Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle

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.

Detecting inbreeding depression in structured populations

“…By analyzing the phenotypes of a large simulated pedigreed polygamous population with strong family structure as well as subsets of the 1,000 genomes project ( 33 ), we demonstrated that, despite population or family structure, ID strength can be efficiently estimated if the data are analyzed with a mixed model including the genomic relationships among individuals as a random effect. While the use of a relationship matrix as a random factor in mixed models for quantitative genetics analyses is standard ( 34 ), and GRMs have been used for the estimation of heritability ( 18 , 35 – 37 ) and in GWAS ( 18 , 37 – 41 ) for a long time, it is seldom used to quantify ID [see McQuillan et al ( 42 ) for a notable exception; we did not discover any follow-up papers using a similar approach until Nishio et al ( 43 ) who used the GCTA based GRM in 2023, although Stoffel et al ( 44 ) use a model with breeding values as random effects]. We evaluate the ability of the LMM approach (including different GRMs) to quantify ID and compare it to the classical LM.…”

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

“…The level of inbreeding in a population is an important parameter for monitoring its genetic diversity and its management. High levels of inbreeding cause inbreeding depression and should be avoided in farm animals [ 49 ]. Moreover, increasing inbreeding is associated with negative effects on the production and reproductive characteristics of dairy cows [ 50 , 51 ].…”

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

“…The calculation of genomic inbreeding coefficients using ROH can be utilized to assess inbreeding in a species or population. A significant advantage of estimating these genomic inbreeding coefficients lies in the availability of chromosomal inbreeding coefficients [ 42 ]. Long ROHs reflect recent generations of inbreeding, while short ROHs indicate more distant generations of inbreeding.…”