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

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 geno...

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Autores principales: Nishio, Motohide, Inoue, Keiichi, Ogawa, Shinichiro, Ichinoseki, Kasumi, Arakawa, Aisaku, Fukuzawa, Yo, Okamura, Toshihiro, Kobayashi, Eiji, Taniguchi, Masaaki, Oe, Mika, Ishii, Kazuo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321020/
https://www.ncbi.nlm.nih.gov/pubmed/37403068
http://dx.doi.org/10.1186/s12864-023-09480-5
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author Nishio, Motohide
Inoue, Keiichi
Ogawa, Shinichiro
Ichinoseki, Kasumi
Arakawa, Aisaku
Fukuzawa, Yo
Okamura, Toshihiro
Kobayashi, Eiji
Taniguchi, Masaaki
Oe, Mika
Ishii, Kazuo
author_facet Nishio, Motohide
Inoue, Keiichi
Ogawa, Shinichiro
Ichinoseki, Kasumi
Arakawa, Aisaku
Fukuzawa, Yo
Okamura, Toshihiro
Kobayashi, Eiji
Taniguchi, Masaaki
Oe, Mika
Ishii, Kazuo
author_sort Nishio, Motohide
collection PubMed
description 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- ([Formula: see text] ) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text] ), correlation between uniting gametes ([Formula: see text] ), the observed vs expected number of homozygous genotypes ([Formula: see text] ), runs of homozygosity (ROH) segments ([Formula: see text] ) and heterozygosity by descent segments ([Formula: see text] ). 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 [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text] , with range 0.33–0.55. Except for [Formula: see text] and [Formula: see text] , there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text] . In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] 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 [Formula: see text] . CONCLUSIONS: Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text] . In particular, [Formula: see text] and [Formula: see text] 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09480-5.
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spelling pubmed-103210202023-07-06 Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle Nishio, Motohide Inoue, Keiichi Ogawa, Shinichiro Ichinoseki, Kasumi Arakawa, Aisaku Fukuzawa, Yo Okamura, Toshihiro Kobayashi, Eiji Taniguchi, Masaaki Oe, Mika Ishii, Kazuo BMC Genomics Research 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- ([Formula: see text] ) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ([Formula: see text] ), correlation between uniting gametes ([Formula: see text] ), the observed vs expected number of homozygous genotypes ([Formula: see text] ), runs of homozygosity (ROH) segments ([Formula: see text] ) and heterozygosity by descent segments ([Formula: see text] ). 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 [Formula: see text] were for [Formula: see text] (0.86) and [Formula: see text] (0.85) whereas [Formula: see text] and [Formula: see text] provided weak correlations with [Formula: see text] , with range 0.33–0.55. Except for [Formula: see text] and [Formula: see text] , there were strong correlations among genome-based inbreeding coefficients ([Formula: see text] 0.94). The estimates of regression coefficients of inbreeding depression for [Formula: see text] was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but [Formula: see text] had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than [Formula: see text] . In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for [Formula: see text] had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, [Formula: see text] 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 [Formula: see text] . CONCLUSIONS: Genome-based inbreeding coefficients can capture more phenotypic variation than [Formula: see text] . In particular, [Formula: see text] and [Formula: see text] 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09480-5. BioMed Central 2023-07-05 /pmc/articles/PMC10321020/ /pubmed/37403068 http://dx.doi.org/10.1186/s12864-023-09480-5 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Nishio, Motohide
Inoue, Keiichi
Ogawa, Shinichiro
Ichinoseki, Kasumi
Arakawa, Aisaku
Fukuzawa, Yo
Okamura, Toshihiro
Kobayashi, Eiji
Taniguchi, Masaaki
Oe, Mika
Ishii, Kazuo
Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title_full Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title_fullStr Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title_full_unstemmed Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title_short Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle
title_sort comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in japanese black cattle
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10321020/
https://www.ncbi.nlm.nih.gov/pubmed/37403068
http://dx.doi.org/10.1186/s12864-023-09480-5
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