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Estimation of relatedness among non-pedigreed Yakutian cryo-bank bulls using molecular data: implications for conservation and breed management.

Tapio I, Tapio M, Li MH, Popov R, Ivanova Z, Kantanen J - Genet. Sel. Evol. (2010)

Bottom Line: In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population.Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck.The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland.

ABSTRACT

Background: Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population.

Methods: To clarify the genetic relatedness between these bulls and to provide recommendations to use their semen in future conservation and breed management programs, we have analysed 30 autosomal microsatellites and mitochondrial DNA sequences in 60 individuals including the six for which semen has been stored. Four relatedness estimators were calculated. In addition, we assessed the value of the cryo-bank bulls for the preservation of genetic variation of the contemporary Yakutian cattle by calculating allelic and gene diversity estimates and mean molecular coancestries.

Results: On the basis of microsatellite variability, including the Yakutian cryo-bank bulls increases the allelic variation in the contemporary population by 3% and in the male subpopulation by 13%. In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population. Although 30 loci are insufficient to resolve definitely their relatedness categories, the data suggest four pairs of cryo-bank bulls as possible half-sibs.

Conclusions: Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.

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Pairwise relatedness of Yakutian cryo-bank bulls. Values are calculated using (A) rW and (B) rQG relatedness estimators plotted on a distribution of four simulated relationship categories: unrelated, half-sibs, full-sibs and parent-offspring; the vertical line represents the 95th percentile for simulated unrelated individuals; the position of pairwise values in regards to the Y-axis was designed based on the estimates from the rK relatedness estimator and was calculated as 3 divided by the cases when the log likelihood of R for the second closest relationship is smaller than the most likely relationship; abbreviations for Yakutian cryo-bank bulls are: K-Keskil, M-Moxsogol, R-Radzu, E-Erel, S-Sarial, A-Alii. Y-axis denotes the distribution of posterior probability density based on the simulations of the four relationship categories using the two relatedness estimators rW and rQG, respectively.
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Figure 1: Pairwise relatedness of Yakutian cryo-bank bulls. Values are calculated using (A) rW and (B) rQG relatedness estimators plotted on a distribution of four simulated relationship categories: unrelated, half-sibs, full-sibs and parent-offspring; the vertical line represents the 95th percentile for simulated unrelated individuals; the position of pairwise values in regards to the Y-axis was designed based on the estimates from the rK relatedness estimator and was calculated as 3 divided by the cases when the log likelihood of R for the second closest relationship is smaller than the most likely relationship; abbreviations for Yakutian cryo-bank bulls are: K-Keskil, M-Moxsogol, R-Radzu, E-Erel, S-Sarial, A-Alii. Y-axis denotes the distribution of posterior probability density based on the simulations of the four relationship categories using the two relatedness estimators rW and rQG, respectively.

Mentions: Ten out of 15 pairwise R-estimates between the six Yakutian cryo-bank bulls approached zero or fell below it. The remaining five bull-pairs exhibited R-values ranging from 0.124 to 0.276 for rW and from 0.180 to 0.295 for rQG (Additional file 2). All pairwise R values were plotted on the distribution of four simulated relatedness categories (Figure 1). When the rW estimator was used, one pair (Radzu:Sarial, R = 0.276) fell outside the 95% confidence interval for simulated UR individuals (the 95th upper quantile = 0.252) and was considered to be related (Figure 1a). Two other pairs were identified as related when the rQG estimator was applied (Keskil:Moxsogol, R = 0.295; Radzu:Erel, R = 0.255; the 95th upper quantile = 0.242) (Figure 1b). The ML-Relate program uses simulation to determine which relationships are consistent with genotype data and to compare putative relationships with alternatives. In order to identify possible misclassified individuals, a maximum-likelihood estimator rK estimated by ML-Relate was applied. Besides the three bull-pairs mentioned above, the Erel:Sarial pair (rW = 0.205; rQG = 0.180) had the highest likelihood of being a half-sib (Additional file 2). The same four pairs of Yakutian cryo-bank bulls were also identified as potential half-sibs in the parentage analysis performed using the pedigree reconstruction method among all individuals in the sample (Additional file 4).


Estimation of relatedness among non-pedigreed Yakutian cryo-bank bulls using molecular data: implications for conservation and breed management.

Tapio I, Tapio M, Li MH, Popov R, Ivanova Z, Kantanen J - Genet. Sel. Evol. (2010)

Pairwise relatedness of Yakutian cryo-bank bulls. Values are calculated using (A) rW and (B) rQG relatedness estimators plotted on a distribution of four simulated relationship categories: unrelated, half-sibs, full-sibs and parent-offspring; the vertical line represents the 95th percentile for simulated unrelated individuals; the position of pairwise values in regards to the Y-axis was designed based on the estimates from the rK relatedness estimator and was calculated as 3 divided by the cases when the log likelihood of R for the second closest relationship is smaller than the most likely relationship; abbreviations for Yakutian cryo-bank bulls are: K-Keskil, M-Moxsogol, R-Radzu, E-Erel, S-Sarial, A-Alii. Y-axis denotes the distribution of posterior probability density based on the simulations of the four relationship categories using the two relatedness estimators rW and rQG, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2909159&req=5

Figure 1: Pairwise relatedness of Yakutian cryo-bank bulls. Values are calculated using (A) rW and (B) rQG relatedness estimators plotted on a distribution of four simulated relationship categories: unrelated, half-sibs, full-sibs and parent-offspring; the vertical line represents the 95th percentile for simulated unrelated individuals; the position of pairwise values in regards to the Y-axis was designed based on the estimates from the rK relatedness estimator and was calculated as 3 divided by the cases when the log likelihood of R for the second closest relationship is smaller than the most likely relationship; abbreviations for Yakutian cryo-bank bulls are: K-Keskil, M-Moxsogol, R-Radzu, E-Erel, S-Sarial, A-Alii. Y-axis denotes the distribution of posterior probability density based on the simulations of the four relationship categories using the two relatedness estimators rW and rQG, respectively.
Mentions: Ten out of 15 pairwise R-estimates between the six Yakutian cryo-bank bulls approached zero or fell below it. The remaining five bull-pairs exhibited R-values ranging from 0.124 to 0.276 for rW and from 0.180 to 0.295 for rQG (Additional file 2). All pairwise R values were plotted on the distribution of four simulated relatedness categories (Figure 1). When the rW estimator was used, one pair (Radzu:Sarial, R = 0.276) fell outside the 95% confidence interval for simulated UR individuals (the 95th upper quantile = 0.252) and was considered to be related (Figure 1a). Two other pairs were identified as related when the rQG estimator was applied (Keskil:Moxsogol, R = 0.295; Radzu:Erel, R = 0.255; the 95th upper quantile = 0.242) (Figure 1b). The ML-Relate program uses simulation to determine which relationships are consistent with genotype data and to compare putative relationships with alternatives. In order to identify possible misclassified individuals, a maximum-likelihood estimator rK estimated by ML-Relate was applied. Besides the three bull-pairs mentioned above, the Erel:Sarial pair (rW = 0.205; rQG = 0.180) had the highest likelihood of being a half-sib (Additional file 2). The same four pairs of Yakutian cryo-bank bulls were also identified as potential half-sibs in the parentage analysis performed using the pedigree reconstruction method among all individuals in the sample (Additional file 4).

Bottom Line: In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population.Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck.The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland.

ABSTRACT

Background: Yakutian cattle, the last remaining native cattle breed in Siberia, are well adapted to the extreme sub-arctic conditions. Nowadays only ca. 1200 purebred animals are left in Yakutia. The semen of six Yakutian bulls was stored in a cryo-bank without any pedigree documentation because of the traditional free herding style of the population.

Methods: To clarify the genetic relatedness between these bulls and to provide recommendations to use their semen in future conservation and breed management programs, we have analysed 30 autosomal microsatellites and mitochondrial DNA sequences in 60 individuals including the six for which semen has been stored. Four relatedness estimators were calculated. In addition, we assessed the value of the cryo-bank bulls for the preservation of genetic variation of the contemporary Yakutian cattle by calculating allelic and gene diversity estimates and mean molecular coancestries.

Results: On the basis of microsatellite variability, including the Yakutian cryo-bank bulls increases the allelic variation in the contemporary population by 3% and in the male subpopulation by 13%. In terms of the mean molecular coancestries, they are less related to the contemporary cow population than the breeding bulls and therefore could be used to reduce inbreeding in the living population. Although 30 loci are insufficient to resolve definitely their relatedness categories, the data suggest four pairs of cryo-bank bulls as possible half-sibs.

Conclusions: Our results show that even relatively limited cryo-bank storage of semen can carry allelic variation through a bottleneck. We propose a breeding scheme based on the rotation of breeding females and the division of cryo-bank bulls into three groups. Thus, if molecular data (e.g. autosomal microsatellite genotypes) for the contemporary population are available and based on relatively small-scale laboratory analyses, it is possible to avoid serious mistakes in their use for breeding applications. The approach suggested here based on the use of Yakutian cryo-bank semen can be easily extended to cryo-bank materials of other animals in future breeding programs.

Show MeSH