Age of admixture; Breed composition; Breeds; Cattle; Genetics; Swiss Fleckvieh
Abstract :
[en] The aim of this study was to predict individual age of admixture in the crossbred Swiss Fleckvieh population. We checked how well the method is dealing with recent admixture with high throughput single nucleotide polymorphism data from the bovine 50K SNP Chip. A total of 101 Red Holstein, 91 Simmental, and 308 crossed animals were available for analysis. Age of admixture was derived from the complete pedigree and molecular markers. The method applied (using SABER software) based on Markov-hidden Markov model was able to derive age of admixture similar to estimates of pedigree data, however the values were often overestimated. Of 21 investigated cases, results from SNP data reflected paternal and maternal age of admixture well for 9 cases but provided results out of range for the other 12 cases. Alternative methods based on breed-specific haplotype blocks need to be evaluated in the future.
Disciplines :
Genetics & genetic processes Animal production & animal husbandry
Author, co-author :
Frkonja, A.; Univ. of Natural Resources and Life Sciences Vienna, Dept. of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria
Druet, Tom ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Curik, I.; Univ. of Zagreb, Fac. of Agriculture, Dept. of Livestock Sciences, Svetosimunska 25, 10000 Zagreb, Croatia
Sölkner, J.; Univ. of Natural Resources and Life Sciences Vienna, Dept. of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria
Language :
English
Title :
Estimating age of admixture in a cattle population based on SNP chip data
Publication date :
2012
Journal title :
Acta Agriculturae Slovenica
ISSN :
1581-9175
eISSN :
1854-1941
Publisher :
Biotehniske Fakultete Univerze v Ljubljani, Slovenia
Falush D., Stephens M., Pritchard J. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164: 1567-1587
Freeman A. R., Hoggart C. J., Hanotte O., Bradley D. G. 2006. Assessing the Relative Ages of Admixture in the Bovine Hybrid Zones of Africa and the Near East Using X ChromosomeHaplotype Mosaicism. Genetics, 173: 1503-1510
Frkonja A., Gredler B., Schnyder U., Curik I., Solkner J. 2012. Prediction of breed composition in an admixed cattle population. Animal genetics (in press). DOI: 10.1111/j.1365-2052.2012.02345.x
Pritchard J. K., Wen X., Falush D. 2010. Documentation for Structure software, Version 2.3. http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/structure_doc.pdf (14 Jan. 2011)
Pritchard J., Stephens M., Donnelly P. 2000. Inference of popu lation structure using multilocus genotype data. Genetics, 155: 945-959
Pugach I., Matveyev R., Wollstein A., Kayser M., Stoneking M. 2011. Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biology. 12: R19.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC.2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81, 3: 559-575
Tang H., Choudhry S., Mei R., Morgan M., Rodriguez-Cintron W., Gonza'lez Burchard E., Risch, N.J. 2007. Recent Genetic Selection in the Ancestral Admixture of Puerto Ricans. The American Journal of Human Genetics, 81: 626-633
