PARALLEL ALGORITHM FOR SORTING ANIMAL PEDIGREES

Maciej Gierdziewicz

Abstract


In many analyses of animal genotype with the methods of quantitative genetics there is a needto account for relationships among individuals. Incorrectly calculated relationship coefficientsmay lead to biased estimates. The number of software packages exist which deal with thatproblem; however, in many of them it is assumed that pedigrees of the individuals are sortedchronologically, but in real data sets – containing information on traits and pedigrees – birthdates are often missing. In extreme cases, when (almost) no birth dates are present, theordering must be made by comparing – at least once – each pair of individuals separately,since it is not sufficient to compare adjacent elements in order to check whether the dataset is sorted. Two versions of parallel computer programs were compared, with constant orvariable distance between elements of compared pairs. The results indicate that the secondalgorithm is more efficient.

Keywords


animal breeding; pedigree; chronological order; parallel computing

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References


Boldman K. G., Kriese L. A., Van Vleck L. D., Van Tassel L. A., Kachman S. D.: A manual for use of MTDFREML, a set of programs to obtain estimates of variances and covariances. Clay Center, Nebraska, USA, USDA–ARS 1993

Gilmour A. R., Cullis B. R., Welham S. J., Thompson R.: ASREML reference manual. Harpedden, UK, IACR-Rothamsted Experimental Station 2000

Henderson C. R.: A simple method of computing the inverse of a numerator relationship matrix used for prediction of breeding values. Biometrics, vol. 32, 1976, 69–79

Kennedy B. W., Quinton M., Van Arendonk J. A. M.: Estimation of effects of single genes on quantitative traits. Journal of Animal Science, vol. 70, 1992, 2000–2012

Lidauer M., Mäntysaari E. A., Stranden I., Kettunen A., Poso J.: DMUIOD: A multitrait BLUP program suitable for random regression testday models. [in:] 6th World Congress „Genetics Applied to Livestock Production”, Armidale, NSW, Australia 1988

Lidauer M., Stranden I.: Fast and flexible program for genetic evaluation in dairy cattle. [in:] „International Workshop On Computational Cattle Breeding”, Tuusula, Finland 1999

Quaas R. L.: Transformed mixed model equations. A recursive algorithm to eliminate A−1. Journal of Dairy Science, vol. 72, 1989, 1937–1941

Stranden I., Lidauer M.: Parallel Computing Applied to Breeding Value Estimation in Dairy Cattle. Journal of Dairy Science, vol. 84, 2001, 276–285

Zhang Z., Li C., Todhunter R. J., Lust G., Goonewardene L., Wang Z.: An Algorithm to Sort Complex Pedigrees Chronologically without Birthdates. Journal of Animal and Veterinary Advances, vol. 8, 2009, 177–182




DOI: https://doi.org/10.7494/csci.2009.10.3.57

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