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), genomic inbreeding (F), pedigree expected future inbreeding (EFI), and genomic expected future inbreeding (EFI) 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. 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 and EFI with 88 million animals in the pedigree and from 19 h to 28 min (41 times faster) for F and EFI for 3,280,753 genotyped animals of 5 breeds. Correlations were high between F computed using either an allele frequency of 0.5 or a base population frequency for most breeds. Mean F was higher for males than for females, but adjustments for the X chromosome made F means more comparable across sexes. The X adjustments did not affect correlations within sex. After adjusting F for the X chromosome using an allele frequency of 0.5, correlations across breeds and sex increased, and X-adjusted F was more similar to F. Using an allele frequency of 0.5, mean correlation with F across breeds was 0.67 for F, 0.67 for X-adjusted F, and 0.54 for F 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 was 0.64. Revision of inbreeding software allowed simpler and more accurate comparison of genomic and pedigree relationships and much faster computation.