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Sood V, Rodas-González A, Valente TS, Virtuoso MCS, Li C, Lam S, López-Campos Ó, Segura J, Basarab J, Juárez M. Genome-wide association study for primal cut lean traits in Canadian beef cattle. Meat Sci 2023; 204:109274. [PMID: 37437385 DOI: 10.1016/j.meatsci.2023.109274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
This study identified genomic variants and underlying candidate genes related to the whole carcass and individual primal cut lean content in Canadian commercial crossbred beef cattle. Genotyping information of 1035 crossbred beef cattle were available alongside estimated and actual carcass lean meat yield and individual primal cut lean content in all carcasses. Significant fixed effects and covariates were identified and included in the animal model. Genome-wide association analysis were implemented using the weighted single-step genomic best linear unbiased prediction (WssGBLUP). A number of candidate genes identified linked to lean tissue production were unrelated to estimated lean meat yield and were specific to the actual lean traits. Among these, 41 genes were common for actual lean traits, on specific regions of BTA4, BTA13 and BTA25 indicating potential involvement in lean mass synthesis. Therefore, the results suggested the inclusion of primal cut lean traits as a selection objective in breeding programs with consideration of further functional studies of the identified genes could help in optimizing lean yield for maximal carcass value.
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Affiliation(s)
- Vipasha Sood
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Food and Human Nutritional Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Argenis Rodas-González
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcos Claudio S Virtuoso
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Jose Segura
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - John Basarab
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits. Cells 2023; 12:cells12040539. [PMID: 36831206 PMCID: PMC9953915 DOI: 10.3390/cells12040539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/21/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.
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Zhang S, Jiang E, Kang Z, Bi Y, Liu H, Xu H, Wang Z, Lei C, Chen H, Lan X. CircRNA Profiling Reveals an Abundant circBDP1 that Regulates Bovine Fat Development by Sponging miR-181b/miR-204 Targeting Sirt1/TRARG1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14312-14328. [PMID: 36269615 DOI: 10.1021/acs.jafc.2c05939] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The proliferation and differentiation of preadipocytes is an important factor determining bovine fat development, which is closely related to the feed conversion ratio, carcass traits, and beef quality. The purpose of this study was to identify the effects of candidate circRNA and miRNA on the proliferation and differentiation of bovine preadipocytes in order to provide basic materials for molecular breeding in cattle. circRNA sequencing was performed on bovine adipocyte samples at different differentiation time points, and a total of 1830 differentially expressed circRNAs were identified. Among them, circBDP1, derived from the bovine BDP1 gene, has potential binding sites for miR-204 (known as a regulator of bovine fat development) and miR-181b, which gives us a hint that circBDP1 may regulate bovine fat development by adsorbing miR-204 and miR-181b. Here, our results revealed that circBDP1 overexpression promoted the proliferation and differentiation of bovine preadipocytes. The miRNA profile of bovine adipocytes at different differentiation time points was also analyzed using the small RNA sequencing method, and a total of 89 differentially expressed miRNAs were identified, including miR-204 and miR-181b. As expected, dual-luciferase reporter results showed that circBDP1 competitively adsorbed miR-181b and miR-204. Overexpression and interference of miR-181b in bovine preadipocytes and 3T3-L1 showed that miR-181b promoted the proliferation and differentiation of preadipocytes. Further results displayed that miR-181b and miR-204 simultaneously targeted the SIRT1 gene, and miR-204 also targeted the 3' UTR region of the TRARG1 gene. In summary, this study found that miR-181b and miR-204 were involved in fat development by targeting SIRT1 and TRARG1. The results of this study will lay a foundation for the research of fat development and beef cattle industry.
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Affiliation(s)
- Sihuan Zhang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei230036, P.R. China
| | - Enhui Jiang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Zihong Kang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100193, China
| | - Yi Bi
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hongfei Liu
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Han Xu
- School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong510006, China
| | - Zhen Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Chuzhao Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Xianyong Lan
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
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