Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population

Zhuo, Yue; Ning, Chao; Zhou, Lei; Liu, Jianfeng

doi:10.1093/g3journal/jkac118

“…In this study, the estimates of , and provided negative values with means below that of . These results were consistent with previous studies of pig [ 54 ] and dairy cattle [ 55 ]. In particular, the minimum value of was the smallest ( ) among all inbreeding coefficients.…”

Section: Discussionsupporting

confidence: 94%

“…Dadousis et al [ 55 ] reported that correlations between and were > 0.85. Zhang et al [ 54 ] also showed that correlations among , and were > 0.85. The correlations between and genome-based inbreeding coefficients obtained in this study were higher than those reported in several previous studies [ 57 , 59 , 60 ].…”

Section: Discussionmentioning

confidence: 99%

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

Nishio

¹

,

Inoue

²

,

Ogawa

³

et al. 2023

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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.

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“…Empirical studies on the performance of molecular markers in estimating ID typically involve samples from multiple generations, which allows for a wide range of inbreeding coefficients among individuals, which facilitates estimation accuracy. For example, most studies include pedigrees spanning seven to 12 pedigree generations (Antonios et al, 2021 ; Bérénos et al, 2016 ; Doekes et al, 2019 ; Ferenčaković et al, 2017 ; Makanjuola et al, 2020 ; Martikainen et al, 2017 ; Zhang et al, 2022 ), with some studies covering more than 20 generations (Saura et al, 2015 ; Silió et al, 2013 ; Sumreddee et al, 2019 ) and a few spanning fewer than five generations (Hidalgo et al, 2021 ; Pryce et al, 2014 ). These studies are also characterized by involving large sample sizes, exceeding 1000 individuals and sometimes reaching over 20,000 individuals (Doekes et al, 2019 ; Makanjuola et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions

Pérez‐Pereira

¹

,

Quesada

²

,

Caballero

³

2023

Evolutionary Applications

1

0

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Inbreeding depression (ID), the reduction in fitness due to inbreeding, is typically measured by the regression of the phenotypic values of individuals for a particular trait on their corresponding inbreeding coefficients (F). While genealogical records can provide these coefficients, they may be unavailable or incomplete, making molecular markers a useful alternative. The power to detect ID and its accuracy depend on the variation of F values of individuals, the sample sizes available, and the accuracy in the estimation of individual fitness traits and F values. In this study, we used Drosophila melanogaster to evaluate the effectiveness of molecular markers in estimating ID under suboptimal conditions. We generated two sets of 100 pairs of unrelated individuals from a large panmictic population and mated them for two generations to produce non‐inbred and unrelated individuals (F = 0) and inbred individuals (full‐sib progeny; F = 0.25). Using these expected genealogical F values, we calculated inbreeding depression for two fitness‐related traits, pupae productivity and competitive fitness. We then sequenced the males from 17 non‐inbred pairs and 17 inbred pairs to obtain their genomic inbreeding coefficients and estimate ID for the two traits. The scenario assumed was rather restrictive in terms of estimation of ID because: (1) the individuals belonged to the same generation of a large panmictic population, leading to low variation in individual F coefficients; (2) the sample sizes were small; and (3) the traits measured depended on both males and females while only males were sequenced. Despite the challenging conditions of our study, we found that molecular markers provided estimates of ID that were comparable to those obtained from simple pedigree estimations with larger sample sizes. The results therefore suggest that genomic measures of inbreeding are useful to provide estimates of inbreeding depression even under very challenging scenarios.

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“…Recently, increased inbreeding has become a concern in livestock populations, as it can be an unwanted consequence of both artificial selection and the widespread use of reproductive biotechnology. It can negatively affect economically important traits, such as fitness, health, reproduction, adaptability, performance and yield (Antonios et al, 2021;Azcona et al, 2020;Doekes et al, 2020Doekes et al, , 2021Zhang et al, 2022). There are three genetic mechanisms which may cause inbreeding depression: partial dominance, overdominance and epistasis.…”

Section: Introductionmentioning

confidence: 99%

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity

Laseca,

Ziadi,

Perdomo‐Gonzalez

et al. 2024

J Animal Breeding Genetics

1

0

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Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic‐level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility is only moderate compared to other livestock species. To explore this further, we evaluated the effect of inbreeding on five reproductive traits (age at first foaling (AFF), average interval between foalings (AIF), total number of foalings (NF), productive life (PL) and reproductive efficiency (RE)) in Pura Raza Español mares using genomic data. Residual predicted phenotypes were obtained by purging these traits through the REML (wgResidual) and ssGREML (gResidual) approaches in reproductive data of 29,847 PRE mares using the BLUPF90+ program. Next, we used pedigree‐based (Fped) and ROH‐based genomic (FROH) inbreeding coefficients derived from 1018 animals genotyped with 61,271 SNPs to estimate the inbreeding depression (linear regression). Our results indicated significant levels of inbreeding depression for all reproductive traits, with the exception of the AIF trait when Fped was used. However, all traits were negatively affected by the increase in genomic inbreeding, and FROH was found to capture more inbreeding depression than Fped. Likewise, REML models (ssGREML) using genomic data for estimated predicted residual phenotypes resulted in higher variance explained by the model compared with the models not using genomics (REML). Finally, a segmented regression analysis was conducted to evaluate the effect of inbreeding depression, revealing that the levels of genealogical and genomic homozygosity do not manifest uniformly in reproductive traits. In contrast, the levels of inbreeding depression ranged from low to high as homozygosity increased. This analysis also showed that reproductive traits are very sensitive to inbreeding depression, even with relatively low levels of homozygosity.

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Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population

Cited by 8 publications

References 41 publications

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

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

An empirical evaluation of the estimation of inbreeding depression from molecular markers under suboptimal conditions

Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity

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