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

Ginja C, Penedo MC, Sobral MF, Matos J, Borges C, Neves D, Rangel-Figueiredo T, Cravador A - Genet. Sel. Evol. (2010)

Bottom Line: Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds.Molecular and morphological results were concordant.Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.

View Article: PubMed Central - HTML - PubMed

Affiliation: IBB/CGB - Universidade do Algarve, Campus de Gambelas, 8005-139 FARO Portugal.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

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Graphical representation of the estimated membership coefficients (q). STRUCTURE was used to obtain q values for each individual of the southern Portuguese breeds and the imported Limousin with K varying from 2 to 6
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Figure 2: Graphical representation of the estimated membership coefficients (q). STRUCTURE was used to obtain q values for each individual of the southern Portuguese breeds and the imported Limousin with K varying from 2 to 6

Mentions: STRUCTURE analyses assume that within a population all loci are in HWE and linkage equilibrium [40]. Although for some breeds a high number of loci showed significant (P < 0.05) deviations from HWE without correction for multiple testing (Additional file 3 Table S1), the assignments with STRUCTURE were conducted to include all loci, because some deviations from HWE are not expected to affect the performance of the test [55]. The HWE deviations found in Brava de Lide and Preta breeds are most probably related with a Wahlund effect and/or inbreeding, considering that the Fis values for these breeds were highly significant [see discussion for Brava de Lide in [12]]. Within breeds, LD was significant (P < 0.001) for one pair of loci in the Alentejana breed, four in the Preta and four in the Brava de Lide, but none of these corresponded to markers located on the same chromosome. The assignment tests of STRUCTURE and GENECLASS were done exclusively for the Algarvia animals, the related southern breeds (Alentejana, Garvonesa, Mertolenga and Preta) and the Limousin cattle to determine which Algarvia animals clustered as an independent group, and to detect admixture. The STRUCTURE assignments without prior information on source breeds showed the highest ΔK at K = 6 (Additional file 4 Figure S3). The estimated genotype membership coefficients (q) obtained for each individual are shown in Figure 2. Algarvia animals clustered with the Alentejana and Mertolenga breeds at K = 2 and only appeared as an independent cluster at K = 6.


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

Ginja C, Penedo MC, Sobral MF, Matos J, Borges C, Neves D, Rangel-Figueiredo T, Cravador A - Genet. Sel. Evol. (2010)

Graphical representation of the estimated membership coefficients (q). STRUCTURE was used to obtain q values for each individual of the southern Portuguese breeds and the imported Limousin with K varying from 2 to 6
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2903498&req=5

Figure 2: Graphical representation of the estimated membership coefficients (q). STRUCTURE was used to obtain q values for each individual of the southern Portuguese breeds and the imported Limousin with K varying from 2 to 6
Mentions: STRUCTURE analyses assume that within a population all loci are in HWE and linkage equilibrium [40]. Although for some breeds a high number of loci showed significant (P < 0.05) deviations from HWE without correction for multiple testing (Additional file 3 Table S1), the assignments with STRUCTURE were conducted to include all loci, because some deviations from HWE are not expected to affect the performance of the test [55]. The HWE deviations found in Brava de Lide and Preta breeds are most probably related with a Wahlund effect and/or inbreeding, considering that the Fis values for these breeds were highly significant [see discussion for Brava de Lide in [12]]. Within breeds, LD was significant (P < 0.001) for one pair of loci in the Alentejana breed, four in the Preta and four in the Brava de Lide, but none of these corresponded to markers located on the same chromosome. The assignment tests of STRUCTURE and GENECLASS were done exclusively for the Algarvia animals, the related southern breeds (Alentejana, Garvonesa, Mertolenga and Preta) and the Limousin cattle to determine which Algarvia animals clustered as an independent group, and to detect admixture. The STRUCTURE assignments without prior information on source breeds showed the highest ΔK at K = 6 (Additional file 4 Figure S3). The estimated genotype membership coefficients (q) obtained for each individual are shown in Figure 2. Algarvia animals clustered with the Alentejana and Mertolenga breeds at K = 2 and only appeared as an independent cluster at K = 6.

Bottom Line: Genetic distance and FCA results confirmed the close relationship between Algarvia and southern Portuguese breeds.Molecular and morphological results were concordant.Results of genetic diversity and conservation analyses provide objective information to establish a management program to reconstitute the Algarvia breed.

View Article: PubMed Central - HTML - PubMed

Affiliation: IBB/CGB - Universidade do Algarve, Campus de Gambelas, 8005-139 FARO Portugal.

ABSTRACT

Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.

Show MeSH