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Inbreeding is usually analysed in terms of autosomes. In contrast, inbreeding on the X- chromosome is rarely studied, although it could be quite different because genes on X-chromosome loci have different genomic population dynamics than autosomal loci. Therefore, inbreeding on the X chromosome should be analysed because it could contribute significantly to inbreeding depression in some traits, such as reproduction. The main objective of this study was to compare inbreeding coefficients on the autosomal (FX) and X- chromosome (FXsex) based on pedigree and genomic data (FROH and FROHsex) in the Old Kladruber horse. We estimated autosomal and X-chromosomal inbreeding coefficients using pedigree (9, 173 individuals) and genomic (180 individuals) data. The mean of complete generation equivalents of genotyped animals was 15.5. Genomic inbreeding coefficients for the X-chromosome (3, 154 SNPs) and autosomes were estimated for ROH>4Mb and ROH>8Mb, respectively. The mean inbreeding coefficients for FXsex and FX in the pedigree were 0.18 (range of 0.01 to 0.40) and 0.13 (range of 0.03 to 0.23), respectively, with a ratio of FXsex/ FX of 1.3. The mean genomic inbreeding coefficients FROHsex>4Mb (0.17, range from 0.00 to 0.72) and FROHsex>8Mb (0.12, range from 0.00 to 0.65) were higher than the estimates from the autosomes of FROH>4Mb (0.11, range from 0.00 to 0.22) and FROHsex>8Mb (0.07, range from 0.00 to 0.10), respectively. More specifically, the FROHsex>4Mb/FROH>4Mb ratio was 1.6 and the FROH- sex>8Mb/FROH>8Mb ratio was 1.7, which was higher than the 1.3 observed between pedigree estimates. Correlations between autosomal and X-chromosomes were highest for pedigree-based estimates (0.65) compared to genomic inbreeding coefficients for distant, ROH>4Mb (0.21) and close ROH>8Mb (0.19) inbreeding. The inbreeding estimates for the X- chromosome showed higher variability, most likely influenced by higher genetic drift. This analysis showed that the X-chromosome, although often ignored, can make an important contribution to the understanding of inbreeding and its negative consequences. Supported by projects QK1910156, MZE-RO0719, and ANAGRAMS-IP -2018-01-8708. |
