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Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Catarina Ginja1, Maria CT Penedo1, Maria F Sobral2, José Matos3, Carla Borges3, Dina Neves4, Teresa Rangel-Figueiredo5 and Alfredo Cravador6*

Author Affiliations

1 University of California, Veterinary Genetics Laboratory, One Shields Avenue, DAVIS, California 95616, USA

2 Direcção Geral de Veterinária-DSPA, Rua Elias Garcia 30, Venda Nova, 2704-507 AMADORA, Portugal

3 L-INIA - Pólo do Lumiar Unidade de Investigação em Recursos Genéticos, Ecofisiologia e Melhoramento de Plantas, Grupo de Biologia Molecular, Estrada do Paço do Lumiar, 22 Ed S 1º andar 1649-038 LISBOA, Portugal

4 Universidade do Algarve, FCT, Campus de Gambelas, 8005-139 FARO, Portugal

5 CECAV - Universidade de Trás-os-Montes e Alto Douro, Departamento de Zootecnia, Apartado 1013, 5000-911 VILA REAL, Portugal

6 IBB/CGB - Universidade do Algarve, Campus de Gambelas, 8005-139 FARO Portugal

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Genetics Selection Evolution 2010, 42:18  doi:10.1186/1297-9686-42-18

Published: 11 June 2010



Decisions to initiate conservation programmes need to account for extant variability, diversity loss and cultural and economic aspects. Molecular markers were used to investigate if putative Algarvia animals could be identified for use as progenitors in a breeding programme to recover this nearly extinct breed.


46 individuals phenotypically representative of Algarvia cattle were genotyped for 27 microsatellite loci and compared with 11 Portuguese autochthonous and three imported breeds. Genetic distances and factorial correspondence analyses (FCA) were performed to investigate the relationship among Algarvia and related breeds. Assignment tests were done to identify representative individuals of the breed. Y chromosome and mtDNA analyses were used to further characterize Algarvia animals. Gene- and allelic-based conservation analyses were used to determine breed contributions to overall genetic diversity.


Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds. Assignment tests without breed information classified 17 Algarvia animals in this cluster with a high probability (q > 0.95). With breed information, 30 cows and three bulls were identified (q > 0.95) that could be used to reconstitute the Algarvia breed. Molecular and morphological results were concordant. These animals showed intermediate levels of genetic diversity (MNA = 6.0 ± 1.6, Rt = 5.7 ± 1.4, Ho = 0.63 ± 0.19 and He = 0.69 ± 0.10) relative to other Portuguese breeds. Evidence of inbreeding was also detected (Fis = 0.083, P < 0.001). The four Algarvia bulls had Y-haplotypes H6Y2 and H11Y2, common in Portuguese cattle. The mtDNA composition showed prevalence of T3 matrilines and presence of the African-derived T1a haplogroup. This analysis confirmed the genetic proximity of Algarvia and Garvonesa breeds (Fst = 0.028, P > 0.05). Algarvia cattle provide an intermediate contribution (CB = 6.18, CW = -0.06 and D1 = 0.50) to the overall gene diversity of Portuguese cattle. Algarvia and seven other autochthonous breeds made no contribution to the overall allelic diversity.


Molecular analyses complemented previous morphological findings to identify 33 animals that can be considered remnants of the Algarvia breed. Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.