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Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients

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Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH Wageningen, The Netherlands
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Centre for Genetic Resources the Netherlands, Wageningen University & Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
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Faculty of Agricultural and Environmental Sciences, Kaposvár University, P.O. Box 16, H-7400 Kaposvár, Hungary
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Faculty of Economic Science, Kaposvár University, P.O. Box 16, H-7400 Kaposvár, Hungary
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Author to whom correspondence should be addressed.
Diversity 2020, 12(4), 155; https://doi.org/10.3390/d12040155
Received: 18 March 2020 / Revised: 14 April 2020 / Accepted: 15 April 2020 / Published: 17 April 2020
(This article belongs to the Section Biodiversity Conservation)
To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski’s ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of FANC and FNEW, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The FANC was systematically underestimated and consequently, FNEW was overestimated. To illustrate this bias, we calculated FANC and FNEW by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of FANC and FNEW, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of FANC and FNEW. View Full-Text
Keywords: ancestral inbreeding; new inbreeding; purging; gene dropping; inbreeding depression ancestral inbreeding; new inbreeding; purging; gene dropping; inbreeding depression
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Doekes, H.P.; Curik, I.; Nagy, I.; Farkas, J.; Kövér, G.; Windig, J.J. Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients. Diversity 2020, 12, 155.

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