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Nishio M, Inoue K, Ogawa S, Ichinoseki K, Arakawa A, Fukuzawa Y, Okamura T, Kobayashi E, Taniguchi M, Oe M, Ishii K. Comparing pedigree and genomic inbreeding coefficients, and inbreeding depression of reproductive traits in Japanese Black cattle. BMC Genomics 2023; 24:376. [PMID: 37403068 DOI: 10.1186/s12864-023-09480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
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- ([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.
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Affiliation(s)
- Motohide Nishio
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan.
| | - Keiichi Inoue
- University of Miyazaki, Miyazaki, Miyazaki, 889-2192, Japan
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Shinichiro Ogawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Kasumi Ichinoseki
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Aisaku Arakawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Yo Fukuzawa
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Toshihiro Okamura
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Eiji Kobayashi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Masaaki Taniguchi
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Mika Oe
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
| | - Kazuo Ishii
- Institute of Livestock and Grassland Science, NARO, Tsukuba, Ibaraki, 3050901, Japan
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Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A. Fine-tuning genomic and pedigree inbreeding rates in equine population with a deep and reliable stud book: the case of the Pura Raza Española horse. J Anim Sci Biotechnol 2022; 13:127. [PMID: 36336696 PMCID: PMC9639299 DOI: 10.1186/s40104-022-00781-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate Classical (F), Ballou's ancestral, Kalinowski's ancestral, Kalinowski's new and the ancestral history coefficient values. In addition, genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques (methods of moments -FHOM-, the diagonal elements of the genomic -FG-, and hybrid matrixes -FH-) and ROH measures (FRZ). The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse, with proven parenteral information for the last 40 years and a high degree of completeness (over 90% for the last 70 years) will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability. RESULTS The mean values of the pedigree-based inbreeding coefficients ranged from 0.01 (F for the last 3 generations -F3-) to 0.44 (ancestral history coefficient) and the mean values of genomic-based inbreeding coefficients varied from 0.05 (FRZ for three generations, FH and FHOM) to 0.11 (FRZ for nine generations). Significant correlations were also found between pedigree and genomic inbreeding values, which ranged between 0.58 (F3 with FHOM) and 0.79 (F with FRZ). In addition, the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values, and the opposite when ancient values are calculated. CONCLUSIONS Ultimately, our results show that it is still useful to work with a deep and reliable pedigree in pedigree-based genetic studies with very large effective population sizes. Obtaining a satisfactory parameter will always be desirable, but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
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Affiliation(s)
- Davinia Isabel Perdomo-González
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain.
| | - Nora Laseca
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Sebastián Demyda-Peyrás
- Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina
| | - Mercedes Valera
- Departamento Agronomía, Escuela Técnica Superior de Ingeniería Agromómica, Universidad de Sevilla, Ctra Utrera Km 1, 41013, Sevilla, Spain
| | - Isabel Cervantes
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Antonio Molina
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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