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Wang Y, Zhang D, Liu Y. Research Progress on the Regulating Factors of Muscle Fiber Heterogeneity in Livestock: A Review. Animals (Basel) 2024; 14:2225. [PMID: 39123750 PMCID: PMC11311112 DOI: 10.3390/ani14152225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
The type of muscle fiber plays a crucial role in the growth, development, and dynamic plasticity of animals' skeletal muscle. Additionally, it is a primary determinant of the quality of both fresh and processed meat. Therefore, understanding the regulatory factors that contribute to muscle fibers' heterogeneity is of paramount importance. Recent advances in sequencing and omics technologies have enabled comprehensive cross-verification of research on the factors affecting the types of muscle fiber across multiple levels, including the genome, transcriptome, proteome, and metabolome. These advancements have facilitated deeper exploration into the related biological questions. This review focused on the impact of individual characteristics, feeding patterns, and genetic regulation on the proportion and interconversion of different muscle fibers. The findings indicated that individual characteristics and feeding patterns significantly influence the type of muscle fiber, which can effectively enhance the type and distribution of muscle fibers in livestock. Furthermore, non-coding RNA, genes and signaling pathways between complicated regulatory mechanisms and interactions have a certain degree of impact on muscle fibers' heterogeneity. This, in turn, changes muscle fiber profile in living animals through genetic selection or environmental factors, and has the potential to modulate the quality of fresh meat. Collectively, we briefly reviewed the structure of skeletal muscle tissue and then attempted to review the inevitable connection between the quality of fresh meat and the type of muscle fiber, with particular attention to potential events involved in regulating muscle fibers' heterogeneity.
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Affiliation(s)
| | | | - Yiping Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, and Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611134, China; (Y.W.); (D.Z.)
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Kong L, Yue Y, Li J, Yang B, Chen B, Liu J, Lu Z. Transcriptomics and metabolomics reveal improved performance of Hu sheep on hybridization with Southdown sheep. Food Res Int 2023; 173:113240. [PMID: 37803553 DOI: 10.1016/j.foodres.2023.113240] [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: 04/11/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/08/2023]
Abstract
Consumers are increasingly demanding high-quality mutton. Cross breeding can improve meat quality and is widely used in sheep breeding. However, little is known about the molecular mechanism of cross breeding sheep meat quality. In this study, male Southdown and female Hu sheep were hybridized. The slaughter performance and longissimus dorsi quality of the 6-month-old hybrid offspring were measured, and the longissimus dorsi of the hybrid offspring was analyzed by transcriptomics and metabolomics to explore the effect of cross breeding on meat quality. The results showed that the production performance of Southdown × Hu F1 sheep was significantly improved, the carcass fat content was significantly decreased, and the eating quality of Southdown × Hu F1 sheep were better. Compared with the HS group (Hu × Hu), the NH group (Southdown × Hu) had 538 differentially expressed genes and 166 differentially expressed metabolites (P < 0.05), which were significantly enriched in amino acid metabolism and other related pathways. Up-regulated genes METTL21C, PPARGC1A and down-regulated gene WFIKKN2 are related to muscle growth and development. Among them, the METTL21C gene, which is related to muscle development, was highly correlated with carnosine, a metabolite related to meat quality (correlation > 0.6 and P < 0.05). Our results provide further understanding of the molecular mechanism of cross breeding for sheep muscle growth and meat quality optimization.
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Affiliation(s)
- Lingying Kong
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bohui Yang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
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Reichhardt CC, Bayles SA, Feuz R, Motsinger LA, Alberto AF, Okamoto LL, Brown BL, Briggs RK, Roholt BW, Bowman BR, Larsen R, Garcia MD, Thornton KJ. Relationship among cattle breed and anabolic implant protocol relative to feedlot performance: Growth, temperament, feeding behavior, carcass traits, and economic return. Domest Anim Endocrinol 2023; 84-85:106806. [PMID: 37392553 DOI: 10.1016/j.domaniend.2023.106806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
Recent research has suggested that different cattle breed types may respond differently to anabolic implant protocols of varying intensity. Therefore, the purpose of this research was to compare anabolic implant protocols in feedlot steers of 2 different breed types. Sixty steers were stratified by weight and breed in a 2 × 3 factorial design examining 2 different breeds: Angus (AN; n=38) or Santa Gertrudis influenced (SG; n=22), and 3 implant strategies: no implant (CON; n=20), a moderate intensity implant protocol (d0 implant: Revalor-G, d56 implant: Revalor-IS, d112 implant: Revalor-S; MI; n=20), or a high intensity implant protocol (d0 implant: Revalor-IS, d56 implant: Revalor-S, d112 implant: Revalor-200; HI; n=20). Steers were randomly placed into pens equipped with GrowSafe bunks to collect dry matter intake and feeding behavior. All animals were fed the same diet. Weight, chute score, exit velocity, serum, rectal temperature, hip height and 12th rib fat thickness were collected approximately every 28 d over a 196 d period. Serum urea nitrogen (SUN) was evaluated as well. Total average daily gain was increased (P < 0.0001) in both the HI and MI steers compared to the CON steers by 29.4% and 26%, respectively. A treatment × breed interaction was observed (P < 0.0001) for hip height, with AN-CON steers being shorter (P < 0.0007) than AN-HI, SG-CON, SG-MI, and SG-HI steers. A breed × treatment interaction was observed (P < 0.004) for chute score and rectal temperature, with SG-HI and SG-MI steers having increased chute scores (P < 0.001) when compared to AN-HI, AN-MI, AN-CON, and SG-CON throughout the course of the trial. Additionally, SG-HI and SG-MI steers had an increased rectal temperature (P < 0.004) compared to AN-HI, AN-MI, AN-CON, and SG-CON steers. A breed effect was observed (P = 0.002) for SUN with AN steers having increased (P = 0.002) SUN concentration compared to SG sired steers, in addition to a treatment effect (P < 0.0001), with CON steers having a higher (P < 0.0001) SUN concentration than MI and HI steers, regardless of breed. The MI implant protocol increased net return per head, on average, by $97.28, regardless of breed, while the HI implant protocol increased net return by only $80.84. Taken together, despite the cattle breed types responding differently to the different anabolic implant protocols at times, a moderate intensity anabolic implant protocol was optimal in this experiment for steers raised in a temperate climate.
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Affiliation(s)
- C C Reichhardt
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA; Department of Human Nutrition, Food and Animal Sciences, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI, 96822, USA
| | - S A Bayles
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - R Feuz
- Department of Applied Economics, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - L A Motsinger
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - A F Alberto
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - L L Okamoto
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - B L Brown
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - R K Briggs
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - B W Roholt
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - B R Bowman
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - R Larsen
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai'i at Mānoa, 1955 East-West Road, Honolulu, HI, 96822, USA
| | - M D Garcia
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA
| | - K J Thornton
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, 4815 Old Main Hill, Logan, UT, 84322, USA.
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Feuz R, Reichhardt CC, Larsen R, Thornton KJ, Garcia MD. Comparing net returns in the feedlot: Bos Taurus vs. Bos Indicus influenced steers with varying anabolic implant intensity. Transl Anim Sci 2022; 6:txac111. [PMID: 36172460 PMCID: PMC9512098 DOI: 10.1093/tas/txac111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
There are two main beef cattle breed types: Bos Taurus (BT) and Bos Indicus (BI). Past research has demonstrated various expected differences in growth, temperament, feeding behavior, and carcass characteristics between these breed types when administered varying levels of anabolic implant. However, little is known about the differences in expected economic returns between these cattle types. The objective of this research is to simulate and compare the expected net returns of BT, Angus (AN) steers and BI influenced, Santa Gertrudis (SG) steers, with moderate or high intensity levels of implants relative to a control with no implant. The animal performance and carcass data for this economic analysis was provided from a recent feeding experiment of AN and SG influenced steers. In the experiment, sixty steers were stratified by weight and breed in a 2 × 3 factorial design examining the two different breeds: AN (N = 38) or SG influenced (N = 22), and three implant strategies: no implant (N = 20), a moderate intensity implant protocol (d0 implant: Revalor-G, d56 implant: Revalor-IS, d112 implant: Revalor-S; n=20), or a high intensity implant protocol (d0 implant: Revalor-IS, d56 implant: Revalor-S, d112 implant: Revalor-200; N = 20). The steers performance and carcass data were used together with publicly available price and input costs data in the simulation of net returns per animal for each of the treatment groups. Results demonstrated that both moderate and high intensity implanted BT steers have higher expected net return (US$78.70/hd. and US$75.84/hd., respectively) compared to BI moderate and high intensity implanted steers (US$47.03/hd. and $6.98/hd., respectively). Stochastic efficiency analysis with respect to a function demonstrated when certainty equivalent values are constrained to those ≥US$0, only the moderate implanted BT steers would be included in the efficient set.
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Affiliation(s)
- Ryan Feuz
- Applied Economics Department, Utah State University , Logan, UT 84322 , USA
| | - Caleb C Reichhardt
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaiʻi at Mānoa , Honolulu, HI 96822 , USA
| | - Ryan Larsen
- Applied Economics Department, Utah State University , Logan, UT 84322 , USA
| | - Kara J Thornton
- Animal, Dairy and Veterinary Science Department, Utah State University , Logan, UT 84322 , USA
| | - Mathew D Garcia
- Animal, Dairy and Veterinary Science Department, Utah State University , Logan, UT 84322 , USA
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Shi J, Wang X, Song Y, Liu T, Cheng S, Zhang Q. Excavation of Genes Related to the Mining of Growth, Development, and Meat Quality of Two Crossbred Sheep Populations Based on Comparative Transcriptomes. Animals (Basel) 2021; 11:ani11061492. [PMID: 34064178 PMCID: PMC8224371 DOI: 10.3390/ani11061492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/04/2022] Open
Abstract
Simple Summary In this study, we measured the performance parameters of two crossbred sheep breeds, using Masson staining of the muscle tissue, and using the Illumina high-throughput sequencing platform to determine the differentially expressed genes (DEGs) in Dorper (DP) × Small-tailed Han (STH) sheep and Mongolia (MG) × Small-tailed Han sheep (STH). New transcripts of the muscle transcriptome were examined for the first time. DP × STH sheep were superior to MG × STH sheep in terms of meat quality and muscle morphology. In addition, 13 DEGs were found to play important roles in growth, development, and meat quality. The findings of this work may provide valuable resources for future research on muscle development in sheep. Abstract Crossbreeding can improve production performance and meat quality in sheep. The objective of this study was to look for genes related to sheep growth, development, and muscle. In this study, Dorper (DP) × Small Tailed Han (STH) sheep and Mongolia (MG) × Small-tailed Han (STH) sheep were used to estimate the productive performance and meat quality in a crossbreed. Subsequently, transcriptome analysis and bioinformatic analysis were performed on the Longissimus dorsi muscles of DP × STH and MG × STH sheep to identify differentially expressed genes (DEGs) related to growth, development, and meat quality. The presence of DEGs was confirmed by real-time PCR (qPCR). Productive performance and meat quality of the DP × STH sheep were better than the MG × STH sheep. Compared to DP × STH, a total of 1445 DEGs were identified in MG × STH sheep (1026 DEG were up-regulated and 419 DEG were down-regulated). Of these, 38 DEGs were related to growth, 161 to development, and 43 to muscle. In addition, 13 co-expressed genes (FGFRL1, SIX1, PLCB1, CRYAB, MYL2, ADIPOQ, GPX1, PPARD, GPC1, CDC42, LOC101106246, IGF1, and LARGE) were identified. The expression of DEGs was consistent with the comparative transcriptome analysis. This work provides genetics resources for future research on muscle development in sheep.
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Affiliation(s)
- Jinping Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Xueying Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China;
| | - Yali Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Ting Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
| | - Shuru Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (J.S.); (Y.S.); (T.L.)
- Correspondence: (S.C.); (Q.Z.); Tel.: +86-931-763-2509 (S.C.)
| | - Quanwei Zhang
- College of Life Science and Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (S.C.); (Q.Z.); Tel.: +86-931-763-2509 (S.C.)
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Grigoletto L, Santana MHA, Bressan FF, Eler JP, Nogueira MFG, Kadarmideen HN, Baruselli PS, Ferraz JBS, Brito LF. Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle. Animals (Basel) 2020; 10:E1185. [PMID: 32668804 PMCID: PMC7401547 DOI: 10.3390/ani10071185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022] Open
Abstract
Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9-65.0 Mb and 109.1-109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.
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Affiliation(s)
- Laís Grigoletto
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Miguel Henrique Almeida Santana
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Fabiana Fernandes Bressan
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Marcelo Fábio Gouveia Nogueira
- Department of Biological Sciences, School of Sciences and Languages, São Paulo State University, Assis, 19806-900 São Paulo, Brazil;
| | - Haja N. Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 102500 Lyngby, Denmark;
| | - Pietro Sampaio Baruselli
- College of Veterinary Medicine and Animal Science, University of Sao Paulo, 05508-270 São Paulo, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900 São Paulo, Brazil; (M.H.A.S.); (F.F.B.); (J.P.E.); (J.B.S.F.)
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
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Cross AJ, King DA, Shackelford SD, Wheeler TL, Nonneman DJ, Keel BN, Rohrer GA. Genome-Wide Association of Myoglobin Concentrations in Pork Loins. MEAT AND MUSCLE BIOLOGY 2018. [DOI: 10.22175/mmb2017.08.0042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Lean color is a major focus for identifying pork loins for export markets, and myoglobin is the primary pigment driving pork color. Thus, increasing myoglobin concentration should increase redness of pork products and the number of loins acceptable for exportation. Therefore, understanding genetic variation and parameters affecting myoglobin concentration is critical for improving pork color. The objective of this study was to identify genetic markers associated with myoglobin concentration in pork loin muscle. Ultimate pH and myoglobin concentrations were measured in longissimus thoracis et lumborum samples of pigs (n = 599) from two different commercial finishing swine facilities. A Bayes-C model implemented in GenSel identified regions within 7 chromosomes that explained greater than 63% of the genetic variance in myoglobin concentration. Chromosome 7 had 1 significant region which accounted for 37% of the genetic variance, while chromosome 14 had 4 significant regions accounting for 9.8% of the genetic variance. Candidate genes in the region on chromosome 7 were involved in iron homeostasis, and genes in the significant regions on chromosome 14 were involved in calcium regulation. Genes identified in this study represent potential biomarkers that could be used to select for higher myoglobin concentrations in pork, which may improve lean meat color.
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Affiliation(s)
| | - David A. King
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
| | - Steven D. Shackelford
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
| | - Tommy L. Wheeler
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
| | - Dan J. Nonneman
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
| | - Brittney N. Keel
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
| | - Gary A. Rohrer
- U.S. Department of Agriculture U.S. Meat Animal Research Center, Agricultural Research Service
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Lu Y, Vandehaar MJ, Spurlock DM, Weigel KA, Armentano LE, Connor EE, Coffey M, Veerkamp RF, de Haas Y, Staples CR, Wang Z, Hanigan MD, Tempelman RJ. Genome-wide association analyses based on a multiple-trait approach for modeling feed efficiency. J Dairy Sci 2018; 101:3140-3154. [PMID: 29395135 DOI: 10.3168/jds.2017-13364] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022]
Abstract
Genome-wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 cows from 16 stations in 4 counties. Of these cows, 4,916 had genotypes on 57,347 single nucleotide polymorphism (SNP) markers. We compared a GWA analysis based on the more classical residual feed intake (RFI) model with one based on a previously proposed multiple trait (MT) approach for modeling FE using an alternative measure (DMI|MILKE,MBW). Both models were based on a single-step genomic BLUP procedure that allowed the use of phenotypes from both genotyped and nongenotyped cows. Estimated effects for single SNP markers were small and not statistically important but virtually identical for either FE measure (RFI vs. DMI|MILKE,MBW). However, upon further refining this analysis to develop joint tests within nonoverlapping 1-Mb windows, significant associations were detected between either measure of FE with a window on each of Bos taurus autosomes BTA12 and BTA26. There was, as expected, no overlap between detected genomic regions for DMI|MILKE,MBW and genomic regions influencing the energy sink traits (i.e., MILKE and MBW) because of orthogonal relationships clearly defined between the various traits. Conversely, GWA inferences on DMI can be demonstrated to be partly driven by genetic associations between DMI with these same energy sink traits, thereby having clear implications when comparing GWA studies on DMI to GWA studies on FE-like measures such as RFI.
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Affiliation(s)
- Y Lu
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - M J Vandehaar
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - D M Spurlock
- Department of Animal Science, Iowa State University, Ames 50011
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - L E Armentano
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - E E Connor
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - M Coffey
- Animal and Veterinary Sciences Group, Scotland's Rural College (SRUC), Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - R F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, the Netherlands
| | - Y de Haas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, the Netherlands
| | - C R Staples
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - Z Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5 Canada
| | - M D Hanigan
- Department of Dairy Science, Virginia Tech, Blacksburg 24061
| | - R J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48824.
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Wright SA, Ramos P, Johnson DD, Scheffler JM, Elzo MA, Mateescu RG, Bass AL, Carr CC, Scheffler TL. Brahman genetics influence muscle fiber properties, protein degradation, and tenderness in an Angus-Brahman multibreed herd. Meat Sci 2018; 135:84-93. [DOI: 10.1016/j.meatsci.2017.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/16/2017] [Accepted: 09/14/2017] [Indexed: 11/25/2022]
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10
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de Oliveira PSN, Cesar ASM, do Nascimento ML, Chaves AS, Tizioto PC, Tullio RR, Lanna DPD, Rosa AN, Sonstegard TS, Mourao GB, Reecy JM, Garrick DJ, Mudadu MA, Coutinho LL, Regitano LCA. Identification of genomic regions associated with feed efficiency in Nelore cattle. BMC Genet 2014; 15:100. [PMID: 25257854 PMCID: PMC4198703 DOI: 10.1186/s12863-014-0100-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 09/10/2014] [Indexed: 01/17/2023] Open
Abstract
Background Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology. Results Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7. Conclusions Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0100-0) contains supplementary material, which is available to authorized users.
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