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grain : a computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach
Author(s) -
Baumung R.,
Farkas J.,
Boichard D.,
Mészáros G.,
Sölkner J.,
Curik I.
Publication year - 2015
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1111/jbg.12145
Subject(s) - inbreeding , pedigree chart , inbreeding depression , biology , statistics , allele , evolutionary biology , genetics , mathematics , gene , demography , population , sociology
Summary GR ain is freely available software intended to enable and promote testing of hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various coefficients from large and complex pedigrees. GR ain calculates, together with the ‘classical’ inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou, (1997) J. Hered ., 88 , 169 and Kalinowski et al ., (2000) Conserv. Biol ., 14 , 1375 as well as an ancestral history coefficient ( A HC ), defined here for the first time. A HC is defined as the number that tells how many times during pedigree segregation (gene dropping) a randomly taken allele has been in IBD status. Furthermore, GR ain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors by calculating partial coefficients for all previously obtained coefficients.