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Haque MA, Iqbal A, Bae H, Lee SE, Park S, Lee YM, Kim JJ. Assessment of genomic breeding values and their accuracies for carcass traits in Jeju Black cattle using whole-genome SNP chip panels. J Anim Breed Genet 2023; 140:519-531. [PMID: 37102238 DOI: 10.1111/jbg.12776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/28/2023]
Abstract
The objective of the present study was to evaluate the breeding value and accuracy of genomic estimated breeding values (GEBVs) of carcass traits in Jeju Black cattle (JBC) using Hanwoo steers and JBC as a reference population using the single-trait animal model. Our research included genotype and phenotype information on 19,154 Hanwoo steers with 1097 JBC acting as the reference population. Likewise, the test population consisted of 418 genotyped JBC individuals with no phenotypic records for those carcass traits. For estimating the accuracy of GEBV, we divided the entire population into three groups. Hanwoo and JBC make up the first group; Hanwoo and JBC, who has both the genotype and phenotypic records, are referred to as the reference (training) population, and JBC, who lacks phenotypic information is referred to as the test (validation) population. The second group consists of the JBC (without phenotype) as the test population and Hanwoo as a reference population with phenotype and genotypic data. The only JBCs in the third group are those who have genotypic and phenotypic data on them as a reference population but no phenotypic data on them as a test population. The single-trait animal model was used in all three groups for statistical purposes. The reference populations estimated heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) as 0.30, 0.26, 0.26, and 0.34 for the Hanwoo steer and 0.42, 0.27, 0.26, and 0.48 for JBC. The average accuracy for carcass traits in Group 1 was 0.80 for the Hanwoo and JBC reference population compared with 0.73 for the JBC test population. Although the average accuracy for carcass traits in Group 2 was 0.80, it was 0.80 for the Hanwoo reference population and only 0.56 for the JBC test population. The average accuracy for the JBC reference and test populations was 0.68 and 0.50, respectively, when they were included in the accuracy comparison without the Hanwoo reference population. Groups 1 and 2 used Hanwoo as reference population, which led to a better average accuracy; however, Group 3 only used the JBC reference and test population, which led to a lower average accuracy. This might be due to the fact that Group 3 used a smaller reference size than the group that came before it and that the genetic makeup of the Hanwoo and JBC breeds differed. The GEBV accuracy for MS was higher than that of other traits across all three analysis groups, followed by CWT, EMA, and BF, which may be partially explained by the MS traits' higher heritability. This study suggests that in order to achieve more accuracy, a large reference population particular to a breed should be established. Therefore, to increase the accuracy of GEBV prediction and the genetic benefit from genomic selection in JBC, individual reference breeds, and large populations are required.
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Affiliation(s)
- Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Asif Iqbal
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Haechang Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Seung Eun Lee
- Department of Biomedical Informatics, Jeju National University, Jeju, Korea
| | - Sepil Park
- Department of Biomedical Informatics, Jeju National University, Jeju, Korea
| | - Yun Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
| | - Jong Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, Korea
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Rostamzadeh Mahdabi E, Tian R, Li Y, Wang X, Zhao M, Li H, Yang D, Zhang H, Li S, Esmailizadeh A. Genomic heritability and correlation between carcass traits in Japanese Black cattle evaluated under different ceilings of relatedness among individuals. Front Genet 2023; 14:1053291. [PMID: 36816045 PMCID: PMC9928846 DOI: 10.3389/fgene.2023.1053291] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 01/18/2023] [Indexed: 02/04/2023] Open
Abstract
The investigation of carcass traits to produce meat with high efficiency has been in focus on Japanese Black cattle since 1972. To implement a successful breeding program in carcass production, a comprehensive understanding of genetic characteristics and relationships between the traits is of paramount importance. In this study, genomic heritability and genomic correlation between carcass traits, including carcass weight (CW), rib eye area (REA), rib thickness (RT), subcutaneous fat thickness (SFT), yield rate (YI), and beef marbling score (BMS) were estimated using the genomic data of 9,850 Japanese Black cattle (4,142 heifers and 5,708 steers). In addition, we investigated the effect of genetic relatedness degree on the estimation of genetic parameters of carcass traits in sub-populations created based on different GRM-cutoff values. Genome-based restricted maximum likelihood (GREML) analysis was applied to estimate genetic parameters. Using all animal data, the heritability values for carcass traits were estimated as moderate to relatively high magnitude, ranging from 0.338 to 0.509 with standard errors, ranging from 0.014 to 0.015. The genetic correlations were obtained low and negative between SFT and REA [-0.198 (0.034)] and between SFT and BMS [-0.096 (0.033)] traits, and high and negative between SFT and YI [-0.634 (0.022)]. REA trait was genetically highly correlated with YI and BMS [0.811 (0.012) and 0.625 (0.022), respectively]. In sub-populations created based on the genetic-relatedness ceiling, the heritability estimates ranged from 0.212 (0.131) to 0.647 (0.066). At the genetic-relatedness ceiling of 0.15, the correlation values between most traits with low genomic correlation were overestimated while the correlations between the traits with relatively moderate to high correlations, ranging from 0.380 to 0.811, were underestimated. The values were steady at the ceilings of 0.30-0.95 (sample size of 5,443-9,850) for most of the highly correlated traits. The results demonstrated that there is considerable genetic variation and also favorable genomic correlations between carcass traits. Therefore, the genetic improvement for the traits can be simultaneously attained through genomic selection. In addition, we observed that depending on the degree of relationship between individuals and sample size, the genomic heritability and correlation estimates for carcass traits may be different.
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Affiliation(s)
| | - Rugang Tian
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China,*Correspondence: Rugang Tian, ; Ali Esmailizadeh,
| | - Yuan Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Xiao Wang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Meng Zhao
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hui Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ding Yang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Hao Zhang
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - SuFan Li
- Institute of Animal Husbandry, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran,*Correspondence: Rugang Tian, ; Ali Esmailizadeh,
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Mehrban H, Naserkheil M, Lee DH, Ibáñez-Escriche N. Genetic parameters and correlations of related feed efficiency, growth, and carcass traits in Hanwoo beef cattle. Anim Biosci 2020; 34:824-832. [PMID: 32898962 PMCID: PMC8100466 DOI: 10.5713/ajas.20.0135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/14/2020] [Indexed: 11/27/2022] Open
Abstract
Objective This study aimed to estimate the genetic parameters and genetic correlations for related feed efficiency, growth, and carcass traits in Hanwoo cattle. Methods Phenotypic data from 15,279 animals born between 1989 and 2015 were considered. The related feed efficiency traits considered were Kleiber ratio (KR) and relative growth rate (RGR). Carcass traits analyzed were backfat thickness (BT), carcass weight, eye muscle area, and marbling score. Growth traits were assessed by the average daily gain (ADG), metabolic body weight (MBW) at mid-test age from 6 to 24 months, and yearling weight (YW). Variance and covariance components were estimated using restricted maximum likelihood using nine multi-trait animal models. Results The heritability estimates for related feed efficiency (0.28±0.04 for KR and RGR) and growth traits (0.26±0.02 to 0.33±0.04) were moderate, but the carcass traits tended to be higher (0.38±0.04 to 0.61±0.06). The related feed efficiency traits were positively genetically correlated with all the carcass traits (0.37±0.09 to 0.47±0.07 for KR, and 0.14±0.09 to 0.37±0.09 for RGR), except for BT, which showed null to weak correlation. Conversely, the genetic correlations of RGR with MBW (−0.36±0.08) and YW (−0.30±0.08) were negative, and those of KR with MBW and YW were close to zero, whereas the genetic correlations of ADG with RGR (0.40±0.08) and KR (0.70±0.05) were positive and relatively moderate to high. The genetic (0.92±0.02) correlations between KR and RGR were very high. Conclusion Sufficient genetic variability and heritability were observed for traits of interest. Moreover, the inclusion of KR and/or RGR in Hanwoo cattle breeding programs could improve the feed efficiency without producing any unfavorable effects on the carcass traits.
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Affiliation(s)
- Hossein Mehrban
- Animal Science, Shahrekord University, Shahrekord, Charmahalo-Bakhteiari 88186-34141, Iran
| | | | - Deuk Hwan Lee
- Animal Life and Environment Sciences, Hankyong National University, Anseong 17579, Korea
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, València 46022, Spain
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Direct and maternal genetic parameters for measures of feed consumption and feed efficiency in young male Japanese Black cattle. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hoque M, Hosono M, Suzuki K. Genetic parameters for dry matter, energy and protein intake, and their relationships with performance and carcass traits in Japanese Black cattle. J Anim Breed Genet 2009; 126:14-21. [DOI: 10.1111/j.1439-0388.2008.00752.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hoque MA, Hosono M, Oikawa T, Suzuki K. Genetic parameters for measures of energetic efficiency of bulls and their relationships with carcass traits of field progeny in Japanese Black cattle1. J Anim Sci 2009; 87:99-106. [DOI: 10.2527/jas.2007-0766] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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