Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
Authors: Nishio Motohide , Inoue Keiichi , Ogawa Shinichiro , Ichinoseki Kasumi , Arakawa Aisaku , Fukuzawa Yo , Okamura Toshihiro , Kobayashi Eiji , Taniguchi Masaaki , Oe Mika , Ishii Kazuo 
Published: July 2023

Abstract
Background
Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ($${F}_{PED}$$

F

PED

) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ($${F}_{GRM}$$

F

GRM

), correlation between uniting gametes ($${F}_{UNI}$$

F

UNI

), the observed vs expected number of homozygous genotypes ($${F}_{HOM}$$

F

HOM

), runs of homozygosity (ROH) segments ($${F}_{ROH}$$

F

ROH

) and heterozygosity by descent segments ($${F}_{HBD}$$

F

HBD

). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle.

Results
The highest correlations with $${F}_{PED}$$

F

PED

were for $${F}_{ROH}$$

F

ROH

(0.86) and $${F}_{HBD}$$

F

HBD

(0.85) whereas $${F}_{GRM}$$

F

GRM

and $${F}_{UNI}$$

F

UNI

provided weak correlations with $${F}_{PED}$$

F

PED

, with range 0.33–0.55. Except for $${F}_{GRM}$$

F

GRM

and $${F}_{UNI}$$

F

UNI

, there were strong correlations among genome-based inbreeding coefficients ($$\ge$$
≥
0.94). The estimates of regression coefficients of inbreeding depression for $${F}_{PED}$$

F

PED

was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but $${F}_{PED}$$

F

PED

had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than $${F}_{PED}$$

F

PED

. In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for $${F}_{UNI}$$

F

UNI

had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, $${F}_{ROH}$$

F

ROH

provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for $${F}_{HBD}$$

F

HBD

.

Conclusions
Genome-based inbreeding coefficients can capture more phenotypic variation than $${F}_{PED}$$

F

PED

. In particular, $${F}_{ROH}$$

F

ROH

and $${F}_{HBD}$$

F

HBD

can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.