest of the analysed breeds and the within-population genetic identity, assessed using molecular coancestry, the highest (0.437). The Pallaresa population showed high levels of differentiation from the other analysed breeds. The lowest kinship distance was assessed for the pairs formed with the Bruna dels Pirineus and Salers breeds (0.417 ± 0.010 and 0.427 ± 0.011, respectively). STRUCTURE analysis showed that most Pallaresa individuals were assigned to one distinct cluster, showing that the breed gathers a unique genetic background.

Despite its dramatic population scenario, the Pallaresa breed still preserves moderate levels of genetic diversity. The results obtained from the current study can contribute to design appropriate conservation strategies to prevent its extinction in the near future. The implementation of a mating programme involving Pallaresa bulls and Bruna dels Pirineus cows selected according to genetic and morphological closeness to the Pallaresa breed is suggested to prevent the genetic impoverishment of the population.

Introduction

Local cattle breeds are important genetic resources for agriculture, but many of them are at risk of extinction because of new market and agricultural demands. Unfortunately, some breeds can disappear before being fully documented. This is the case with some autochthonous Iberian breeds, such as the Pallaresa, which have suffered a dramatic reduction in their population sizes due to the loss of their economic importance.

The Pallaresa is a white-coated cattle breed that was traditionally distributed through three counties of the western Catalan Pyrenees (Pallars Sobirà, Pallars Jussà and Vall d'Aran), in north-eastern Spain. According to orally transmitted knowledge, it was descended from breeds from northern Europe that arrived in the western Catalan Pyrenees in about 1750. In relation to its morphology and geographical origin, it can be included in the Turdetanus Trunk (Red Convex trunk), together with the Pirenaica breed, which has shared the same habitat for centuries.

The Pallaresa enjoyed its golden age during the first half of the twentieth century, largely due to three main aptitudes: good capacity for field work and the quality of its meat and milk. However, after the beginning of the twentieth century, farmers began to crossbreed Pallaresa cows with dairy cattle breeds imported from Switzerland particularly the Brown-Alpine. The result of these crossbreeds, together with selection for meat production, was the Bruna dels Pirineus breed, which is now widely distributed throughout the Catalan Pyrenees. In the middle of the twentieth century, between the 50 and 70% of cattle in the western Catalan Pyrenees were Pallaresa, but after this the population size decreased dramatically in favour of the Bruna dels Pirineus (Servei de Producció Ramadera, 2003, Parés et al., 2005). The Pallaresa is now classified as a relic breed by the Food and Agriculture Organization of the United Nations (FAO, http://www.fao.org/dad-is/). At the moment, only twenty-two breeding animals remain alive (two bulls and twenty cows), grouped in a single herd in the village of Besan (Vall Ferrera, Pallars Sobirà).

The historical, cultural and genetic heritage of the Pallaresa cattle breed is unquestionable. Moreover, productively, the Pallaresa is quite similar to the Bruna dels Pirineus and it is well adapted to extreme mountainous environments. The withers height for adult cows is around 136 cm; the weight of living individuals ranges from 575 to 625 for cows, and from 625 to 650 kg for bulls. Calves are fattened up and slaughtered at one year-old. The carcass yield is 60% (carcass weight around 350–375 kg) (Parés et al., 2005).

The loss of this autochthonous breed would represent the extinction of selected genotypes for adaptation to mountainous regions, contributing to the genetic impoverishment of the species. Despite its long history, the Pallaresa is not yet included in the Spanish Official Breed Catalogue. In addition, neither genetic nor morphological studies have been previously performed to characterise this breed. Due to the extreme risk of extinction, it is necessary to obtain data from this breed urgently, at least in order to document its main morphological and genetic characteristics and also to explore whether its recovery is possible. For this reason, in 2001, the Department of Agriculture, Food and Rural Action (DAR) of the Catalan Government, in collaboration with the Universitat Autònoma de Barcelona (UAB), began the Pallaresa Cattle Breed Conservation Programme (Avellanet et al., 2002). The objectives of this Conservation Programme were the genetic and morphological characterisation of the Pallaresa population to describe the breed standard, the levels of genetic variability and its phylogenetic relationships. Here we report the results obtained since the beginning of the Conservation Programme and discuss the possibilities for recovering the Pallaresa cattle breed.

Section snippets

Material and methods

Genetic characterisation was carried out using pedigree analysis together with microsatellite markers. We analysed the information contained in the Pallaresa cattle Herd Book, in which 66 animals were registered between 1962 and 2009. This information belonged to one only herd located at Besan (Vall Ferrera, Pallars Sobirà). The level of pedigree completeness was characterised by computing the maximum number of generations and full generations traced, as well as equivalent generations. In order

Pedigree analysis

In 2009, a total of 66 individuals belonging to the same herd was registered in the Pallaresa breed Herd Book. The sex ratio between males and females was close to 1:2 (21 males and 45 females). The living population consisted of 31 individuals (22 females). The base population consisted of nine founders – eight females and a single male – from which all other ancestors of living individuals were descended. As a consequence, all non-founder individuals turned out to be related. The maximum

Discussion

Despite its extremely low population size, the sole extant population of the Pallaresa cattle breed still preserves moderate levels of genetic diversity. The average number of alleles per locus found in the Pallaresa was lower than the range of values obtained in other western European cattle breeds using the same microsatellite markers (5.5 for Mirandesa; 7.2 for Gasconne) (Cañón et al., 2001). This parameter is one of the most important in conservation genetics because it provides information

Conclusion

Despite its extremely low population size and high consanguinity, the sole extant population of the Pallaresa cattle breed still preserves relatively good levels of genetic diversity. The proven fact that the northern regions of the Iberian Peninsula, such as the Pyrenees, are an important reservoir of diversity, endorses the priority of the recovery of the Pallaresa breed for conservation purposes. Thus, the management of the breed must include a careful planning of crossings between

Acknowledgements

We wish to thank the breeder Ignasi Sinfreu Canturri for providing samples of the animals and their genealogical data. This work has been supported by the Department of Agriculture, Food and Rural Action (DAR) of the Government of Catalonia.

References (37)

J.L. Bossart et al.
Genetic estimates of population structure and gene flow: limitations, lessons and new directions
Trend Ecol. Evol.
(1998)
J.A. Aranguren-Méndez et al.
Genetic diversity measures of local cattle Majorcan breed for conservation purposes
Rev. Cient-Fac. Cien. V.
(2002)
F.M. Ausubel et al.
Current Protocols in Molecular Biology
(1987)
R. Avellanet et al.
Programa de recuperación de la raza bovina Pallaresa
A. Beja-Pereira et al.
Genetic characterization of Southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites
J. Hered.
(2003)
K. Belkhir et al.
GENETIX 4.02, Logiciel sous Windows TM pour la Génétique des Populations. Laboratoire Génome, Populations, Interactions: CNRS UMR 5000, Université de Montpellier II, Montpellier, France
(2001)
A. Caballero et al.
Analysis of genetic diversity for the management of conserved subdivided populations
Conserv. Genet.
(2002)
J. Cañón et al.
Genetic diversity measures of local European beef cattle breeds for conservation purposes
Genet. Sel. Evol.
(2001)
J. Carlsson
Effects of microsatellite null alleles on assignment testing
J. Hered.
(2008)
J. Casellas et al.
Genetic diversity measures of the bovine Alberes breed using microsatellites: variability among herds and types of coat colour
J. Anim. Breed. Genet.
(2004)

A. Di Rienzo et al.

Mutational processes of simple-sequence repeat loci in human populations

Proc. Natl Acad. Sci. USA

(1994)

European Cattle Genetic Diversity Consortium

Marker-assisted conservation of European cattle breeds: an evaluation

Anim. Genet.

(2006)

L. Excoffier et al.

Arlequin ver. 3.0: an integrated software package for population genetics data analysis

Evolutionary Bioinformatics Online

(2005)

D. Falush et al.

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies

Genetics

(2003)

J. Goudet

FSTAT (version 1.2): a computer program to calculate F-statistics

J. Hered.

(1995)

J.P. Gutiérrez et al.

A note on ENDOG: a computer program for analysing pedigree information

J. Anim. Breed. Genet.

(2005)

J.P. Gutiérrez et al.

Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed

J. Anim. Breed. Genet.

(2005)

J.P. Gutiérrez et al.

MolKin (v.2.0) a computer program for genetic analysis of populations using molecular coancestry information

J. Hered.

(2005)

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Molecular, genealogical and morphometric characterisation of the Pallaresa, a Pyrenean relic cattle breed: Insights for conservation

Abstract

Introduction

Section snippets

Material and methods

Pedigree analysis

Discussion

Conclusion

Acknowledgements

Trend Ecol. Evol.

Genetic diversity measures of local cattle Majorcan breed for conservation purposes

Rev. Cient-Fac. Cien. V.

Current Protocols in Molecular Biology

Programa de recuperación de la raza bovina Pallaresa

Genetic characterization of Southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites

J. Hered.

GENETIX 4.02, Logiciel sous Windows TM pour la Génétique des Populations. Laboratoire Génome, Populations, Interactions: CNRS UMR 5000, Université de Montpellier II, Montpellier, France

Analysis of genetic diversity for the management of conserved subdivided populations

Conserv. Genet.

Genetic diversity measures of local European beef cattle breeds for conservation purposes

Genet. Sel. Evol.

Effects of microsatellite null alleles on assignment testing

J. Hered.

Genetic diversity measures of the bovine Alberes breed using microsatellites: variability among herds and types of coat colour

J. Anim. Breed. Genet.

Mutational processes of simple-sequence repeat loci in human populations

Proc. Natl Acad. Sci. USA

Marker-assisted conservation of European cattle breeds: an evaluation

Anim. Genet.

Arlequin ver. 3.0: an integrated software package for population genetics data analysis

Evolutionary Bioinformatics Online

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies

Genetics

FSTAT (version 1.2): a computer program to calculate F-statistics

J. Hered.

A note on ENDOG: a computer program for analysing pedigree information

J. Anim. Breed. Genet.

Pedigree information reveals moderate to high levels of inbreeding and a weak population structure in the endangered Catalonian donkey breed

J. Anim. Breed. Genet.

MolKin (v.2.0) a computer program for genetic analysis of populations using molecular coancestry information

J. Hered.