Performance of using opposing homozygotes for paternity testing in Japanese Black cattle

Komiya, Ryota; Ogawa, Shinichiro; Aonuma, Tatsuya; Satoh, Masahiro

doi:10.1111/jbg.12649

“…Figure 1 shows a histogram of MAFs in the 575 cows for the 36,426 SNP markers used in the ssGBLUP approach. The shape of the histogram is similar to those in previous studies on different Japanese Black cattle populations [37][38][39]; that is, the proportion of SNPs with low MAFs was slightly greater than that of the others. The ET center introduces cows from various parts of Japan to meet a wide demand of embryo buyers, which might confer results on the MAF distribution similar to those in previous studies.…”

Section: Comparing a And G Matrices For The 575 Cowssupporting

confidence: 82%

Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows

Zoda

¹

,

Ogawa

²

,

Kagawa

³

et al. 2023

Biology

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We assessed the performance of single-step genomic prediction of breeding values for superovulatory response traits in Japanese Black donor cows. A total of 25,332 records of the total number of embryos and oocytes (TNE) and the number of good embryos (NGE) per flush for 1874 Japanese Black donor cows were collected during 2008 and 2022. Genotype information on 36,426 autosomal single-nucleotide polymorphisms (SNPs) for 575 out of the 1,874 cows was used. Breeding values were predicted exploiting a two-trait repeatability animal model. Two genetic relationship matrices were used, one based on pedigree information (A matrix) and the other considering both pedigree and SNP marker genotype information (H matrix). Estimated heritabilities of TNE and NGE were 0.18 and 0.11, respectively, when using the H matrix, which were both slightly lower than when using the A matrix (0.26 for TNE and 0.16 for NGE). Estimated genetic correlations between the traits were 0.61 and 0.66 when using H and A matrices, respectively. When the variance components were the same in breeding value prediction, the mean reliability was greater when using the H matrix than when using the A matrix. This advantage seems more prominent for cows with low reliability when using the A matrix. The results imply that introducing single-step genomic prediction could boost the rate of genetic improvement of superovulatory response traits, but efforts should be made to maintain genetic diversity when performing selection.

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“…GCA I,popB , GCX I,popB , GCY I,popB , and GCM I,popB of each G1 mouse to G8 population were calculated using pedigree information with errors. According to estimated pedigree error rates by previous studies (e.g., [17][18][19]), the error size was set to 1%, 2%, 4%, 8%, and 16% of the total number of known parents (Table 2). Within the same error rate, we ran this simulation for 10,000 iterations to obtain the root mean squared error (RMSE) of the average genetic contributions calculated with and without pedigree errors.…”

Section: Discussionmentioning

confidence: 99%

“…Pedigree errors could have effects not only on genetic diversity evaluation but also on genetic parameter estimation, breeding value prediction, evaluating the degree of inbreeding and inferring inbreeding depression, and so on (e.g., [20,21,64]). Thus, efforts should be still paid to collect and accumulate accurate pedigree information (e.g., [19,65,66]). 1 GCA I,popB , GCX I,popB , GCY I,popB , and GCM I,popB average genetic contribution of individual I to target population B with respect to genes on autosomes, X chromosome, Y chromosome, and mitochondrial DNA, respectively.…”

Section: Effect Of Pedigree Errors On Genetic Contribution Calculationmentioning

confidence: 99%

“…Therefore, developing a tool to effectively manage and secure genetic diversity is an urgent need (e.g., [14][15][16]). Existing theories assume the use of 100% accurate pedigree data, although low but nonzero pedigree error rates, partly due to human errors, have been reported (e.g., [17][18][19]). This indicates the importance of investigating the effect of pedigree error on evaluation of genetic diversity (e.g., [20][21][22]).…”

Section: Introductionmentioning

confidence: 99%

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Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

Ogawa

¹

,

Satoh

²

2022

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The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population. Here, we developed a method to calculate the genetic contribution with respect to genes on sex chromosomes and mitochondrial DNA through pedigree analysis. To demonstrate the performance, we applied the methods for calculating genetic contributions to example pedigree data. To verify the results of genetic contribution calculations, we performed gene-dropping simulations mimicking flows of genes on autosomes, X and Y chromosomes, and mitochondrial DNA, and then compared the results from the simulation with the corresponding genetic contributions. To investigate the effect of pedigree error, we compared the results of genetic contribution calculations using pedigree data with and without errors. The results of gene-dropping simulation showed good agreement with the results of the genetic contribution calculation. The effect of pedigree errors on the calculation of genetic contribution depended on the error rate. Since the patterns of the genetic contributions of such genes might be different from those on autosomes, the novel approach could provide new information on the genetic composition of populations. The results are expected to contribute to the development of methods for sustainable breeding and population management.

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“…The quality of imputation using this reference population was valid for genomic prediction and genome-wide association study [ 35 , 36 ]. Moreover, several studies previously evaluated the genetic diversity and structure in Japanese Black cattle using BovineSNP50 BeadChip or GGP BovineLD v4.0 [ 37 – 39 ]. All SNP were filtered for call rate < 95%, minor allele frequency (MAF) < 0.01 and extreme deviation from Hardy–Weinberg equilibrium ( p < 0.0001).…”

Section: Methodsmentioning

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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Performance of using opposing homozygotes for paternity testing in Japanese Black cattle

Cited by 7 publications

References 55 publications

Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows

Single-Step Genomic Prediction of Superovulatory Response Traits in Japanese Black Donor Cows

Genetic Contributions of Genes on Sex Chromosomes and Mitochondrial DNA in a Pedigreed Population

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

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