1
|
Halli K, König S, Giambra IJ. Association study between SNP markers located in meat quality candidate genes with intramuscular fat content in an endangered dual-purpose cattle population. Transl Anim Sci 2024; 8:txae066. [PMID: 38737521 PMCID: PMC11088282 DOI: 10.1093/tas/txae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
The aim of this study was to associate single nucleotide polymorphisms (SNP) of the bovine calcium-activated neutral protease µ-calpain, calpastatin, diacylglycerol-O-acyltransferase, adipose fatty acid binding protein, retinoic acid receptor-related orphan receptor C (RORC), and thyroglobulin (TG) gene with intramuscular fat content (IMF). Therefore, 542 animals of the cattle breed "Rotes Höhenvieh" (RHV) were phenotyped for IMF. Genotyping of the animals was performed using polymerase chain reaction-restriction fragment length polymorphism tests for six SNP from candidate genes for meat quality traits. In addition, we calculated allele substitution and dominance effects on IMF. A subgroup of animals (n = 44, reduced dataset) with extraordinary high IMF was analyzed separately. The mean IMF content was 2.5% (SD: 2.8) but ranged from 0.02% to 23.9%, underlining the breeds' potential for quality meat production. Allele and genotype frequencies for all SNP were similar in the complete and reduced dataset. Association analyses in the complete dataset revealed the strongest effects of RORC on IMF (P = 0.075). The log-transformed least-squares mean for IMF of genotype g.3290GG was 0.45 ± 0.16, 0.26 ± 0.14 for genotype g.3290GT, and 0.32 ± 0.14 for genotype g.3290TT. In the reduced dataset, we found a significant effect (P < 0.05) of the g.422C>T-SNP of TG on IMF, with highest IMF for genotype CT (0.91 ± 0.17), lowest IMF for genotype TT (0.37 ± 0.25), and medium IMF for genotype CC (0.59 ± 0.16; log-transformed values). Compared to the complete dataset, allele substitution effects increased in the reduced dataset for most of the SNP, possibly due to the selective genotyping strategy, with focus on animals with highest IMF implying strong phenotypic IMF contrast. Dominance effects were small in both datasets, related to the high heritability of IMF. Results indicated RHV breed particularities regarding the effects of meat quality genes on IMF. An explanation might be the breeding history of RHV with focus on adaptation and resilience in harsh outdoor systems. Consequently, it is imperative to develop breed-specific selection strategies. Allele substitution and dominance effects were in a similar direction in both datasets, suggesting the same breeding approaches for different RHV strains in different regions. Nevertheless, a selective genotyping approach (reduced dataset), contributed to more pronounced genotype effect differences on IMF and dominance values.
Collapse
Affiliation(s)
- Kathrin Halli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, 35390 Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, 35390 Giessen, Germany
| | - Isabella J Giambra
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, 35390 Giessen, Germany
| |
Collapse
|
2
|
Kostusiak P, Slósarz J, Gołębiewski M, Grodkowski G, Puppel K. Polymorphism of Genes and Their Impact on Beef Quality. Curr Issues Mol Biol 2023; 45:4749-4762. [PMID: 37367051 DOI: 10.3390/cimb45060302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
The single-nucleotide polymorphism (SNP) form of genes is a valuable source of information regarding their suitability for use as specific markers of desirable traits in beef cattle breeding. For several decades, breeding work focused on improving production efficiency through optimizing the feed conversion ratio and improving daily gains and meat quality. Many research teams previously undertook research work on single-nucleotide polymorphism in myostatin (MSTN), thyroglobulin (TG), calpain (CAPN), and calpastatin (CAST) proteins. The literature review focuses on the most frequently addressed issues concerning these genes in beef cattle production and points to a number of relevant studies on the genes' polymorphic forms. The four genes presented are worth considering during breeding work as a set of genes that can positively influence productivity and production quality.
Collapse
Affiliation(s)
- Piotr Kostusiak
- Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Jan Slósarz
- Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Marcin Gołębiewski
- Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Grzegorz Grodkowski
- Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Kamila Puppel
- Institute of Animal Science, Warsaw University of Life Sciences, Ciszewskiego 8, 02-786 Warsaw, Poland
| |
Collapse
|
3
|
Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle. Curr Issues Mol Biol 2022; 44:6075-6092. [PMID: 36547075 PMCID: PMC9777506 DOI: 10.3390/cimb44120414] [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: 09/19/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.
Collapse
|
4
|
Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness. Animals (Basel) 2022; 12:ani12212976. [PMID: 36359100 PMCID: PMC9654910 DOI: 10.3390/ani12212976] [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: 09/29/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary A bibliometric analysis was carried out to know the evolution of research on genes associated with meat tenderness, of interest for the development of selection programs. Since 1993, studies have been limited to a few researchers in high-income countries due to the costs associated with the techniques. The main findings showed that the scientific production had a discontinuous growth because science experienced a significant change since approximately 2010. Marker-assisted selection was widely used, evaluating mainly CAPN (calpain) and CAST (calpastatin) genes for their contribution to meat tenderness, especially in cattle. However, the effects are small; therefore, genomic selection was implemented by genotyping thousands of single nucleotide polymorphisms (SNPs) for further explanation of genetic variation. The results shown are important for scholars to identify emerging methodologies and gaps in the literature and to know who the prolific authors and institutions in the field for possible collaborations, etc., are. Abstract Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness.
Collapse
|
5
|
Foraker BA, Johnson B, Rathmann RJ, Legako JF, Brooks JC, Miller M, Woerner DR. Expression of beef- versus dairy-type in crossbred beef × dairy cattle does not impact shape, eating quality, or color of strip loin steaks. MEAT AND MUSCLE BIOLOGY 2022. [DOI: 10.22175/mmb.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Phenotypic expression of dairy-influence often carries negative implications in beef production; thus, considerable variation in expression of beef- versus dairy-type might adversely affect value of crossbred beef × dairy cattle. This study evaluated effects of beef- versus dairy-type on meat quality in crossbred beef × dairy cattle. Effects were blocked within commercial feedlot pens because cattle within a pen were contemporaries for sex, age, management, and source. On their harvest date, 592 Angus or [Simmental × Angus] × Holstein cattle from 9 pens were assessed by 3 expert evaluators. Scores for muscling and frame size were used to categorize and subset cattle in a pen into 4 phenotype groups: (1) fully dairy-type, (2) partially dairy-type, (3) partially beef-type, and (4) fully beef-type. Strip loin steaks were obtained from selected cattle (n = 82 to 84 per group) and evaluated for descriptive sensory attributes, shear force, pH, color at retail display, steak dimensions, muscle fiber type, and fatty acid composition. Data were tested for fixed effects of phenotype group with random effects of pen. Despite distinct expression of visual beef- versus dairy-type among cattle sampled, phenotype groups were largely not different (P > 0.05) in shape, sensory attributes, color, or biochemical properties of strip loin steaks. Other body regions, separate from the loin, were likely responsible for differences in live animal muscling. Additional research is needed on effects of sire breed, individual sire, and management strategies on meat quality in beef × dairy crossbreds. Because expression of beef- versus dairy-type does not affect meat quality, the beef × dairy mating system should focus on increasing complementarity of beef breeds and sires to produce more profitable, beef-type cattle. Finally, marketing programs rooted in production of consistent and premium products may benefit from including beef from beef × dairy crossbreds.
Collapse
Affiliation(s)
| | - Bradley Johnson
- Texas Tech University Department of Animal and Food Sciences
| | | | | | | | - Mark Miller
- Texas Tech University Department of Animal and Food Sciences
| | | |
Collapse
|
6
|
Sustained Effects of Muscle Calpain System Genotypes on Tenderness Phenotypes of South African Beef Bulls during Ageing up to 20 Days. Animals (Basel) 2022; 12:ani12060686. [PMID: 35327083 PMCID: PMC8944438 DOI: 10.3390/ani12060686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/25/2022] [Accepted: 02/02/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary When searching for genetic markers for the selection of more tender beef, it is important to maintain minimal environmental variation from pre-slaughter, right through to the ageing process, to ensure the accuracy of the obtained phenotypes. This is because beef quality traits have a large environmental component that can greatly alter the characteristics of the meat, which would not reflect a true genetic effect. We propose that variable ageing times are especially important in determining whether markers are associated with tenderization or not. Our analyses included candidate genes for the protein degrading enzyme system for calpains, because they contribute the most to tenderization. We were able to validate these markers in South African beef cattle, where they could be useful for selection. The timing of the collection of tenderness data was critical, as only a few (6/134) genetic markers sustained their association with tenderization over ageing to 20 days. A larger tenderization effect earlier in ageing, as shown here for the capn1_187 and capn1_4751 markers, would decrease the length of ageing. This would not only increase profits, but also decrease the energy needed during the storage and refrigeration of aged beef, decreasing the carbon footprint of beef production. Abstract The most important factor that determines beef tenderness is its proteolytic activity, and the balance between calpain-1 protease activity and calpastatin inhibition is especially important, while contributions can also arise from calpain-2 and, possibly, calpain-3. The meat ageing process itself affects these processes. To determine whether genotypes in the calpain–calpastatin system can enhance tenderness through a 20-day ageing period, South African purebred beef bulls (n = 166) were genotyped using the Illumina BovineHD SNP BeadChip through a gene-based association analysis targeting the cast, capn3, capn2 and capn1 genes. The Warner–Bratzler shear force (WBSF) and myofibril fragment length (MFL) of Longissimus thoracis et lumborum (LTL) steaks were evaluated between d 3 and d 20 of ageing, with protease enzyme activity in the first 20 h post-mortem. Although several of the 134 SNPs are associated with tenderness, only seven SNP in the cast, capn2 and capn1 genes sustained genetic associations, additive to the ageing-associated increases in tenderness for at least three of the four ageing periods. While most genomic associations were relatively stable over time, some genotypes within the SNP responded differently to ageing, resulting in altered genomic effects over time. The level of ageing at which genomic associations are performed is an important factor that determines whether SNPs affect tenderness phenotypes.
Collapse
|
7
|
Connecting Heat Tolerance and Tenderness in Bos indicus Influenced Cattle. Animals (Basel) 2022; 12:ani12030220. [PMID: 35158544 PMCID: PMC8833572 DOI: 10.3390/ani12030220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Bos indicus (also known as zebu or humped) cattle are heat tolerant and parasite resistant, which is advantageous in hot, humid climates. However, Bos indicus cattle are also known for excitable temperaments, slower growth, and variation in meat quality characteristics. The relationships between thermotolerance, temperament, and meat production traits are poorly understood. Due to its contribution to body weight, muscle may play an important role in determining the thermoregulatory capacity of Bos indicus cattle. Ultimately, defining relationships between muscle metabolism and heat tolerance are necessary in order to enhance tenderness, without sacrificing heat tolerance of Bos indicus breeds. Abstract Bos indicus cattle are widely utilized in tropical and subtropical climates. Their heat tolerance and parasite resistance are integral for beef production in these regions; however, a reputation for excitable temperaments, slower growth, and variation in tenderness has limited their use in commercial beef production. This suggests that there is antagonism between heat tolerance and meat production traits. Meat quality characteristics are determined by the properties of skeletal muscle as well as conditions during slaughter and processing. Thus, it is possible that adaptations related to heat tolerance in the living animal affect tenderness and other meat quality attributes. Since muscle represents a large proportion of body mass, relatively small changes at the cellular level could impact overall heat production of the animal. Specifically, protein degradation and mitochondria function are aspects of organ and cellular metabolism that may help limit heat production and also have a connection to tenderness. Protein degradation postmortem is critical to structural changes that enhance tenderness whereas mitochondria may influence tenderness through their roles in energy metabolism, calcium regulation, cell death signaling, and oxidative stress. This review explores potential relationships between cellular metabolism in vivo and beef quality development in Bos indicus and Bos indicus influenced cattle.
Collapse
|
8
|
Fonseca PADS, Caldwell T, Mandell I, Wood K, Cánovas A. Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages. Meat Sci 2022; 186:108733. [PMID: 35007800 DOI: 10.1016/j.meatsci.2022.108733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.
Collapse
Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tim Caldwell
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ira Mandell
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Katharine Wood
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
| |
Collapse
|
9
|
Frezarim GB, Fonseca LFS, Salatta BM, Silva DBDS, Bresolin T, Seno LDO, Barufatti A, Ferro JA, Albuquerque LG. Genes and proteins associated with ribeye area and meat tenderness in a commercial Nellore cattle population. Genome 2021; 65:229-240. [PMID: 34860606 DOI: 10.1139/gen-2020-0163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite several studies on genetic markers and differently expressed genes related to ribeye area (REA) and tenderness traits in beef cattle, there is divergence in the results regarding the genes associated with these traits. Thirteen genes that had been associated or have biological functions that may influence such phenotypes were included in this study. A total of five genes for REA (IGF-1, IGF-2, MSTN, NEDD4, and UBE4A) and eight genes for meat tenderness (CAPN1, CAPN2, CAST, HSPB1, DNAJA1, FABP4, SCD, and PRKAG3) were selected from previously studies in beef cattle. Genes and its respective proteins expression were validated in a commercial population of Nellore cattle using quantitative real-time PCR (RT-qPCR) and advanced mass spectrometry (LC / MS-MS) techniques, respectively. MSTN gene was upregulated in animals with low REA. CAPN1, CAPN2, CAST, HSPB1, and DNAJA1 genes were upregulated in animals with tougher meat. The proteins translated by these genes were not differentially expressed. Our results could confirm the potential of some studied genes as biomarkers for carcass and meat quality in Nellore cattle.
Collapse
Affiliation(s)
- Gabriela Bonfá Frezarim
- School of Agricultural and Veterinary Studies, Animal Science, Via de Acesso Professor Paulo Donato Castelane Castellane S/N Vila Industrial, 14884-900, Jaboticabal , SP, Brazil, 14884-900;
| | | | - Bruna Maria Salatta
- School of Agricultural and Veterinary Studies, Animal Science , Jaboticabal , Brazil;
| | | | - Tiago Bresolin
- University of Wisconsin-Madison, 5228, Madison, Wisconsin, United States;
| | | | | | | | | |
Collapse
|
10
|
Warner RD, Wheeler TL, Ha M, Li X, Bekhit AED, Morton J, Vaskoska R, Dunshea FR, Liu R, Purslow P, Zhang W. Meat tenderness: advances in biology, biochemistry, molecular mechanisms and new technologies. Meat Sci 2021; 185:108657. [PMID: 34998162 DOI: 10.1016/j.meatsci.2021.108657] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022]
Abstract
Meat tenderness is an important quality trait critical to consumer acceptance, and determines satisfaction, repeat purchase and willingness-to-pay premium prices. Recent advances in tenderness research from a variety of perspectives are presented. Our understanding of molecular factors influencing tenderization are discussed in relation to glycolysis, calcium release, protease activation, apoptosis and heat shock proteins, the use of proteomic analysis for monitoring changes, proteomic biomarkers and oxidative/nitrosative stress. Each of these structural, metabolic and molecular determinants of meat tenderness are then discussed in greater detail in relation to animal variation, postmortem influences, and changes during cooking, with a focus on recent advances. Innovations in postmortem technologies and enzymes for meat tenderization are discussed including their potential commercial application. Continued success of the meat industry relies on ongoing advances in our understanding, and in industry innovation. The recent advances in fundamental and applied research on meat tenderness in relation to the various sectors of the supply chain will enable such innovation.
Collapse
Affiliation(s)
- Robyn D Warner
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne University, Parkville 3010, Australia.
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska 68933, USA
| | - Minh Ha
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne University, Parkville 3010, Australia
| | - Xin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | | | - James Morton
- Department of Wine Food and Molecular Biosciences, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Rozita Vaskoska
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne University, Parkville 3010, Australia
| | - Frank R Dunshea
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, Melbourne University, Parkville 3010, Australia; Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rui Liu
- School of Food Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225127, PR China
| | - Peter Purslow
- Tandil Centre for Veterinary Investigation (CIVETAN), National University of Central Buenos Aires Province, Tandil B7001BBO, Argentina
| | - Wangang Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
11
|
Cushman RA, Bennett GL, Tait RG, McNeel AK, Casas E, Smith TPL, Freetly HC. Relationship of molecular breeding value for beef tenderness with heifer traits through weaning of their first calf. Theriogenology 2021; 173:128-132. [PMID: 34375939 DOI: 10.1016/j.theriogenology.2021.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
Polymorphisms in μ-calpain (CAPN1) that beneficially associate with beef tenderness are reported to antagonistically associate with calving day in beef heifers and post-partum interval to estrus in beef cows. We, therefore, hypothesized that a molecular breeding value for slice shear force, calculated based on CAPN1 and calpastatin (CAST) genotypes, would demonstrate an antagonistic relationship between genomically predicted slice shear force and ordinal calving date in replacement beef heifers. A secondary objective of this study was to evaluate the association of a polymorphism in diacylglycerol O-acyltransferase (DGAT1) with reproductive traits in beef heifers. One hundred eighty-seven MARC III heifers (¼ Angus, ¼ Hereford, ¼ Red Poll, and ¼ Pinzgauer) that had been selectively bred to increase the frequency of these polymorphisms were submitted for monthly ultrasound exams beginning at 333 d of age and continuing until the start of breeding to determine pubertal status. At the last exam before breeding, all antral follicles were counted, and the length and height of each ovary was measured to determine if genomic selection for slice shear force associated with ovarian follicle number. Calving date, calf gender, and calf birth weight were recorded at parturition. Regression analysis of the molecular breeding value for slice shear force of the heifers on ordinal calving date indicated no association between genomic prediction of tenderness and calving date (P = 0.16); however, there was a tendency for age at puberty to be delayed in heifers as genetic merit for tenderness improved (P = 0.09). The results of the present study indicate that within experimental precision, selecting for tenderness using genomic predictions had minimal or no antagonistic association with reproductive performance in heifers. Further analysis of reproductive performance as cows is needed within this population but applying these genetic markers to select for tenderness in steers does not antagonize reproductive traits influencing conception or first calf birth date and birth weight in replacement beef heifers.
Collapse
Affiliation(s)
- Robert A Cushman
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States.
| | - Gary L Bennett
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Richard G Tait
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Anthony K McNeel
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Eduardo Casas
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Timothy P L Smith
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| | - Harvey C Freetly
- USDA, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, United States
| |
Collapse
|
12
|
Lee HJ, Chung YJ, Jang S, Seo DW, Lee HK, Yoon D, Lim D, Lee SH. Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle). PLoS One 2020; 15:e0241848. [PMID: 33264312 PMCID: PMC7710051 DOI: 10.1371/journal.pone.0241848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/21/2020] [Indexed: 11/24/2022] Open
Abstract
It was hypothesized that single-nucleotide polymorphisms (SNPs) extracted from text-mined genes could be more tightly related to causal variant for each trait and that differentially weighting of this SNP panel in the GBLUP model could improve the performance of genomic prediction in cattle. Fitting two GRMs constructed by text-mined SNPs and SNPs except text-mined SNPs from 777k SNPs set (exp_777K) as different random effects showed better accuracy than fitting one GRM (Im_777K) for six traits (e.g. backfat thickness: + 0.002, eye muscle area: + 0.014, Warner–Bratzler Shear Force of semimembranosus and longissimus dorsi: + 0.024 and + 0.068, intramuscular fat content of semimembranosus and longissimus dorsi: + 0.008 and + 0.018). These results can suggest that attempts to incorporate text mining into genomic predictions seem valuable, and further study using text mining can be expected to present the significant results.
Collapse
Affiliation(s)
- Hyo Jun Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Yoon Ji Chung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Sungbong Jang
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States of America
| | - Dong Won Seo
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, Korea
| | - Duhak Yoon
- Department of Animal Science, Kyungpook National University, Sangju, Korea
| | - Dajeong Lim
- Animal Genome & Bioinformatics, National Institute of Animal Science, Wanju, Korea
- * E-mail: (DL); (SHL)
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
- * E-mail: (DL); (SHL)
| |
Collapse
|
13
|
Leal-Gutiérrez JD, Rezende FM, Reecy JM, Kramer LM, Peñagaricano F, Mateescu RG. Whole Genome Sequence Data Provides Novel Insights Into the Genetic Architecture of Meat Quality Traits in Beef. Front Genet 2020; 11:538640. [PMID: 33101375 PMCID: PMC7500205 DOI: 10.3389/fgene.2020.538640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
Tenderness is a major quality attribute for fresh beef steaks in the United States, and meat quality traits in general are suitable candidates for genomic research. The objectives of the present analysis were to (1) perform genome-wide association (GWA) analysis for marbling, Warner-Bratzler shear force (WBSF), tenderness, and connective tissue using whole-genome data in an Angus population, (2) identify enriched pathways in each GWA analysis; (3) construct a protein-protein interaction network using the associated genes and (4) perform a μ-calpain proteolysis assessment for associated structural proteins. An Angus-sired population of 2,285 individuals was assessed. Animals were transported to a commercial packing plant and harvested at an average age of 457 ± 46 days. After 48 h postmortem, marbling was recorded by graders' visual appraisal. Two 2.54-cm steaks were sampled from each muscle for recording of WBSF, and tenderness, and connective tissue by a sensory panel. The relevance of additive effects on marbling, WBSF, tenderness, and connective tissue was evaluated on a genome-wide scale using a two-step mixed model-based approach in single-trait analysis. A tissue-restricted gene enrichment was performed for each GWA where all polymorphisms with an association p-value lower than 1 × 10-3 were included. The genes identified as associated were included in a protein-protein interaction network and a candidate structural protein assessment of proteolysis analyses. A total of 1,867, 3,181, 3,926, and 3,678 polymorphisms were significantly associated with marbling, WBSF, tenderness, and connective tissue, respectively. The associate region on BTA29 (36,432,655-44,313,046 bp) harbors 13 highly significant markers for meat quality traits. Enrichment for the GO term GO:0005634 (Nucleus), which includes transcription factors, was evident. The final protein-protein network included 431 interations between 349 genes. The 42 most important genes based on significance that encode structural proteins were included in a proteolysis analysis, and 81% of these proteins were potential μ-Calpain substrates. Overall, this comprehensive study unraveled genetic variants, genes and mechanisms of action responsible for the variation in meat quality traits. Our findings can provide opportunities for improving meat quality in beef cattle via marker-assisted selection.
Collapse
Affiliation(s)
| | - Fernanda M. Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luke M. Kramer
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| |
Collapse
|
14
|
Genome association of carcass and palatability traits from Bos indicus-Bos taurus crossbred steers within electrical stimulation status and correspondence with steer temperament 2. Palatability. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
15
|
Validation Study of SNPs in CAPN1-CAST Genes on the Tenderness of Muscles ( Longissimus thoracis and Semimembranosus) in Hanwoo (Korean Cattle). Animals (Basel) 2019; 9:ani9090691. [PMID: 31533240 PMCID: PMC6770136 DOI: 10.3390/ani9090691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary For meat tenderness, single nucleotide polymorphisms (SNPs) in the μ-calpain (CAPN1) and calpastatin (CAST) genes have been reported to be associated with Warner-Bratzler shear force (WBSF) in different cattle populations, including Korean Hanwoo cattle. In this study, we validated the association of seven SNPs in CAPN1 and CAST genes with meat tenderness in two different muscle cuts tenderness in the Longissimus thoracis (LT) and Semimembranosus (SM) muscles. Two SNPs in CAPN1 and one SNPs in CAST genes showed association with WBSF of both muscle types. Furthermore, of twelve reconstructed haplotypes, six demonstrated significant associations with WBSF values. These findings may be one of the strong evidences that CAPN1 and CAST gene mutations are strongly associated with WBSF. The information of significantly-associated SNPs and the resulted haplotypes could be utilized in the Hanwoo breeding program for further genetic improvement of tenderness traits. Abstract Previous studies demonstrated that polymorphisms in the μ-calpain (CAPN1) and calpastatin (CAST) genes had significant effects on meat tenderness in different cattle populations. The aim of this study was to validate the potential association of seven single nucleotide polymorphisms (SNPs) harbored in these two candidate genes with meat tenderness in the Longissimus thoracis (LT) and Semimembranosus (SM) muscles. A total of 1000 animals were genotyped using TaqMan SNP genotyping arrays, and the meat tenderness of two muscle (LT and SM at 7 days post-slaughter) was assessed based on Warner-Bratzler WBSF (WBSF) testing. We observed significant associations of the CAPN1:c.580T>C, CAPN1:c.658T>C and CAST:c.1985G>C polymorphisms (p < 0.05) with the WBSF values in the LT and SM muscles. Additive effects of the C allele in CAPN1:c.580T>C and CAST:c.1985G>C were associated with an increase of 0.16 and 0.15 kg, and 0.08 and 0.26 kg WBSF in the LT and SM, respectively; CAPN1:c.658T>C had negative effects on the WBSFs. Furthermore, six reconstructed haplotypes demonstrated significant associations with WBSF values (p < 0.05). In conclusion, the significant associations identified between the SNPs in CAPN1, CAST and WBSF values could be utilized in marker-assisted selection programs in order to improve the beef tenderness of Hanwoo cattle.
Collapse
|
16
|
Leal-Gutiérrez JD, Mateescu RG. Genetic basis of improving the palatability of beef cattle: current insights. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2019.1616299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
17
|
Wang Z, Ma H, Xu L, Zhu B, Liu Y, Bordbar F, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. Animals (Basel) 2019; 9:ani9060296. [PMID: 31151238 PMCID: PMC6617538 DOI: 10.3390/ani9060296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5'-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population.
Collapse
Affiliation(s)
- Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haoran Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
18
|
Bennett GL, Tait RG, Shackelford SD, Wheeler TL, King DA, Casas E, Smith TPL. Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and µ-calpain genes. J Anim Sci 2019; 97:569-577. [PMID: 30476168 DOI: 10.1093/jas/sky451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/21/2018] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to enhance estimates of additive, dominance, and epistatic effects of marker polymorphisms on beef carcass and quality traits. Myostatin (MSTN) F94L SNP and the µ-calpain (CAPN1) 316 and 4751 SNP haplotype have previously been associated with fat and muscle traits in beef cattle. Multiyear selection in a composite population segregating these polymorphisms increased minor allele (F94L L) and chosen haplotype (CAPN1 CC and GT) frequencies to intermediate levels resulting in more precise estimates of additive and nonadditive genetic effects. During the 3 yr after selection, 176 steers were evaluated for growth, carcass, meat quality, tenderness (n = 103), and meat color traits. The statistical model included year, age of dam, age of the steer, and genotype in a random animal model. The 9 genotypes (3 CAPN1 diplotypes × 3 F94L genotypes) affected marbling score, ribeye area, adjusted fat thickness, vision yield grade (all P < 0.001), slice shear force (P = 0.03), and CIE L* reflectance (P = 0.01). Linear contrasts of the 9 genotypes estimated additive, recessive, and epistatic genetic effects. Significant additive effects of the F94L L allele decreased marbling score, adjusted fat thickness, vision yield grade, and slice shear force; and increased ribeye area and CIE L* reflectance. The homozygous F94L FF and LL genotypes differed by 1.3 to 1.9 phenotypic SD for most carcass traits and by 0.8 to 0.9 SD for slice shear force and CIE L* reflectance but carcass weight differed by only 3 kg (0.1 SD). The L allele was partially recessive to F for ribeye area (P = 0.02) and the heterozygous FL means tended to be closer to the FF genotype than the LL genotype for other carcass traits but differences from additive were not significant. The CAPN1 additive × F94L additive effect on slice shear force was the only significant epistatic estimate. The F94L L allele is prevalent in Limousin but nearly absent in other U.S. purebreds. This allele had about half of the effects on birth weight, muscle, and fat traits reported for severe MSTN mutations in Belgian Blue and Piedmontese breeds. The interaction between MSTN and CAPN1 genotypes may reflect the strong additive effects of MSTN F94L L allele on fat and muscle traits interfering with the phenotypic effect of CAPN1 genotype on meat tenderness.
Collapse
Affiliation(s)
- Gary L Bennett
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Richard G Tait
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Steven D Shackelford
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Tommy L Wheeler
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - David A King
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Eduardo Casas
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Timothy P L Smith
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| |
Collapse
|
19
|
Braz CU, Taylor JF, Decker JE, Bresolin T, Espigolan R, Garcia DA, Gordo DGM, Magalhães AFB, de Albuquerque LG, de Oliveira HN. Polymorphism analysis in genes associated with meat tenderness in Nelore cattle. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
20
|
Tait RG, Cushman RA, McNeel AK, Casas E, Smith TP, Freetly HC, Bennett GL. μ-Calpain (CAPN1), calpastatin (CAST), and growth hormone receptor (GHR) genetic effects on Angus beef heifer performance traits and reproduction. Theriogenology 2018; 113:1-7. [DOI: 10.1016/j.theriogenology.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/11/2018] [Accepted: 02/03/2018] [Indexed: 12/27/2022]
|
21
|
Leal-Gutiérrez JD, Elzo MA, Johnson DD, Scheffler TL, Scheffler JM, Mateescu RG. Association of μ-Calpain and Calpastatin Polymorphisms with Meat Tenderness in a Brahman-Angus Population. Front Genet 2018. [PMID: 29520298 PMCID: PMC5827160 DOI: 10.3389/fgene.2018.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Autogenous proteolytic enzymes of the calpain family are implicated in myofibrillar protein degradation. As a result, the μ-calpain gene and its specific inhibitor, calpastatin, have been repeatedly investigated for their association with meat quality traits in cattle; however, no functional mutation has been identified for these two genes. The objectives of this study were: (1) to assess breed composition effect on tenderness; (2) to perform a linkage disequilibrium (LD) analysis in μ-calpain and calpastatin genes as well as an association analyses with tenderness; and (3) to analyze putative functional SNPs inside the significant LD block for an effect on tenderness. Tenderness measurements and genotypes for 16 SNPs in μ-calpain gene and 28 SNPs in calpastatin gene from 673 steers were analyzed. A bioinformatic analysis identified “putative functional SNPs” inside the associated LD block – polymorphisms able to produce a physical and/or chemical change in the DNA, mRNA, or translated protein in silico. Breed composition had a significant (P < 0.0001) effect on tenderness where animals with more than 80% Angus composition had the most tender meat. One 11-kb LD-block and three LD-blocks of 37, 17, and 14 kb in length were identified in the μ-calpain and calpastatin genes, respectively. Out of these, the LD-block 3 in calpastatin, tagged by SNPs located at 7-98566391 and 7-98581038, had a significant effect on tenderness with the TG-CG diplotype being approximately 1 kg more tender than the toughest diplotype, TG-CG. A total of 768 SNPs in the LD-block 3 of calpastatin were included in the bioinformatic analysis, and 28 markers were selected as putative functional SNPs inside the LD-block 3 of calpastatin; however, none of them were polymorphic in this population. Out of 15 initial polymorphisms segregating inside the LD-block 3 of calpastatin in this population, markers ARSUSMARC116, Cast5, rs730723459, and rs210861835 were found to be significantly associated with tenderness.
Collapse
Affiliation(s)
- Joel D Leal-Gutiérrez
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Mauricio A Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Dwain D Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Tracy L Scheffler
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Jason M Scheffler
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| |
Collapse
|
22
|
Animal breeding strategies can improve meat quality attributes within entire populations. Meat Sci 2017; 132:6-18. [DOI: 10.1016/j.meatsci.2017.04.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/15/2017] [Accepted: 04/18/2017] [Indexed: 12/28/2022]
|
23
|
Experimental Verification of CAPN1 and CAST Gene Polymorphisms in Different Generations of Da-Heng Broilers. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7968450. [PMID: 28713829 PMCID: PMC5497636 DOI: 10.1155/2017/7968450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/09/2017] [Accepted: 05/02/2017] [Indexed: 12/02/2022]
Abstract
The micromolar calcium activated neutral protease (CAPN1) and calpastatin (CAST) have been widely regarded as genes related to muscle growth and meat tenderness. The objective of this study was to verify the association of SNPs of CAPN1 and CAST genes with carcass and tenderness traits and search the possible change patterns of SNPs in CAPN1 and CAST genes in six generations of broiler breeding process for growth rate, efficiency, and reproduction, during the third generation and the ninth generation, respectively. We found that, for CAPN1, genetic effects between SNPs (G3535A, C7198A) and meat tenderness were similar in different generations, while SNP3 (G7324A) was a novel polymorphism and had significant association with carcass and tenderness traits (P < 0.05) in this study. Furthermore, there was significant association between SNP4 (G9950A) and carcass indexes instead of tenderness traits (P < 0.05) which was consistent in the two generations. Moreover, although SNP6 (G37868A) of CAST had no relevance to carcass traits or tenderness traits in the third generation, it showed significant association with LW and CW in the ninth generation (P < 0.05).
Collapse
|
24
|
Grochowska E, Borys B, Grześkowiak E, Mroczkowski S. Effect of the calpain small subunit 1 gene ( CAPNS1 ) polymorphism on meat quality traits in sheep. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
25
|
Casas E, Kehrli ME. A Review of Selected Genes with Known Effects on Performance and Health of Cattle. Front Vet Sci 2016; 3:113. [PMID: 28018909 PMCID: PMC5156656 DOI: 10.3389/fvets.2016.00113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 11/28/2016] [Indexed: 11/21/2022] Open
Abstract
There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions.
Collapse
Affiliation(s)
- Eduardo Casas
- National Animal Disease Center, USDA, ARS, Ames, IA, USA
| | | |
Collapse
|
26
|
Bernal Rubio YL, Gualdrón Duarte JL, Bates RO, Ernst CW, Nonneman D, Rohrer GA, King DA, Shackelford SD, Wheeler TL, Cantet RJC, Steibel JP. Implementing meta-analysis from genome-wide association studies for pork quality traits. J Anim Sci 2016; 93:5607-17. [PMID: 26641170 DOI: 10.2527/jas.2015-9502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.
Collapse
|
27
|
Association of single nucleotide polymorphisms in CAPN1, CAST and MB genes with meat color of Brahman and crossbreed cattle. Meat Sci 2016; 117:44-9. [DOI: 10.1016/j.meatsci.2016.02.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 11/24/2022]
|
28
|
Parr T, Mareko MHD, Ryan KJP, Hemmings KM, Brown DM, Brameld JM. The impact of growth promoters on muscle growth and the potential consequences for meat quality. Meat Sci 2016; 120:93-99. [PMID: 27179582 DOI: 10.1016/j.meatsci.2016.04.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 12/21/2022]
Abstract
To meet the demands of increased global meat consumption, animal production systems will have to become more efficient, or at least maintain the current efficiency utilizing feed ingredients that are not also used for human consumption. Use of growth promoters is a potential option for increasing production animal feed efficiency and increased muscle growth. The objective of this manuscript is to describe the mechanisms by which the growth promoters, beta-adrenergic agonists and growth hormone, mediate their effects, with specific consideration of the aspects which have implications for meat quality.
Collapse
Affiliation(s)
- Tim Parr
- Division of Nutritional Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, University of Nottingham, Loughborough, Leics LE12 5RD, UK.
| | | | - Kevin J P Ryan
- Division of Nutritional Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, University of Nottingham, Loughborough, Leics LE12 5RD, UK
| | - Krystal M Hemmings
- College of Life and Natural Sciences, Department of Natural Sciences, University of Derby, Derby DE22 1GB, UK
| | - David M Brown
- Division of Nutritional Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, University of Nottingham, Loughborough, Leics LE12 5RD, UK
| | - John M Brameld
- Division of Nutritional Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, University of Nottingham, Loughborough, Leics LE12 5RD, UK
| |
Collapse
|
29
|
Bolormaa S, Hayes BJ, van der Werf JHJ, Pethick D, Goddard ME, Daetwyler HD. Detailed phenotyping identifies genes with pleiotropic effects on body composition. BMC Genomics 2016; 17:224. [PMID: 26968377 PMCID: PMC4788919 DOI: 10.1186/s12864-016-2538-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 02/05/2016] [Indexed: 12/27/2022] Open
Abstract
Background Genetic variation in both the composition and distribution of fat and muscle in the body is important to human health as well as the healthiness and value of meat from cattle and sheep. Here we use detailed phenotyping and a multi-trait approach to identify genes explaining variation in body composition traits. Results A multi-trait genome wide association analysis of 56 carcass composition traits measured on 10,613 sheep with imputed and real genotypes on 510,174 SNPs was performed. We clustered 71 significant SNPs into five groups based on their pleiotropic effects across the 56 traits. Among these 71 significant SNPs, one group of 11 SNPs affected the fatty acid profile of the muscle and were close to 8 genes involved in fatty acid or triglyceride synthesis. Another group of 23 SNPs had an effect on mature size, based on their pattern of effects across traits, but the genes near this group of SNPs did not share any obvious function. Many of the likely candidate genes near SNPs with significant pleiotropic effects on the 56 traits are involved in intra-cellular signalling pathways. Among the significant SNPs were some with a convincing candidate gene due to the function of the gene (e.g. glycogen synthase affecting glycogen concentration) or because the same gene was associated with similar traits in other species. Conclusions Using a multi-trait analysis increased the power to detect associations between SNP and body composition traits compared with the single trait analyses. Detailed phenotypic information helped to identify a convincing candidate in some cases as did information from other species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2538-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sunduimijid Bolormaa
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia. .,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.
| | - Ben J Hayes
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Julius H J van der Werf
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - David Pethick
- Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Michael E Goddard
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.,School of Land and Environment, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hans D Daetwyler
- AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.,Cooperative Research Centre for Sheep Industry Innovation, Armidale, NSW, 2351, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| |
Collapse
|
30
|
Rubio Lozano MS, Alfaro-Zavala S, Sifuentes-Rincón AM, Parra-Bracamonte GM, Braña Varela D, Medina RDM, Pérez Linares C, Ríos Rincón F, Sánchez Escalante A, Torrescano Urrutia G, Figueroa Saavedra F. Meat Tenderness Genetic and Genomic Variation Sources in Commercial Beef Cattle. J FOOD QUALITY 2015. [DOI: 10.1111/jfq.12185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- María Salud Rubio Lozano
- Facultad Medicina Veterinaria y Zootecnia; Universidad Nacional Autónoma de México; México DF Mexico
| | - Selene Alfaro-Zavala
- Facultad Medicina Veterinaria y Zootecnia; Universidad Nacional Autónoma de México; México DF Mexico
| | - Ana María Sifuentes-Rincón
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Boulevard del Maestro, SN, Esq. Elías Piña, Col. Narciso Mendoza Reynosa Tamaulipas 88710 Mexico
| | - Gaspar Manuel Parra-Bracamonte
- Centro de Biotecnología Genómica; Instituto Politécnico Nacional; Boulevard del Maestro, SN, Esq. Elías Piña, Col. Narciso Mendoza Reynosa Tamaulipas 88710 Mexico
| | - Diego Braña Varela
- Agrícolas y Pecuarias-Fisiología; Instituto Nacional de Investigaciones Forestales; Colón Querétaro Mexico
| | | | - Cristina Pérez Linares
- Instituto de Investigaciones en Ciencias Veterinarias; Universidad Autónoma de Baja California; Mexicali Baja California Mexico
| | - Francisco Ríos Rincón
- Facultad de Medicina Veterinaria y Zootecnia; Universidad Autónoma de Sinaloa; Culiacán Sinaloa Mexico
| | | | | | - Fernando Figueroa Saavedra
- Instituto de Investigaciones en Ciencias Veterinarias; Universidad Autónoma de Baja California; Mexicali Baja California Mexico
| |
Collapse
|
31
|
Gurgul A, Szmatoła T, Ropka-Molik K, Jasielczuk I, Pawlina K, Semik E, Bugno-Poniewierska M. Identification of genome-wide selection signatures in the Limousin beef cattle breed. J Anim Breed Genet 2015; 133:264-76. [PMID: 26611546 DOI: 10.1111/jbg.12196] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/24/2015] [Indexed: 02/03/2023]
Abstract
The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection footprints were detected on chromosomes 1, 4, 8 and 14, which are known to carry several quantitative trait loci for growth traits and meat quality. The study provides information about the genes and metabolic pathways potentially modified under the influence of directional selection, aimed at improving beef production characteristics in Limousin cattle.
Collapse
Affiliation(s)
- A Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - T Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - K Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - I Jasielczuk
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - K Pawlina
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - E Semik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - M Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| |
Collapse
|
32
|
Parra-Bracamonte GM, Martínez-González JC, Sifuentes-Rincón AM, Moreno-Medina VR, Ortega-Rivas E. Meat tenderness genetic polymorphisms occurrence and distribution in five Zebu breeds in Mexico. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
33
|
Liu X, Usman T, Wang Y, Wang Z, Xu X, Wu M, Zhang Y, Zhang X, Li Q, Liu L, Shi W, Qin C, Geng F, Wang C, Tan R, Huang X, Liu A, Wu H, Tan S, Yu Y. Polymorphisms in epigenetic and meat quality related genes in fourteen cattle breeds and association with beef quality and carcass traits. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:467-75. [PMID: 25656186 PMCID: PMC4341095 DOI: 10.5713/ajas.13.0837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Revised: 02/21/2014] [Accepted: 08/14/2014] [Indexed: 01/19/2023]
Abstract
Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.
Collapse
Affiliation(s)
- Xuan Liu
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tahir Usman
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China ; Department of Animal Health, The University of Agriculture, Peshawar, Peshawar 25000, Pakistan
| | - Yachun Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zezhao Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xianzhou Xu
- Dalian Xuelong Industry Limited Group, Dalian 116001, China
| | - Meng Wu
- Dalian Xuelong Industry Limited Group, Dalian 116001, China
| | - Yi Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xu Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiang Li
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lin Liu
- Beijing Dairy Cattle Center, Beijing 100193, China
| | - Wanhai Shi
- Beijing Dairy Cattle Center, Beijing 100193, China
| | - Chunhua Qin
- Ningxia Sygen BioEngineering Research Center, Yinchuan 750000, China
| | - Fanjun Geng
- Dingyuan Seedstock Bulls Breeding Ltd. Company, Zhengzhou 450000, China
| | - Congyong Wang
- Dingyuan Seedstock Bulls Breeding Ltd. Company, Zhengzhou 450000, China
| | - Rui Tan
- Xinjiang General Livestock Service, Urumqi 830000, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agriculture University, Urumqi 830000 China
| | - Airong Liu
- Xiertala Breeding Farm, Hailaer Farm Buro, Hailaer 021008, China
| | - Hongjun Wu
- Hailaer Farm Buro, Hailaer 021008, China
| | - Shixin Tan
- Xinjiang Tianshan Animal Husbandry Bio-Eng. Co. Ltd, Urumqi 830000, China
| | - Ying Yu
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
34
|
Cushman RA, Tait RG, McNeel AK, Forbes ED, Amundson OL, Lents CA, Lindholm-Perry AK, Perry GA, Wood JR, Cupp AS, Smith TPL, Freetly HC, Bennett GL. A polymorphism in myostatin influences puberty but not fertility in beef heifers, whereas µ-calpain affects first calf birth weight1. J Anim Sci 2015; 93:117-26. [DOI: 10.2527/jas.2014-8505] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
35
|
Tait RG, Shackelford SD, Wheeler TL, King DA, Keele JW, Casas E, Smith TPL, Bennett GL. CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization1,2,3,4. J Anim Sci 2014; 92:5382-93. [DOI: 10.2527/jas.2014-8211] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- R. G. Tait
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - S. D. Shackelford
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - T. L. Wheeler
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - D. A. King
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - J. W. Keele
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - E. Casas
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - T. P. L. Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - G. L. Bennett
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| |
Collapse
|
36
|
Dang CG, Cho SH, Sharma A, Kim HC, Jeon GJ, Yeon SH, Hong SK, Park BY, Kang HS, Lee SH. Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1328-35. [PMID: 25178377 PMCID: PMC4150200 DOI: 10.5713/ajas.2013.13690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/02/2014] [Accepted: 04/11/2014] [Indexed: 01/23/2023]
Abstract
Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10−6) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.
Collapse
Affiliation(s)
- C G Dang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Cho
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - A Sharma
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H C Kim
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - G J Jeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Yeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S K Hong
- National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - B Y Park
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H S Kang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Lee
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| |
Collapse
|
37
|
Lian T, Wang L, Liu Y. A New Insight into the Role of Calpains in Post-mortem Meat Tenderization in Domestic Animals: A review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:443-54. [PMID: 25049808 PMCID: PMC4093471 DOI: 10.5713/ajas.2012.12365] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 11/22/2012] [Accepted: 09/15/2012] [Indexed: 01/07/2023]
Abstract
Tenderness is the most important meat quality trait, which is determined by intracellular environment and extracellular matrix. Particularly, specific protein degradation and protein modification can disrupt the architecture and integrity of muscle cells so that improves the meat tenderness. Endogenous proteolytic systems are responsible for modifying proteinases as well as the meat tenderization. Abundant evidence has testified that calpains (CAPNs) including calpain I (CAPN1) and calpastatin (CAST) have the closest relationship with tenderness in livestock. They are involved in a wide range of physiological processes including muscle growth and differentiation, pathological conditions and post-mortem meat aging. Whereas, Calpain3 (CAPN3) has been established as an important activating enzyme specifically expressed in livestock's skeletal muscle, but its role in domestic animals meat tenderization remains controversial. In this review, we summarize the role of CAPN1, calpain II (CAPN2) and CAST in post-mortem meat tenderization, and analyse the relationship between CAPN3 and tenderness in domestic animals. Besides, the possible mechanism affecting post-mortem meat aging and improving meat tenderization, and current possible causes responsible for divergence (whether CAPN3 contributes to animal meat tenderization or not) are inferred. Only the possible mechanism of CAPN3 in meat tenderization has been confirmed, while its exact role still needs to be studied further.
Collapse
Affiliation(s)
- Ting Lian
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Yiping Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| |
Collapse
|
38
|
Polymorphisms in twelve candidate genes are associated with growth, muscle lipid profile and meat quality traits in eleven European cattle breeds. Mol Biol Rep 2014; 41:4721-31. [DOI: 10.1007/s11033-014-3343-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
|
39
|
Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, Kemper K, Tier B, Savin K, Hayes BJ, Goddard ME. A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genet 2014; 10:e1004198. [PMID: 24675618 PMCID: PMC3967938 DOI: 10.1371/journal.pgen.1004198] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 01/02/2014] [Indexed: 12/14/2022] Open
Abstract
Polymorphisms that affect complex traits or quantitative trait loci (QTL) often affect multiple traits. We describe two novel methods (1) for finding single nucleotide polymorphisms (SNPs) significantly associated with one or more traits using a multi-trait, meta-analysis, and (2) for distinguishing between a single pleiotropic QTL and multiple linked QTL. The meta-analysis uses the effect of each SNP on each of n traits, estimated in single trait genome wide association studies (GWAS). These effects are expressed as a vector of signed t-values (t) and the error covariance matrix of these t values is approximated by the correlation matrix of t-values among the traits calculated across the SNP (V). Consequently, t'V−1t is approximately distributed as a chi-squared with n degrees of freedom. An attractive feature of the meta-analysis is that it uses estimated effects of SNPs from single trait GWAS, so it can be applied to published data where individual records are not available. We demonstrate that the multi-trait method can be used to increase the power (numbers of SNPs validated in an independent population) of GWAS in a beef cattle data set including 10,191 animals genotyped for 729,068 SNPs with 32 traits recorded, including growth and reproduction traits. We can distinguish between a single pleiotropic QTL and multiple linked QTL because multiple SNPs tagging the same QTL show the same pattern of effects across traits. We confirm this finding by demonstrating that when one SNP is included in the statistical model the other SNPs have a non-significant effect. In the beef cattle data set, cluster analysis yielded four groups of QTL with similar patterns of effects across traits within a group. A linear index was used to validate SNPs having effects on multiple traits and to identify additional SNPs belonging to these four groups. We describe novel methods for finding significant associations between a genome wide panel of SNPs and multiple complex traits, and further for distinguishing between genes with effects on multiple traits and multiple linked genes affecting different traits. The method uses a meta-analysis based on estimates of SNP effects from independent single trait genome wide association studies (GWAS). The method could therefore be widely used to combine already published GWAS results. The method was applied to 32 traits that describe growth, body composition, feed intake and reproduction in 10,191 beef cattle genotyped for approximately 700,000 SNP. The genes found to be associated with these traits can be arranged into 4 groups that differ in their pattern of effects and hence presumably in their physiological mechanism of action. For instance, one group of genes affects weight and fatness in the opposite direction and can be described as a group of genes affecting mature size, while another group affects weight and fatness in the same direction.
Collapse
Affiliation(s)
- Sunduimijid Bolormaa
- Victorian Department of Environment and Primary Industries, Bundoora, Victoria, Australia
- * E-mail:
| | - Jennie E. Pryce
- Victorian Department of Environment and Primary Industries, Bundoora, Victoria, Australia
| | - Antonio Reverter
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Queensland, Australia
| | - Yuandan Zhang
- Animal Genetics and Breeding Unit, University of New England, Armidale, New South Wales, Australia
| | - William Barendse
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Queensland, Australia
| | - Kathryn Kemper
- School of Land and Environment, University of Melbourne, Parkville, Victoria, Australia
| | - Bruce Tier
- Animal Genetics and Breeding Unit, University of New England, Armidale, New South Wales, Australia
| | - Keith Savin
- Victorian Department of Environment and Primary Industries, Bundoora, Victoria, Australia
| | - Ben J. Hayes
- Victorian Department of Environment and Primary Industries, Bundoora, Victoria, Australia
| | - Michael E. Goddard
- Victorian Department of Environment and Primary Industries, Bundoora, Victoria, Australia
- School of Land and Environment, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
40
|
Tait RG, Shackelford SD, Wheeler TL, King DA, Casas E, Thallman RM, Smith TPL, Bennett GL. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies1,2,3. J Anim Sci 2014; 92:456-66. [DOI: 10.2527/jas.2013-7075] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. G. Tait
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - S. D. Shackelford
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - T. L. Wheeler
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - D. A. King
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - E. Casas
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - R. M. Thallman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - T. P. L. Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| | - G. L. Bennett
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166
| |
Collapse
|
41
|
Calvo J, Iguácel L, Kirinus J, Serrano M, Ripoll G, Casasús I, Joy M, Pérez-Velasco L, Sarto P, Albertí P, Blanco M. A new single nucleotide polymorphism in the calpastatin (CAST) gene associated with beef tenderness. Meat Sci 2014; 96:775-82. [DOI: 10.1016/j.meatsci.2013.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 09/27/2013] [Accepted: 10/03/2013] [Indexed: 11/25/2022]
|
42
|
Effects of genetic variants for the bovine calpain gene on meat tenderness. Mol Biol Rep 2014; 41:2963-70. [DOI: 10.1007/s11033-014-3152-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 01/13/2014] [Indexed: 10/25/2022]
|
43
|
Nattrass GS, Cafe LM, McIntyre BL, Gardner GE, McGilchrist P, Robinson DL, Wang YH, Pethick DW, Greenwood PL. A post-transcriptional mechanism regulates calpastatin expression in bovine skeletal muscle. J Anim Sci 2014; 92:443-55. [PMID: 24664555 DOI: 10.2527/jas.2013-6978] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to investigate whether single nucleotide polymorphisms (SNP) in the calpain 1 (CAPN1), calpain 3 (CAPN3) and calpastatin (CAST) genes, which have been shown to be associated with shear force and tenderness differences in the skeletal muscle of cattle, contribute to phenotypic variation in muscle tenderness by modulating the transcriptional activity of their respective gene. The mRNA expression of the calpain and CAST genes was assessed in the longissimus lumborum muscle (LLM) of cattle from two herds located in distinct production zones on the east (New South Wales, NSW) and west (Western Australia, WA) of Australia. The cattle in the herds were mainly Brahman cattle (Bos indicus) with smaller populations of Angus cattle (Bos taurus). There were 191 steers in the WA herd and 107 steers and 106 heifers in the NSW herd. These herds were established by choosing cattle from the diverse population which had different single nucleotide polymorphism (SNP) genotypes at the CAPN1, CAPN3 and CAST loci. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), the transcriptional activities of the CAPN1 and the CAST genes, but not the CAPN3 gene, were found to differ between favorable, positively associated with tenderness, and unfavorable, negatively associated with tenderness, allelic variants of these genes. These findings suggest that the muscle shear force and consumer taste panel differences in tenderness explained by the CAPN1 and CAST gene markers are a consequence of alterations in their mRNA levels, which may ultimately influence the protein activity of these genes, thereby altering the rate and(or) the extent of postmortem proteolysis in skeletal muscle. Of particular importance were the significantly lower type II and type III CAST 5' splice variant mRNA levels that were detected in the LLM muscle of Brahman and Angus cattle with 2 favourable alleles of the CAST:c.2832A > G polymorphism. Moreover, a reduction in the abundance of an alternative polyadenylated variant of the CAST transcript, terminated at the proximal polyadenylation site, provides a unique insight into the potential involvement of a post-transcriptional regulatory mechanism which may influence protein expression levels in bovine skeletal muscle.
Collapse
Affiliation(s)
- G S Nattrass
- Australian Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, NSW 2351, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Lee SH, Kim SC, Chai HH, Cho SH, Kim HC, Lim D, Choi BH, Dang CG, Sharma A, Gondro C, Yang BS, Hong SK. Mutations in calpastatin and μ-calpain are associated with meat tenderness, flavor and juiciness in Hanwoo (Korean cattle): molecular modeling of the effects of substitutions in the calpastatin/μ-calpain complex. Meat Sci 2013; 96:1501-8. [PMID: 24468663 DOI: 10.1016/j.meatsci.2013.11.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 10/14/2013] [Accepted: 11/26/2013] [Indexed: 10/25/2022]
Abstract
The objective of this study was to evaluate the effects of seven single nucleotide polymorphisms (SNPs) in Calpain 1 and Calpastatin genes previously associated with meat tenderness attributes in other cattle breeds in Korean Hanwoo cattle. The Hanwoo resource population was used to study association of 7 SNPs with beef tenderness, flavor, juiciness, intramuscular fat and shear force. In this association study, CAST:c.182A>G (+0.14, P=0.04) and CAST:c.1985G>C (-0.12, P=0.02) had significant effects on juiciness, but no effects on other traits. In contrast, CAPN1:c.1589G>A was associated with meat tenderness (P=0.01) and juiciness (P=0.04). The CAPN1:c.1589G>A (Val530Ile) SNP marker displayed significant effect on the meat tenderness score which is strongly supported by molecular modeling of the CAPN1:c.1589G>A (Val530Ile) variant that inhibits CAST protein from binding more strongly than the wild-type protein, which may explain its effect on meat tenderness.
Collapse
Affiliation(s)
- Seung-Hwan Lee
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, PyeongChang 232-950, Republic of Korea.
| | - Seung-Chang Kim
- Animal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| | - Han-Ha Chai
- Animal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| | - Soo-Hyun Cho
- Animal Production Research and Development Division, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| | - Hyeong-Cheol Kim
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, PyeongChang 232-950, Republic of Korea
| | - Dajeong Lim
- Animal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| | - Bong-Hwan Choi
- Animal Genome & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| | - Chang-Gwan Dang
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, PyeongChang 232-950, Republic of Korea
| | - Aditi Sharma
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, PyeongChang 232-950, Republic of Korea
| | - Cedric Gondro
- School of Environment & Rural Science, University of New England, Armidale, NSW 2350, Australia
| | - Boh-Suk Yang
- Hanwoo Experiment Station, National Institute of Animal Science, RDA, PyeongChang 232-950, Republic of Korea
| | - Seong-Koo Hong
- Department of Life and Environment, National Institute of Animal Science, RDA, Suwon, Republic of Korea
| |
Collapse
|
45
|
Casas E, Duan Q, Schneider MJ, Shackelford SD, Wheeler TL, Cundiff LV, Reecy JM. Polymorphisms in calpastatin and mu-calpain genes are associated with beef iron content. Anim Genet 2013; 45:283-4. [PMID: 24303986 DOI: 10.1111/age.12108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2013] [Indexed: 01/19/2023]
Abstract
The objective of this study was to assess the association of markers in the calpastatin and mu-calpain loci with iron in beef cattle muscle. The population consisted of 259 cross-bred steers from Beefmaster, Brangus, Bonsmara, Romosinuano, Hereford and Angus sires. Total iron and heme iron concentrations were measured. Markers in the calpastatin (referred to as CAST) and mu-calpain (referred to as CAPN4751) genes were used to assess their association with iron levels. The mean and standard error for iron and heme iron content in the population was 35.6 ± 1.3 μg and 27.1 ± 1.4 μg respectively. Significant associations (P < 0.01) of markers were observed for both iron and heme iron content. For CAST, animals with the CC genotype had higher levels of iron and heme iron in longissimus dorsi muscle. For CAPN4751, individuals with the TT genotype had higher concentrations of iron and heme iron than did animals with the CC and CT genotypes. Genotypes known to be associated with tougher meat were associated with higher levels of iron concentration.
Collapse
Affiliation(s)
- E Casas
- National Animal Disease Center, USDA, ARS, Ames, IA, 50010, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Bolormaa S, Pryce JE, Kemper KE, Hayes BJ, Zhang Y, Tier B, Barendse W, Reverter A, Goddard ME. Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies. Genet Sel Evol 2013; 45:43. [PMID: 24168700 PMCID: PMC4176739 DOI: 10.1186/1297-9686-45-43] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 10/14/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The apparent effect of a single nucleotide polymorphism (SNP) on phenotype depends on the linkage disequilibrium (LD) between the SNP and a quantitative trait locus (QTL). However, the phase of LD between a SNP and a QTL may differ between Bos indicus and Bos taurus because they diverged at least one hundred thousand years ago. Here, we test the hypothesis that the apparent effect of a SNP on a quantitative trait depends on whether the SNP allele is inherited from a Bos taurus or Bos indicus ancestor. METHODS Phenotype data on one or more traits and SNP genotype data for 10 181 cattle from Bos taurus, Bos indicus and composite breeds were used. All animals had genotypes for 729 068 SNPs (real or imputed). Chromosome segments were classified as originating from B. indicus or B. taurus on the basis of the haplotype of SNP alleles they contained. Consequently, SNP alleles were classified according to their sub-species origin. Three models were used for the association study: (1) conventional GWAS (genome-wide association study), fitting a single SNP effect regardless of subspecies origin, (2) interaction GWAS, fitting an interaction between SNP and subspecies-origin, and (3) best variable GWAS, fitting the most significant combination of SNP and sub-species origin. RESULTS Fitting an interaction between SNP and subspecies origin resulted in more significant SNPs (i.e. more power) than a conventional GWAS. Thus, the effect of a SNP depends on the subspecies that the allele originates from. Also, most QTL segregated in only one subspecies, suggesting that many mutations that affect the traits studied occurred after divergence of the subspecies or the mutation became fixed or was lost in one of the subspecies. CONCLUSIONS The results imply that GWAS and genomic selection could gain power by distinguishing SNP alleles based on their subspecies origin, and that only few QTL segregate in both B. indicus and B. taurus cattle. Thus, the QTL that segregate in current populations likely resulted from mutations that occurred in one of the subspecies and can have both positive and negative effects on the traits. There was no evidence that selection has increased the frequency of alleles that increase body weight.
Collapse
Affiliation(s)
- Sunduimijid Bolormaa
- Victorian Department of Environment and Primary Industries, Bundoora 3083, VIC, Australia.
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Knight MI, Daetwyler HD, Hayes BJ, Hayden MJ, Ball AJ, Pethick DW, McDonagh MB. An independent validation association study of carcass quality, shear force, intramuscular fat percentage and omega-3 polyunsaturated fatty acid content with gene markers in Australian lamb. Meat Sci 2013; 96:1025-33. [PMID: 23948658 DOI: 10.1016/j.meatsci.2013.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 05/17/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022]
Abstract
Previous association studies revealed several single nucleotide polymorphisms (SNPs) that explained the observed phenotypic variation for meat tenderness and long-chain omega-3 polyunsaturated fatty acid (PUFA) content of Australian lamb. To confirm the validity of these associated SNPs at predicting meat tenderness and omega-3 PUFA content, an independent validation study was designed. The OvineSNP50 genotypes of these animals were used to impute the 192 SNP Meat Quality Research (MQR) panel genotypes on nearly 6200 animals from the Cooperative Research Centre for Sheep Industry Innovation Information Nucleus Flock and Sheep Genomics Falkiner Memorial Field Station flock. Association analysis revealed numerous SNP from the 192 SNP MQR panel that were associated with carcass quality - fat depth at the C-site and eye muscle depth; shear force at day 1 and day 5 after slaughter (SF1 and SF5); and omega-3 PUFA content at P<0.01. However, 1 SNP was independently validated for SF5 (i.e. CAST_101781475). The magnitude of the effect of each significant SNP and the relative allele frequencies across Merino-, Maternal- and Terminal-sired progeny was determined. The independently validated SNP for SF5 and the associated SNP with omega-3 PUFA content will accelerate efforts to improve these phenotypic traits in Australian lamb.
Collapse
Affiliation(s)
- Matthew I Knight
- Cooperative Research Centre for Sheep Industry Innovation, CJ Hawkins Homestead Building, University of New England, Armidale, NSW, 2351, Australia; Biosciences Research Division, Department of Primary Industries, AgriBio Building, 5 Ring Road, Bundoora, Vic, 3083, Australia; Future Farming Systems Research Division, Department of Primary Industries, 915 Mt Napier Road, Hamilton, Vic, 3300, Australia.
| | | | | | | | | | | | | |
Collapse
|
48
|
Dunner S, Sevane N, García D, Cortés O, Valentini A, Williams J, Mangin B, Cañón J, Levéziel H. Association of genes involved in carcass and meat quality traits in 15 European bovine breeds. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
49
|
Rasouli Z, Zerehdaran S, Azari MA, Shargh MS. Genetic polymorphism of the CAPN1 gene is associated with meat quality traits in Japanese quail. Br Poult Sci 2013; 54:171-5. [PMID: 23647179 DOI: 10.1080/00071668.2013.770128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. The objective of the study was to investigate the polymorphisms in two regions of the calpain 1 (CAPN1) gene and their association with breast and thigh meat quality in Japanese quail (ultimate pH (pHu), lightness, redness, yellowness, drip loss, thawing-cooking loss, water holding capacity and shear force, SF). 2. Blood samples were collected randomly from 100 birds and DNA was extracted using a commercial kit. Genotypes were determined by PCR amplification followed by single-strand conformation polymorphism (SSCP) analysis. The effect of CAPN1 genotypes on meat quality traits were analysed using a general linear model (GLM) procedure. 3. Genotypes of the CAPN1 gene in the first region (217-bp) analysed were significantly associated with yellowness and SF. The TT genotype showed significantly higher yellowness and lower shear force (more tenderness) than CT and CC genotypes. Genotypes of the second region of the gene (intron 4, 800-bp) were significantly associated with pHu, redness and SF of the breast meat. The BB genotype showed significantly lower pHu and redness and higher SF (lower tenderness) than other genotypes. 4. Information on polymorphisms of the CAPN1 gene will eventually provide useful information for improving meat quality of Japanese quail through marker-assisted selection.
Collapse
Affiliation(s)
- Z Rasouli
- Department of Animal Science, Gorgan University of Agricultural Sciences and Natural Resources, Golestan, Iran
| | | | | | | |
Collapse
|
50
|
Bolormaa S, Pryce JE, Kemper K, Savin K, Hayes BJ, Barendse W, Zhang Y, Reich CM, Mason BA, Bunch RJ, Harrison BE, Reverter A, Herd RM, Tier B, Graser HU, Goddard ME. Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. J Anim Sci 2013; 91:3088-104. [PMID: 23658330 DOI: 10.2527/jas.2012-5827] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction [BayesR and genomic BLUP (GBLUP)] either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identified many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.
Collapse
Affiliation(s)
- S Bolormaa
- Victorian Department of Primary Industries, Bundoora, VIC 3083, Australia.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|