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Genetic components of grey cattle in Estonia as revealed by microsatellite analysis using two Bayesian clustering methods.

Li MH, Kantanen J, Michelson A, Saarma U - BMC Res Notes (2011)

Bottom Line: It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock.Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components.This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland. menghua.li@mtt.fi.

ABSTRACT

Background: It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock. Genotypes at 17 microsatellite loci from a total of 243 cattle from North European breeds and 11 grey cattle in Estonia were used in an attempt to clarify the genetic composition of the grey cattle.

Findings: We characterize the genetic components of 11 examples of the grey cattle in Estonia at the population and individual levels. Our results show that the grey cattle in Estonia are most genetically similar to the Holstein-Friesian breed and secondarily to the Estonian Red cattle.

Conclusions: Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components. This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds.

No MeSH data available.


Related in: MedlinePlus

Population structure of 7 cattle populations using: (A) model-based STRUCTURE program (Pritchard et al. 2000) and (B) BAPS program (Tang et al. 2009). Each animal is represented by a single vertical line divided into K colours, where K is the number of clusters assumed. The coloured segment shows the individual's estimated proportion of membership (averaged across 10 runs at K = 6) in that cluster for the STRUCTURE program and indicates the average probability of assignment to the "correct" cluster for the BAPS program. Black lines separate the populations labelled above the figure. The labels above the figure indicate the number of animals analysed in each breed and the names of the cattle populations analysed are indicated below the figure.
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Figure 2: Population structure of 7 cattle populations using: (A) model-based STRUCTURE program (Pritchard et al. 2000) and (B) BAPS program (Tang et al. 2009). Each animal is represented by a single vertical line divided into K colours, where K is the number of clusters assumed. The coloured segment shows the individual's estimated proportion of membership (averaged across 10 runs at K = 6) in that cluster for the STRUCTURE program and indicates the average probability of assignment to the "correct" cluster for the BAPS program. Black lines separate the populations labelled above the figure. The labels above the figure indicate the number of animals analysed in each breed and the names of the cattle populations analysed are indicated below the figure.

Mentions: Based on the population Q-values, the STRUCTURE program identified six clusters among the seven populations, but could not discern all seven populations (Figure 2A). More exactly, it failed to differentiate between the grey cattle in Estonia and Finnish Holstein-Friesian. Over the entire cattle populations, Ln P(D) increased from K = 2 to K = 6, after which it began to decline, indicating the most likely value to be K = 6 (results not shown). When we used ΔK to infer the number of clusters, we found that K = 6 was clearly favoured (results not shown). At K = 6, all the grey cattle in Estonia were characterized, with the highest proportion of membership from the Finnish Holstein-Friesian cluster (QFiHF). Five grey cattle (Le1, Le4, Le9, Le10 and Le11) showed high values of QFiHF > 0.9 and the remaining grey cattle are suggested to have large membership fractions in multiple clusters for the sampled populations. In particular, the grey cattle Le8 have similar values of Q for two distinct populations, Finnish Holstein-Friesian (QFiHF = 0.480) and the Estonian Red (QEsR = 0.351; Table 1).


Genetic components of grey cattle in Estonia as revealed by microsatellite analysis using two Bayesian clustering methods.

Li MH, Kantanen J, Michelson A, Saarma U - BMC Res Notes (2011)

Population structure of 7 cattle populations using: (A) model-based STRUCTURE program (Pritchard et al. 2000) and (B) BAPS program (Tang et al. 2009). Each animal is represented by a single vertical line divided into K colours, where K is the number of clusters assumed. The coloured segment shows the individual's estimated proportion of membership (averaged across 10 runs at K = 6) in that cluster for the STRUCTURE program and indicates the average probability of assignment to the "correct" cluster for the BAPS program. Black lines separate the populations labelled above the figure. The labels above the figure indicate the number of animals analysed in each breed and the names of the cattle populations analysed are indicated below the figure.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045957&req=5

Figure 2: Population structure of 7 cattle populations using: (A) model-based STRUCTURE program (Pritchard et al. 2000) and (B) BAPS program (Tang et al. 2009). Each animal is represented by a single vertical line divided into K colours, where K is the number of clusters assumed. The coloured segment shows the individual's estimated proportion of membership (averaged across 10 runs at K = 6) in that cluster for the STRUCTURE program and indicates the average probability of assignment to the "correct" cluster for the BAPS program. Black lines separate the populations labelled above the figure. The labels above the figure indicate the number of animals analysed in each breed and the names of the cattle populations analysed are indicated below the figure.
Mentions: Based on the population Q-values, the STRUCTURE program identified six clusters among the seven populations, but could not discern all seven populations (Figure 2A). More exactly, it failed to differentiate between the grey cattle in Estonia and Finnish Holstein-Friesian. Over the entire cattle populations, Ln P(D) increased from K = 2 to K = 6, after which it began to decline, indicating the most likely value to be K = 6 (results not shown). When we used ΔK to infer the number of clusters, we found that K = 6 was clearly favoured (results not shown). At K = 6, all the grey cattle in Estonia were characterized, with the highest proportion of membership from the Finnish Holstein-Friesian cluster (QFiHF). Five grey cattle (Le1, Le4, Le9, Le10 and Le11) showed high values of QFiHF > 0.9 and the remaining grey cattle are suggested to have large membership fractions in multiple clusters for the sampled populations. In particular, the grey cattle Le8 have similar values of Q for two distinct populations, Finnish Holstein-Friesian (QFiHF = 0.480) and the Estonian Red (QEsR = 0.351; Table 1).

Bottom Line: It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock.Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components.This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology and Food Research, MTT Agrifood Research Finland, FI-31600 Jokioinen, Finland. menghua.li@mtt.fi.

ABSTRACT

Background: It was recently postulated that a few individual grey cattle still found in Estonia might be a relict of the old native cattle stock. Genotypes at 17 microsatellite loci from a total of 243 cattle from North European breeds and 11 grey cattle in Estonia were used in an attempt to clarify the genetic composition of the grey cattle.

Findings: We characterize the genetic components of 11 examples of the grey cattle in Estonia at the population and individual levels. Our results show that the grey cattle in Estonia are most genetically similar to the Holstein-Friesian breed and secondarily to the Estonian Red cattle.

Conclusions: Both Bayesian approaches gave similar results in terms of the identification of numbers of clusters and the estimation of proportions of genetic components. This study suggested that the Estonian grey cattle included in the analysis are a genetic composite resulting from cross-breeding of European dairy breeds.

No MeSH data available.


Related in: MedlinePlus