Population structure and genomic inbreeding in nine Swiss dairy cattle populations

Table 3 Number of sires, pedigree completeness index for five generations (PCI_5G), average pedigree inbreeding (F _PED) and average genomic inbreeding (F _HOM, F _ROH and \(F_{{{\text{ROH}} > 5{\text{Mb}}}}\)) for nine Swiss dairy cattle populations

Population	Number of sires	Avg. PCI_5G	Avg. F _PED (± SD) (p < 2.2e−16)*	Avg. F _HOM (± SD) (p < 2.2e−16)*	Avg. F _ROH (± SD) (p < 2.2e−16)*	Avg. \(F_{{{\text{ROH}} > 5Mb}}\) (± SD) (p < 2.2e−16)*
BS	281	0.993	0.071 (± 0.028)^A	0.115 (± 0.037)^A	0.091 (± 0.029)^A	0.084 (± 0.029)^A
BV	3386	0.995	0.059 (± 0.023)^B	0.100 (± 0.039)^B	0.074 (± 0.028)^B	0.067 (± 0.027)^B
OB	167	0.992	0.023 (± 0.017)^C	0.052 (± 0.029)^C	0.029 (± 0.017)^C	0.025 (± 0.016)^C
HO	2568	0.991	0.057 (± 0.023)^D	0.066 (± 0.035)^D	0.058 (± 0.025)^D	0.053 (± 0.025)^D
RH	1960	0.993	0.042 (± 0.022)^E	0.047 (± 0.037)^C	0.045 (± 0.023)^E	0.041 (± 0.023)^E
SF	547	0.992	0.027 (± 0.020)^C	0.012 (± 0.033)^E	0.029 (± 0.021)^C	0.027 (± 0.021)^B
SI	248	0.991	0.028 (± 0.024)^C	0.092 (± 0.030)^B	0.039 (± 0.023)^F	0.033 (± 0.022)^F
ER	36	0.808	0.015 (± 0.012)^C	0.056 (± 0.018)^C,D	0.027 (± 0.014)^C,F	0.022 (± 0.013)^B,F
EV	21	0.358	0.012 (± 0.026)^C	0.109 (± 0.059)^A,B	0.074 (± 0.042)^B,D	0.070 (± 0.041)^A,B,D

BS Brown Swiss, BV Braunvieh, OB Original Braunvieh, HO Holstein, RH Red Holstein, SF Swiss Fleckvieh, SI Simmental, ER Eringer, EV Evolèner
* p value, Kruskal–Wallis test, R: kruskal.test()
^A,B,C,D,E,FDifferent letters indicate significant Bonferroni-adjusted differences between breeds, as assessed in the R-package DUNN.TEST

ISSN: 1297-9686