Original scientific paper
Runs of Homozygosity Reveal Genome-wide Autozygosity in the Austrian Fleckvieh Cattle
Maja Ferencakovic
; University of Zagreb, Faculty of Agriculture, Department of Animal Science, Svetošimunska 25, 10000 Zagreb, Croatia
Edin Hamzic
; University of Natural Resources and Life Sciences Vienna, Department of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria
Birgit Gredler
; University of Natural Resources and Life Sciences Vienna, Department of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria
Ino Curik
; University of Zagreb, Faculty of Agriculture, Department of Animal Science, Svetošimunska 25, 10000 Zagreb, Croatia
Johann Sölkner
; University of Natural Resources and Life Sciences Vienna, Department of Sustainable Agricultural Systems, Division of Livestock Sciences, Gregor Mendel Str. 33, A-1180 Vienna, Austria
Abstract
Runs of homozygosity (ROH) are recognized as potential inbreeding measure in studies on humans. Inbreeding coefficients derived from ROH (FROH) measure proportion of the genome arranged in long homozygous segments and highly correlate with those derived from pedigree (Fped). From that we assumed that ROH represent an alternative to pedigree inbreeding levels in studies on animals too, because pedigree can be incorrect, incomplete and can not fully explain what happened in meiosis. To confirm our premise we used pedigree and genotype data from 500 Austrian dual purpose Simmental bulls to determine correlation between FROH and Fped. ROH were obtainedusing Fortran 90 soft ware created by the authors. Proportions of genome in ROH were calculated for lengths of ROH of >1, >2, >4, >8 and >16 Mb. Pedigree data were analyzed and inbreeding coefficients for complete pedigree (FpedT) and five generations (Fped5) were calculated using ENDOG soft ware. We found low FpedT and Fped5 (means of 1.5% and 0.9%) while FROH for segments >1Mb suggested much higher values (9.0%) indicating old inbreeding that can not be traced using pedigree. The highest correlations were found between FROH calculated from ROH of length >4Mb and FpedT (0.68) that is consistent with studies on humans. We conclude that inbreeding coefficients derived from ROH are useful for measuring levels of inbreeding in cattle, because ROH are not subject to mistakes as pedigrees and calculations made from those.
Keywords
inbreeding; runs of homozygosity; genome-wide autozygosity; pedigree; cattle
Hrčak ID:
72108
URI
Publication date:
4.10.2011.
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