Improved computation of genomic and pedigree inbreeding and relationships accounting for the X chromosome

Breeders for many decades used pedigrees to limit increases in inbreeding, but genomic measures of relationship and inbreeding provide more precise control. Previous calculations of pedigree inbreeding (F_ped), genomic inbreeding (F_gen), pedigree expected future inbreeding (EFI_ped), and genomic expected future inbreeding (EFI_gen) included the X chromosome but ignored its influence when estimating relationships. The X chromosome contributes to inbreeding in female progeny, for example, if parents with the same X chromosome are mated. Because the X-specific region has 3.0% of the 79,060 markers used in US genomic evaluation and those markers are coded as 100% homozygous in males, homozygosity of females appeared to be 3% less than for males. Allele frequency also affects the computation of F_gen. Programs to compute pedigree and genomic measures were revised to improve speed and memory use, as well as to better account for the X chromosome. Revised software reduced computational time from 33 h to 13 min (152 times faster) using 32 processors for F_ped and EFI_ped with 88 million animals in the pedigree and from 19 h to 28 min (41 times faster) for F_gen and EFI_gen for 3,280,753 genotyped animals of 5 breeds. Correlations were high between F_gen computed using either an allele frequency of 0.5 or a base population frequency for most breeds. Mean F_gen was higher for males than for females, but adjustments for the X chromosome made F_gen means more comparable across sexes. The X adjustments did not affect correlations within sex. After adjusting F_gen for the X chromosome using an allele frequency of 0.5, correlations across breeds and sex increased, and X-adjusted F_gen was more similar to F_ped. Using an allele frequency of 0.5, mean correlation with F_ped across breeds was 0.67 for F_gen, 0.67 for X-adjusted F_gen, and 0.54 for F_gen with base population allele frequency; corresponding EFI correlations were 0.83, 0.83, and 0.84. Breeds with smaller populations were more sensitive to the use of different allele frequencies. Mean correlation of haplotype-based inbreeding with F_ped was 0.64. Revision of inbreeding software allowed simpler and more accurate comparison of genomic and pedigree relationships and much faster computation.