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
|
Berry DP, Spangler ML. Animal board invited review: Practical applications of genomic information in livestock. Animal 2023; 17:100996. [PMID: 37820404 DOI: 10.1016/j.animal.2023.100996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic evaluations exploit genome-wide genotype information to improve the accuracy of predicting an animal's (and by extension its progeny's) genetic merit. Genomic data also provide a huge resource for research, albeit the outcome from this research, if successful, should eventually be realised through one of the ten applications already mentioned. The process for generating a genotype all the way from sample procurement to identifying erroneous genotypes is described, as are the steps that should be considered when developing a bespoke genotyping panel for practical application.
Collapse
Affiliation(s)
- D P Berry
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland.
| | - M L Spangler
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| |
Collapse
|
3
|
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
|
4
|
Castillo-Salas CA, Luna-Nevárez G, Reyna-Granados JR, Luna-Ramirez RI, Limesand SW, Luna-Nevárez P. Molecular markers for thermo-tolerance are associated with reproductive and physiological traits in Pelibuey ewes raised in a semiarid environment. J Therm Biol 2023; 112:103475. [PMID: 36796920 DOI: 10.1016/j.jtherbio.2023.103475] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/18/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
Pelibuey sheep exhibit reproductive activity through the year, but warm weather lowers their fertility and demonstrates physiological limitations of environmental heat stress. Single nucleotide polymorphisms (SNPs) associated with heat stress tolerance in sheep have been reported previously. The objective was to validate the association of seven thermo-tolerance SNP markers with reproductive and physiological traits in Pelibuey ewes raised in a semiarid region. Pelibuey ewes were assigned to a cool (January 1st.- March 31st.; n = 101) or warm (April 1st.- August 31st.; n = 104) experimental group. All ewes were exposed to fertile rams and assessed for pregnancy diagnosis 90 days later; lambing day was reported at birth. These data served to calculate the reproductive traits of services per conception, prolificacy, days to estrus, days to conception, conception rate and lambing rate. Rectal temperature, rump/leg skin temperature and respiratory rate were measured and reported as physiological traits. Blood samples were collected and processed to extract DNA, which was genotyped using the TaqMan allelic discrimination method and qPCR. A mixed effects statistical model was used to validate associations between SNP genotypes and phenotypic traits. The SNPs rs421873172, rs417581105 and rs407804467 were confirmed as markers associated with reproductive and physiological traits (P < 0.05), and these SNPs were in the genes PAM, STAT1 and FBXO11, respectively. Interestingly, these SNP markers resulted as predictors for the evaluated traits but only in ewes from the warm group, which indicated their association with heat-stress tolerance. An additive SNP effect was confirmed with the highest contribution (P < 0.01) of the SNP rs417581105 for the evaluated traits. Reproductive performance improved (P < 0.05) and physiological parameters decreased in ewes carrying favorable SNP genotypes. In conclusion, three thermo-tolerance SNP markers were associated with improved reproductive and physiological traits in a prospective population of heat-stressed ewes raised in a semiarid environment.
Collapse
Affiliation(s)
- Candelario A Castillo-Salas
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Guillermo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Javier R Reyna-Granados
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México
| | - Rosa I Luna-Ramirez
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Sean W Limesand
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Pablo Luna-Nevárez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, 85000, México.
| |
Collapse
|
5
|
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
|
6
|
Halli K, Bohlouli M, Schulz L, Sundrum A, König S. Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed. Transl Anim Sci 2022; 6:txac022. [PMID: 35308836 PMCID: PMC8925308 DOI: 10.1093/tas/txac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw), and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix), or both (H-matrix). Genome-wide association studies (GWASs) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW, and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW, and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27, and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), −0.13 (G), and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1, and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW, and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1, and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB, and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.
Collapse
Affiliation(s)
- K Halli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - M Bohlouli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - L Schulz
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - A Sundrum
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - S König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| |
Collapse
|
7
|
Nack MF, DelCurto Wyffels HM, Wyffels SA, DelCurto T. Relationship of gene markers to residual feed intake, ADG, and marbling of 4 years of MSU Steer-A-Year steers. Transl Anim Sci 2021; 4:S160-S164. [PMID: 33381743 PMCID: PMC7754223 DOI: 10.1093/tas/txaa131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Makae F Nack
- Northern Agricultural Research Center, Montana State University, Havre, MT
| | | | - Samuel A Wyffels
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT
| | - Timothy DelCurto
- Northern Agricultural Research Center, Montana State University, Havre, MT
| |
Collapse
|
8
|
Berry DP, Conroy S, Hegarty PJ, Evans RD, Pabiou T, Judge MM. Inter-animal genetic variability exist in organoleptic properties of prime beef meat. Meat Sci 2020; 173:108401. [PMID: 33310548 DOI: 10.1016/j.meatsci.2020.108401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 01/27/2023]
Abstract
The objective of the present study was to estimate genetic parameters for four organoleptic traits in beef meat, namely tenderness, juiciness, flavour and chewiness using data from 5380 young crossbred progeny of 748 different sires. As well as using the mean animal sensory score across all panellists for a given trait, other aggregate functions such as the median and modal values were also investigated. The heritability (SE) of mean tenderness, juiciness, flavour and chewiness was 0.16 (0.04), 0.14 (0.04), 0.11 (0.03) and 0.21 (0.06), respectively; heritability estimates for the other aggregate values of these traits were generally lower. All genetic correlations between tenderness, juiciness and flavour were positive (0.52 to 0.68) while the genetic correlations between these three traits with chewiness were all negative varying from -0.95 to -0.48. Weak genetic correlations (≤|0.16|) were evident between the sensory traits and all of carcass weight, conformation and subcutaneous fat cover.
Collapse
Affiliation(s)
- D P Berry
- Teagasc, Animal & Grassland Research and Innovation Center, Moorepark, Fermoy, Co. Cork, Ireland.
| | - S Conroy
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - P J Hegarty
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - R D Evans
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - T Pabiou
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - M M Judge
- Teagasc, Animal & Grassland Research and Innovation Center, Moorepark, Fermoy, Co. Cork, Ireland
| |
Collapse
|
9
|
Biosensors in Evaluation of Quality of Meat and Meat Products – A Review. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Abstract
Biosensors can find application in meat and meat products testing for safety, including microbial and other contaminants, and quality, including meat freshness, beef tenderness and pork quality defects. The available biosensors enable the evaluation of freshness, the classification of tenderness of meat products, the evaluation of the glycolysis extent and the presence of the microbial and other contaminants. Since biosensors depend on receptor types, the expansion of knowledge on metabolic transformations occurring in meat contributes to the development of new potential markers and indicators. Examples include assays for glucose, lactates, hypoxanthines, calpastastins, microbial and other contaminants in meat products, augmenting conventional methods. At the same time, biosensors rely on transducers for detection, requiring achievement in many fields including nanotechnology and optics, among others. Biosensors have potential to become a fundamental tool for monitoring and controlling safety and quality of meat products in the future. Hence the aim of the present paper is to present the current state of knowledge on the application of biosensors in meat.
Collapse
|
10
|
Raza SHA, Khan S, Amjadi M, Abdelnour SA, Ohran H, Alanazi KM, Abd El-Hack ME, Taha AE, Khan R, Gong C, Schreurs NM, Zhao C, Wei D, Zan L. Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle. Arch Biochem Biophys 2020; 694:108543. [PMID: 32798459 DOI: 10.1016/j.abb.2020.108543] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/26/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
Genomic selection has an essential role in the livestock economy by increasing selection productivity. Genomics provides a mechanism to increase the rate of genetic gain using marker-assisted selection. Various quantitative trait loci (QTL) associated with body, carcass and meat quality traits in beef cattle have been found. It is widely accepted that QTL traits in livestock species are regulated by several genes and factors from the environment. Genome-wide association studies (GWAS) are a powerful approach in identifying QTL and to establish genomic regions harboring the genes and polymorphisms associated with specific characteristics in beef cattle. Due to their impact on economic returns, growth, carcass and meat quality traits of cattle are frequently used as essential criteria in selection in breeding programs., GWAS has been used in beef cattle breeding and genetic program and some progress has been made. Furthermore, numerous genes and markers related to productivity traits in beef cattle have been found. This review summarizes the advances in the use of GWAS in beef cattle production and outlines the associations with growth, carcass, and meat quality.
Collapse
Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Samiullah Khan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Motahareh Amjadi
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Hussien Ohran
- Department of Physiology, University of Sarajevo, Veterinary Faculty, Zmajaod Bosne 90, 71000, Sarajevo, Bosnia and Herzegovina
| | - Khalid M Alanazi
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ayman E Taha
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22578, Egypt
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Cheng Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola M Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
11
|
Weber TM, Colle MJ, Murdoch GK, Buseman BJ, Lancaster JM, Van Buren JB, Nasados JA, Bass PD. Using Genetic Panels to Predict Tenderness in Beef Cattle. MEAT AND MUSCLE BIOLOGY 2020. [DOI: 10.22175/mmb.9549] [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
Genetic panel use as a selection tool has grown in popularity in the beef industry. The objective of the study was to determine whether beef cattle genetically selected for tenderness generated a tender product. Igenity® (IT) panel results were provided by a cattle producer for 52 steers, which were harvested at a commercial harvest facility. Boneless strip loins (Institutional Meat Purchase Specifications #180; United States Department of Agriculture [USDA] Choice, n = 32; USDA Prime n = 20) were collected from the left side of each carcass and transported to the University of Idaho Meat Science Laboratory. Four steaks were cut from each subprimal and assigned to aging periods of 7, 14, and 21 d for Warner-Bratzler Shear Force (WBSF) analysis or 21 d for consumer sensory analysis. Carcasses were assigned to tenderness groups based on their IT tenderness indexes (Low IT, 3 – 6, n = 30; High IT, 7 – 10, n = 22). Data were analyzed using the mixed model procedure of SAS version 9.4 (SAS Institute Inc., Cary, NC). An interaction was observed between tenderness group and USDA quality grade (P = 0.015) when analyzing WBSF. All of the cattle had less than 4.14 kg of WBSF; however, USDA Prime steers that were in the High IT tenderness group produced more tender steaks than High IT USDA Choice, Low IT USDA Prime, and Low IT USDA Choice steers. Consumers were not able to detect tenderness differences between IT tenderness groups (P = 0.11) or USDA quality grades (P = 0.11), but they found USDA Prime steaks to be more acceptable (P = 0.01), juicier (P = 0.01), and more flavorful (P = 0.02) than USDA Choice steaks. In conclusion, regardless of tenderness group, USDA Prime steaks were preferred by consumers over USDA Choice steaks in terms of flavor, juiciness, and acceptability.
Collapse
Affiliation(s)
- Tanya M. Weber
- University of Idaho Department of Animal and Veterinary Science
| | | | | | | | | | | | | | - Phillip D. Bass
- University of Idaho Department of Animal and Veterinary Science
| |
Collapse
|
12
|
Weber TM, Buseman BJ, Nasados JA, Lancaster JM, Van Buren JB, Smart JH, Bass PD, Murdoch GK, Insausti K, Colle MJ. Assessing outcomes of genetic selection panels to predict marbling in crossbred beef cattle. Transl Anim Sci 2020; 4:txaa077. [PMID: 32705071 PMCID: PMC7316178 DOI: 10.1093/tas/txaa077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/02/2020] [Indexed: 11/13/2022] Open
Abstract
The objective of this study was to evaluate the effectiveness of genetic panel marbling indexes [Igenity (IT) and PredicGEN (PG)] to predict marbling and tenderness of crossbred cattle. Steers (n = 23) were harvested at the University of Idaho Meat Science Laboratory, and blood samples were submitted to Neogen and Zoetis for genetic panel analysis. Forty-eight hours postharvest, one boneless strip loin was collected from each carcass, and six 2.54-cm thick steaks were cut from each strip loin. Steaks were aged for 14 and 21 d and assigned to consumer sensory evaluation or Warner–Bratzler Shear Force (WBSF) analysis. Results were analyzed using the Mixed Model procedure of the Statistical Analysis System (SAS Institute, Inc., Cary, NC). Carcasses were grouped by marbling index score into Low IT (IT indexes 3–6; n = 16; marbling score (MS) = 410), High IT (IT indexes 7–10; n = 7; MS = 496), Low PG (PG index <50; n = 9; MS = 398), or High PG (PG index ≥50; n = 14; MS = 458). Mean MS was observed to be greater in High IT steaks than Low IT (P < 0.01) and greater in High PG steaks than Low PG (P = 0.01). There was a trend observed in WBSF between IT marbling groups (P = 0.06); however, no difference in WBSF was observed between PG marbling groups (P = 0.83). Consumers did not report differences between IT marbling groups in terms of acceptability (P = 0.99) or tenderness (P = 0.24). Additionally, consumers could not detect differences between PG marbling groups in terms of acceptability (P = 0.75) or tenderness (P = 0.40). Consumers consistently preferred Choice steaks over Select steaks in terms of acceptability (P = 0.02) and tenderness (P = 0.02). In conclusion, though consumers were not able to tell the difference between steaks from each of the genetic panels, using genetic panels to predict marbling, in conjunction with proper nutrition and handling practices, could be a beneficial tool to producers making decisions about retaining ownership at the feedlot.
Collapse
Affiliation(s)
- Tanya M Weber
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Brianna J Buseman
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - James A Nasados
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Jessica M Lancaster
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Jessie B Van Buren
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Jaxon H Smart
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Phillip D Bass
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Gordon K Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| | - Kizkitza Insausti
- Agricultural Engineering School-IS FOOD, Public University of Navarra, Pamplona, Spain
| | - Michael J Colle
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID
| |
Collapse
|
13
|
Rossafa Garcia OS, Simões Araújo JL, Gasparino E, Teixeira Rodrigues M, de Souza Khatlab A, Veiga Rodrigues Paulino P, Chaves da Silva J, Nehme de Azevedo PC, Menck Soares MA. Association of CAST-gene polymorphism with mRNA levels and meat tenderness in goats. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context Meat tenderness is affected by numerous factors that can cause considerable economic loss as it is one of the characteristics of meat most appreciated by consumers. Higher expression of the calpastatin gene (CAST) has been associated with a reduced meat tenderness in different animal species. Aims Our main objective of the present study was to evaluate the association of the expression of the CAST gene with the shear force of goat muscle. We also assessed whether variations in gene expression could be explained by the polymorphism already identified by other authors or whether the polymorphism may be associated with phenotypic characteristics such as meat tenderness, slaughter weight and carcass weight. Methods Forty crossbred goats (Saanen × Alpine) were slaughtered at ~150 days of age. So as to obtain the genotype of each animal, blood samples were collected on the day of slaughter for subsequent DNA isolation. On the same day, samples of muscle tissue (Longissimus lumborum) were collected to analyse both gene expression and shear force. Key results Among the seven alleles already known from A to G, the C allele, which is the only one exhibiting exon variation, was not observed in our samples. We found, for the first time, that in goat, the highest CAST-gene expression levels are directly related to an increase in the muscle shear force, as has been described for other species. No statistical difference was observed for shear force, slaughter weight or carcass weight among the different genotypic groups evaluated. However, we observed that the level of expression of the CAST gene within Group 7 (Genotypes GG and GE) presented a higher value that in the other genotypes (P < 0.05), although we did not find a satisfactory explanation for the increase in expression in those genotypes. Conclusions Our results gave support what has already been verified in studies with other species, namely that the calpastatin-gene expression is related to the postmortem meat-tenderising process. Implications The tenderness is an important feature in the choice of meat. Several factors can alter this characteristic, such as breed, age, sex and slaughter weight of animals. The molecular mechanisms involved in ante-morten and postmortem processes are important for improving understanding of how we can identify animals that tend to have softer meat after slaughter by applying new technologies, such as molecular marker.
Collapse
|
14
|
Iguácel LP, Calvo JH, Casasús I, Serrano M, Ripoll G, Sarto P, Villalba D, Blanco M. Association of two single nucleotide polymorphisms in the calpastatin gene with tenderness under varying lengths of meat ageing in two native Spanish cattle breeds. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.103820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
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
|
Damiran D, Penner GB, Larson KA, Añez-Osuna F, Lardner HAB. Relationships between beef heifer feed efficiency traits and Igenity panel scores in western Canada. Transl Anim Sci 2018; 2:S66-S70. [PMID: 32704739 PMCID: PMC7200480 DOI: 10.1093/tas/txy022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/14/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daalkhaijav Damiran
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada.,Western Beef Development Centre, Humboldt, SK, Canada
| | - Gregory B Penner
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Federico Añez-Osuna
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - H A Bart Lardner
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK, Canada.,Western Beef Development Centre, Humboldt, SK, Canada
| |
Collapse
|
18
|
Abo-Ismail MK, Lansink N, Akanno E, Karisa BK, Crowley JJ, Moore SS, Bork E, Stothard P, Basarab JA, Plastow GS. Development and validation of a small SNP panel for feed efficiency in beef cattle. J Anim Sci 2018; 96:375-397. [PMID: 29390120 DOI: 10.1093/jas/sky020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022] Open
Abstract
The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.
Collapse
Affiliation(s)
- M K Abo-Ismail
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt
| | - N Lansink
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - E Akanno
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - B K Karisa
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J J Crowley
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Canadian Beef Breeds Council, Calgary, AB, Canada
| | - S S Moore
- Centre for Animal Science, University of Queensland, St Lucia, Australia
| | - E Bork
- Rangeland Research Institute, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - P Stothard
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J A Basarab
- Alberta Agriculture and Forestry, Lacombe Research Centre, Lacombe, AB, Canada
| | - G S Plastow
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
19
|
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]
|
20
|
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]
|
21
|
Kononoff PJ, Defoor PJ, Engler MJ, Swingle RS, Gleghorn JF, James ST, Marquess FLS. Impacts of a leptin SNP on growth performance and carcass characters in finishing steers studied over time. J Anim Sci 2017; 95:194-200. [PMID: 28177355 DOI: 10.2527/jas.2016.0926] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A total of 2,948 steers (mean initial BW = 568.9 ± 49.4 kg) were used to evaluate the effect of the LEP R25C SNP genotype on feed intake, growth performance, and carcass characteristics over time. Steers were grouped into 5 blocks, each consisting of 10 pens initially, and then at approximately 24 d prior to the assigned slaughter date, cattle in each pen were randomly selected either to remain in the pen they were in (group A) or to be assigned to a new pen (group B). Steers were allocated to 5 blocks and 6 harvest weeks (-3, -2, 0, 2, 3, and 4 wk) relative to the projected end point. Steers were weighed and ultrasound scanned at 60 and 1 d prior to harvest. Leptin genotype affected ( ≤ 0.011) 12th-rib fat and i.m. fat percentage (IMF) for each slaughter group at both 60 and 1 d prior to slaughter, although rib eye area (REA) was not affected ( = 0.773) by leptin genotype 60 d prior to slaughter in any group. Time affected ( < 0.001) live BW as well as 12th-rib fat, REA, and IMF measured 60 and 1 d prior to each slaughter time. Dry matter intake was also higher ( = 0.003) for cattle of the animals homozygous for the T allele (TT) genotype compared to those with the animals homozygous for the C allele (CC) genotype (9.59 vs. 9.29 ± 0.075 kg). The LEP R25C genotype affected key traits related to carcass fatness; specifically, compared to cattle of the CC genotype, cattle of the TT genotype had a higher ( = 0.016) calculated empty body fat (29.1 vs. 28.8 ± 0.133%) and higher ( = 0.020 calculated yield grade (2.62 vs. 2.52 ± 0.035). Additionally, like for live measures, TT cattle tended ( = 0.093) to have a higher 12th-rib fat (13.2 vs. 12.8 ± 0.26 mm). However, the LEP R25C genotype did not affect KPH ( = 0.854) or marbling score ( = 0.240), nor did it affect any USDA quality measure ( ≥ 0.350). The leptin genotype also affected ( = 0.048) HCW, which was highest for steers of the TT genotype (400.9 vs. 403.5 ± 3.41kg). Results indicate that the leptin R25C genotype and time impacted most traits associated with fatness.
Collapse
|
22
|
Proteolysis in meat tenderization from the point of view of each single protein: A proteomic perspective. J Proteomics 2016; 147:85-97. [DOI: 10.1016/j.jprot.2016.02.011] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/05/2016] [Accepted: 02/15/2016] [Indexed: 12/21/2022]
|
23
|
Evaluation of the innate immune response of Angus heifers with genetic marker variation for intramuscular fat deposition following a lipopolysaccharide challenge. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
24
|
Ramayo-Caldas Y, Renand G, Ballester M, Saintilan R, Rocha D. Multi-breed and multi-trait co-association analysis of meat tenderness and other meat quality traits in three French beef cattle breeds. Genet Sel Evol 2016; 48:37. [PMID: 27107817 PMCID: PMC4842279 DOI: 10.1186/s12711-016-0216-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/13/2016] [Indexed: 01/19/2023] Open
Abstract
Background Studies to identify markers associated with beef tenderness have focused on Warner–Bratzler shear force (WBSF) but the interplay between the genes associated with WBSF has not been explored. We used the association weight matrix (AWM), a systems biology approach, to identify a set of interacting genes that are co-associated with tenderness and other meat quality traits, and shared across the Charolaise, Limousine and Blonde d’Aquitaine beef cattle breeds. Results Genome-wide association studies were performed using ~500K single nucleotide polymorphisms (SNPs) and 17 phenotypes measured on more than 1000 animals for each breed. First, this multi-trait approach was applied separately for each breed across 17 phenotypes and second, between- and across-breed comparisons at the AWM and functional levels were performed. Genetic heterogeneity was observed, and most of the variants that were associated with WBSF segregated within rather than across breeds. We identified 206 common candidate genes associated with WBSF across the three breeds. SNPs in these common genes explained between 28 and 30 % of the phenotypic variance for WBSF. A reduced number of common SNPs mapping to the 206 common genes were identified, suggesting that different mutations may target the same genes in a breed-specific manner. Therefore, it is likely that, depending on allele frequencies and linkage disequilibrium patterns, a SNP that is identified for one breed may not be informative for another unrelated breed. Well-known candidate genes affecting beef tenderness were identified. In addition, some of the 206 common genes are located within previously reported quantitative trait loci for WBSF in several cattle breeds. Moreover, the multi-breed co-association analysis detected new candidate genes, regulators and metabolic pathways that are likely involved in the determination of meat tenderness and other meat quality traits in beef cattle. Conclusions Our results suggest that systems biology approaches that explore associations of correlated traits increase statistical power to identify candidate genes beyond the one-dimensional approach. Further studies on the 206 common genes, their pathways, regulators and interactions will expand our knowledge on the molecular basis of meat tenderness and could lead to the discovery of functional mutations useful for genomic selection in a multi-breed beef cattle context. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0216-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Maria Ballester
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Genètica i Millora Animal, IRTA, 08140, Torre Marimon, Caldes de Montbui, Spain
| | | | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| |
Collapse
|
25
|
Tait RG, Cushman RA, McNeel AK, Casas E, Smith TPL, Freetly HC, Bennett GL. Estimates of epistatic and pleiotropic effects of () and () genetic markers on beef heifer performance traits enhanced by selection. J Anim Sci 2016; 94:920-6. [PMID: 27065254 DOI: 10.2527/jas.2015-9860] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC II) was subjected to marker assisted selection for 2 yr to equalize and genetic marker frequencies to evaluate the epistatic and pleiotropic effects of these markers on BW, reproduction, and first calf performance traits in replacement beef females ( = 171) managed under 2 postweaning development protocols. Traits evaluated on the heifers were birth BW, weaning BW, 11-mo BW, 12-mo BW, 13-mo BW, first breeding season pregnancy evaluation BW, first calving season BW, 11-mo puberty, 12-mo puberty, 13-mo puberty, first breeding season pregnancy, and first calf weaning rate. Additionally, heifer's first calf performance traits of ordinal calving date, first calf birth BW, and first calf weaning BW (with and without age adjustment) were analyzed. Selection to increase minor allele frequencies and balanced sampling across genotype classes enhanced the ability to detect all genetic effects except dominance × dominance epistasis. The × genotype effect was significant ( < 0.05) for 11-mo BW and 12-mo BW and tended to be significant ( = 0.08) for 13-mo BW. Consistently, for all 3 traits, the most significant effect among epistatic × genotype effects was the additive effect, with the G allele decreasing BW. There were no associations between × genotype and fertility related traits ( ≥ 0.46) in this study. Additionally, there were no × genotype associations with first progeny performance traits ( ≥ 0.14). The large effect of the additive × additive interaction on first calf weaning BW was imprecisely estimated, which may warrant further investigation.
Collapse
|
26
|
Lisa C, Di Stasio L. Variability of μ-Calpain and Calpastatin genes in cattle. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2009.s2.99] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Claudio Lisa
- Dipartimento di Scienze Zootecniche, Università di Torino, Italy
| | | |
Collapse
|
27
|
Sudrajad P, Sharma A, Dang CG, Kim JJ, Kim KS, Lee JH, Kim S, Lee SH. Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1541-1546. [PMID: 26954199 PMCID: PMC5088372 DOI: 10.5713/ajas.15.0836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/12/2016] [Accepted: 02/23/2016] [Indexed: 12/25/2022]
Abstract
Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.
Collapse
Affiliation(s)
- Pita Sudrajad
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea.,Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Jakarta Selatan 12540, Indonesia
| | - Aditi Sharma
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Jeonju 565-851, Korea
| | - Chang Gwon Dang
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Jong Joo Kim
- School of Biotechnology, Yeungnam University, Daegu 717-749, Korea
| | - Kwan Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| | - Sidong Kim
- Hanwoo Research Institute, National Institute of Animal Science, RDA, Pyeongchang 232-950, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 305-764, Korea
| |
Collapse
|
28
|
Berry D, Garcia J, Garrick D. Development and implementation of genomic predictions in beef cattle. Anim Front 2016. [DOI: 10.2527/af.2016-0005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D.P. Berry
- Teagasc Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - J.F. Garcia
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP- Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - D.J. Garrick
- Department of Animal Science, Iowa State University, Ames, 50011, USA
| |
Collapse
|
29
|
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
|
30
|
Kononoff PJ, Defoor PJ, Engler MJ, Swingle RS, James ST, Deobald HM, Deobald JL, Woronuk GN, Marquess FLS. Performance and carcass characteristics when sorting feedlot cattle on the basis of phenotype, and leptin genotype along with differential use of β-adrenergic agonists. CANADIAN JOURNAL OF ANIMAL SCIENCE 2015. [DOI: 10.4141/cjas-2014-052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Kononoff, P. J., Defoor, P. J., Engler, M. J., Swingle, R. S., James, S. Y., Deobald, H. M., Deobald, R. L., Woronuk, G. N. and Marquess, F. L. S. 2015. Performance and carcass characteristics when sorting feedlot cattle on the basis of phenotype, and leptin genotype along with differential use of β-adrenergic agonists. Can. J. Anim. Sci. 95: 455–463. Crossbred steers were used in a randomized complete block design to evaluate a feedlot cattle sorting system. The sorting system combined information on live body weight, ultrasound fat thickness, coat color, and genotype on the leptin R25C genotype. Using described sorting criteria, a total of four groups (Groups 1–4) of cattle were created along with a randomly selected unsorted control (Group 5), with Groups 1 through 5 representing experimental treatments, and placed in one of five pens within each block. Block was replicated 10 times thus n equaled 50. All cattle were administered zilpaterol hydrochloride except Group 3, which we hypothesized would have a greater proportion of cattle reaching a higher value Quality Grade, and as a result administered ractopamine hydrochloride. The initial body weight of cattle was similar (P=0.426) between the control Group and Groups 1–4. Initial fat, as measured by ultrasound, was also observed to be similar (P=0.256) between these two groups. Overall, when cattle included in Groups 1–4 were compared with Group 5, hot carcass weight was greater (P=0.040), while the proportion of excessively heavy weight carcasses was less (P=0.049). Additionally, hot carcass weight gain tended (P=0.096) to be higher for Groups 1–4 compared with Group 5. No differences (P≥0.129) were observed for calculated yield grade. On average, cattle included in the Sorting Groups 1–4 returned $23 more per head than those in Group 5.
Collapse
Affiliation(s)
- P. J. Kononoff
- Department of Animal Science, C220j Animal Science, Lincoln, NE, 68582-0908, USA
- Participation through consulting agreement with Quantum Genetix, Canada Inc
| | | | | | | | - S. T. James
- Quantum Genetix Canada Inc., Saskatoon, Saskatchewan, Canada S7N 3R3
| | - H. M. Deobald
- Quantum Genetix Canada Inc., Saskatoon, Saskatchewan, Canada S7N 3R3
| | - J. L. Deobald
- Quantum Genetix Canada Inc., Saskatoon, Saskatchewan, Canada S7N 3R3
| | - G. N. Woronuk
- Quantum Genetix Canada Inc., Saskatoon, Saskatchewan, Canada S7N 3R3
| | - F. L. S. Marquess
- Quantum Genetix Canada Inc., Saskatoon, Saskatchewan, Canada S7N 3R3
| |
Collapse
|
31
|
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
|
32
|
Association analysis of polymorphism in thyroglobulin gene promoter with milk production traits in riverine buffalo (Bubalus bubalis). Meta Gene 2015; 5:157-61. [PMID: 26273563 PMCID: PMC4532728 DOI: 10.1016/j.mgene.2015.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 07/13/2015] [Accepted: 07/13/2015] [Indexed: 11/21/2022] Open
Abstract
Polymorphism within the promoter region of bovine thyroglobulin has been reported to be associated with milk and meat quality. In this study, we investigated the genetic variation within thyroglobulin promoter region of swamp and riverine buffaloes using PCR-SSCP technique and sequencing, and also analyzing association of polymorphism with the milk production traits. The study revealed four conformational patterns, A, B, C, and D among 323 buffaloes of two riverine breeds and different swamp populations. The frequency of SSCP variant 'A' was found to be invariably high among all buffalo populations. Variant 'C' was found to be absent in pure swamp population and present with higher frequency among riverine dairy breeds Mehsana and Nili Ravi. Frequency of D variant was observed to be highest in buffalo population, representing riverine and hybrid types. Sequencing of three representative PCR products of each of the SSCP variants, revealed three polymorphic sites responsible, 33C > T, 176G > T and 221C > T, in the buffalo TG promoter region. Further, association studies of SSCP variants with various milk production and milk quality traits indicated significant effect on fat percentage in buffaloes belonging to Mehsana and Nili Ravi dairy breeds. The preliminary results also showed the substantial variations in the distribution of SSCP variants' frequencies across swamp and riverine buffaloes, two distinct populations being reared for meat and milk production, respectively.
Collapse
|
33
|
Thompson NM, DeVuyst EA, Brorsen BW, Lusk JL. Yield and quality grade outcomes as affected by molecular breeding values for commercial beef cattle1. J Anim Sci 2015; 93:2045-55. [DOI: 10.2527/jas.2014-8511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
34
|
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
|
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
|
Dubey P, Goyal S, Yadav A, Sahoo B, Kumari N, Mishra S, Niranjan S, Arora R, Mukesh M, Kataria R. Genetic diversity analysis of the thyroglobulin gene promoter in buffalo and other bovines. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
37
|
Sharma A, Dang CG, Kim KS, Kim JJ, Lee HK, Kim HC, Yeon SH, Kang HS, Lee SH. Validation of genetic polymorphisms on BTA14 associated with carcass trait in a commercial Hanwoo population. Anim Genet 2014; 45:863-7. [DOI: 10.1111/age.12204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2014] [Indexed: 11/26/2022]
Affiliation(s)
- A. Sharma
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| | - C. G. Dang
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| | - K. S. Kim
- Department of Animal Science; Chungbuk National University; Cheongju 361-763 Korea
| | - J. J. Kim
- School of Biotechnology; Yeungnam University; Daegu 717-749 Korea
| | - H. K. Lee
- Department of Biotechnology; Hankyung National University; An-sung 456-749 Korea
| | - H. C. Kim
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| | - S. H. Yeon
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| | - H. S. Kang
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| | - S. H. Lee
- Hanwoo Experiment Station; National Institute of Animal Science; RDA; Pyeongchang 232-950 Korea
| |
Collapse
|
38
|
Possibilities to improve the genetic evaluation of a rare breed using limited genomic information and multivariate BLUP. Animal 2014; 8:685-94. [PMID: 24739347 PMCID: PMC4000164 DOI: 10.1017/s1751731114000330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The use of molecular genetic information in the evaluation of livestock has become more
common. This study looks at the efficacy of using such information to improve the genetic
evaluation of a rare breed of dual-purpose cattle. Data were available in the form of
pedigree information on the Gloucester cattle breed in the United Kingdom and recorded
milk and beef performance on a small number of animals. In addition, molecular genetic
information in the form of multi-marker, multiple regression results converted to a 1 to
10 score (Igenity scores) and 123 single nucleotide polymorphism (SNP) genotypes for 199
non-recorded animals were available. Appropriate mixed-animal models were explored for the
recorded traits and these were used to calculate estimated breeding values (EBV), and
their accuracies, for 6527 animals in the breed’s pedigree file. Various ways to improve
the accuracy of these EBV were explored. This involved using multivariate BLUP analyses,
genomic estimated breeding values (GEBV) and combining Igenity scores with recorded traits
in a series of bivariate genetic analyses. Using the milk recording traits as an example,
the accuracy of a number of traits could be improved using multivariate analyses by up to
14%, depending on the combination of traits used. The level of increase in accuracy
largely corresponded to the absolute difference between the genetic and residual
correlations between two traits, but this was not always symmetrical. The use of GEBV did
not increase the accuracy of milk trait EBV owing to the low proportion of variance
explained by the 101 SNPs used. Using Igenity scores in bivariate analyses with the
recorded data was more successful in increasing EBV accuracy. The largest increases were
found in genotyped animals with no recorded performance (e.g. a 58% increase in fat weight
in milk); however, the size of the increase depended on the level of the genetic
correlation between the recorded trait and the Igenity score for that trait. Lower levels
of improvements in accuracy were seen in animals that were recoded but not genotyped, and
ancestors which were neither genotyped nor recorded. This study demonstrated that it was
possible to improve the accuracy of EBV estimation by including Igenity score information
in genetic analyses but it also concluded that increasing the level of performance
recording in the breed would be beneficial.
Collapse
|
39
|
Sevane N, Levéziel H, Nute GR, Sañudo C, Valentini A, Williams J, Dunner S. Phenotypic and genotypic background underlying variations in fatty acid composition and sensory parameters in European bovine breeds. J Anim Sci Biotechnol 2014; 5:20. [PMID: 24735897 PMCID: PMC4019361 DOI: 10.1186/2049-1891-5-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 04/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients. In this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. METHODS A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids (FA) profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. RESULTS The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA (PUFA) were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between flavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis (PCA) mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. CONCLUSIONS The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic information on polymorphisms previously associated with different lipid traits, provide a broad characterization of beef meat, which allows giving a better response to the variety of consumers' preferences. Also, the development and implementation of low-density SNP panels with predictive value for economically important traits, such as those summarized here, may be used to improve production efficiency and meat quality in the beef industry.
Collapse
Affiliation(s)
- Natalia Sevane
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - Hubert Levéziel
- INRA, UMR 1061, F-87000 Limoges, France ; Université de Limoges, UMR 1061, F-87000 Limoges, France
| | - Geoffrey R Nute
- Division of Farm Animal Science, University of Bristol, Bristol BS40 5DU, UK
| | - Carlos Sañudo
- Departimento de Producción Animal y Ciencia de los Alimentos, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Alessio Valentini
- Dipartimento di Produzioni Animali, Università della Tuscia, via De Lellis, 01100 Viterbo, Italy
| | - John Williams
- Parco Tecnologico Padano, Via Einstein, Polo Universitario, 26900 Lodi, Italy
| | - Susana Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| |
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
|
Heo EJ, Ko EK, Seo KH, Chon JW, Kim YJ, Park HJ, Wee SH, Moon JS. Comparison of the Microsatellite and Single Nucleotide Polymorphism Methods for Discriminating among Hanwoo (Korean Native Cattle), Imported, and Crossbred Beef in Korea. Korean J Food Sci Anim Resour 2014; 34:763-8. [PMID: 26761672 PMCID: PMC4662190 DOI: 10.5851/kosfa.2014.34.6.763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 10/08/2014] [Accepted: 10/12/2014] [Indexed: 11/16/2022] Open
Abstract
The identity of 45 Hanwo and 47 imported beef (non-Hanwoo) samples from USA and Australia were verified using the microsatellite (MS) marker and single nucleotide polymorphism (SNP) methods. Samples were collected from 19 supermarkets located in the city of Seoul and Gyeonggi province, South Korea, from 2009 to 2011. As a result, we obtained a 100% concordance rate between the MS and SNP methods for identifying Hanwoo and non-Hanwoo beef. The MS method presented a 95% higher individual discriminating value for Hanwoo (97.8%) than for non-Hanwoo (61.7%) beef. For further comparison of the MS and SNP methods, blood samples were collected and tested from 54 Hanwoo × Holstein crossbred cattle (first, second, and third generations). By using the SNP and MS methods, we correctly identified all of the first-generation crossbred cattle as non-Hanwoo; in addition, among the second and third generation crossbreds, the ratio identified as Hanwoo was 20% and 10%, respectively. The MS method used in our study provides more information, but requires sophisticated techniques during each experimental process. By contrast, the SNP method is simple and has a lower error rate. Our results suggest that the MS and SNP methods are useful for discriminating Hanwoo from non-Hanwoo breeds.
Collapse
Affiliation(s)
- Eun-Jeong Heo
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Eun-Kyung Ko
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Kun-Ho Seo
- KU Center for Food Safety, College of Veterinary Medicine, Konkuk University, Seoul 143-701, Korea
| | - Jung-Whan Chon
- KU Center for Food Safety, College of Veterinary Medicine, Konkuk University, Seoul 143-701, Korea
| | - Young-Jo Kim
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Hyun-Jung Park
- Ministry of Food and Drug Safety, Cheongwon 363-951, Korea
| | - Sung-Hwan Wee
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| | - Jin-San Moon
- Animal and Plant Quarantine Agency, Anyang 430-757, Korea
| |
Collapse
|
45
|
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
|
46
|
Ribeca C, Bonfatti V, Cecchinato A, Albera A, Gallo L, Carnier P. Effect of polymorphisms in candidate genes on carcass and meat quality traits in double muscled Piemontese cattle. Meat Sci 2013; 96:1376-83. [PMID: 24361557 DOI: 10.1016/j.meatsci.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/25/2013] [Accepted: 11/26/2013] [Indexed: 11/27/2022]
Abstract
The aim of this study was to investigate the association between 10 candidate genes and carcass weight and conformation, carcass daily gain, and meat quality (pH, color, cooking loss, drip loss and shear force) in 990 double-muscled Piemontese young bulls. Animals were genotyped at each of the following genes: growth hormone, growth hormone receptor, pro-opiomelanocortin, pro-opiomelanocortin class 1 homeobox 1, melanocortin-4 receptor, corticotrophin-releasing hormone, diacylglycerol O-acyltransferase-1, thyroglobulin, carboxypeptidase E and gamma-3 regulatory subunit of the AMP-activated protein kinase. All the investigated SNPs had additive effects which were relevant for at least one of the traits. Relevant associations between the investigated SNPs and carcass weight, carcass daily gain and carcass conformation were detected, whereas associations of SNPs with meat quality were moderate. Results confirmed some of previously reported associations, but diverged for others. Validation in other cattle breeds is required to use these SNPs in gene-assisted selection programs for enhancement of carcass traits and meat quality.
Collapse
Affiliation(s)
- C Ribeca
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - V Bonfatti
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy.
| | - A Cecchinato
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - A Albera
- Piemontese Cattle Breeders Association (ANABoRaPi), strada Trinità 32/a, Carrù, 12061, Italy
| | - L Gallo
- Department of Agriculture, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - P Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| |
Collapse
|
47
|
Van Eenennaam AL, Weigel KA, Young AE, Cleveland MA, Dekkers JCM. Applied animal genomics: results from the field. Annu Rev Anim Biosci 2013; 2:105-39. [PMID: 25384137 DOI: 10.1146/annurev-animal-022513-114119] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic selection (GS) is the use of statistical methods to estimate the genetic merit of a genotyped animal based on prediction equations derived from large ancestral populations with both phenotypes and genotypes. It has revolutionized the dairy cattle breeding industry and has been implemented with varying degrees of success in other animal breeding programs, including swine, poultry, and beef cattle. The findings of empirical field studies applying GS to the breeding sectors of these main animal protein industries are reviewed. Several translational considerations must be addressed before implementing GS in genetic improvement programs. These include determining and obtaining economically relevant phenotypes and determining the optimal size of the training population, cost-effective genotyping strategies, the practicality of field implementation, and the relative costs versus the benefits of the realized rate of genetic gain. GS may additionally change the optimal breeding scheme design, and studies that address this consideration are also reviewed briefly.
Collapse
|
48
|
Magolski J, Buchanan D, Maddock-Carlin K, Anderson V, Newman D, Berg E. Relationship between commercially available DNA analysis and phenotypic observations on beef quality and tenderness. Meat Sci 2013; 95:480-5. [DOI: 10.1016/j.meatsci.2013.05.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 05/07/2013] [Accepted: 05/20/2013] [Indexed: 11/29/2022]
|
49
|
Greenwood PL, Cafe LM, McIntyre BL, Geesink GH, Thompson JM, Polkinghorne R, Pethick DW, Robinson DL. Molecular value predictions: associations with beef quality, carcass, production, behavior, and efficiency phenotypes in Brahman cattle. J Anim Sci 2013; 91:5912-25. [PMID: 24126277 DOI: 10.2527/jas.2013-6960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Data from 2 previously published experiments, New South Wales (NSW; n = 161) and Western Australia (WA; n = 135), were used to test molecular value predictions (MVP), generated from commercially available gene markers, on economically important traits of Bos indicus (Brahman) cattle. Favorable tenderness MVP scores were associated with reduced shear force values of strip loin (LM) steaks aged 7 d from Achilles-hung carcasses (P ≤ 0.06), as well as steaks aged 1 (P ≤ 0.08) or 7 d (P ≤ 0.07) from carcasses hung from the pelvis (tenderstretch). Favorable tenderness MVP scores were also associated with improved consumer tenderness ratings for strip loin steaks aged 7 d and either Achilles hung (P ≤ 0.006) or tenderstretched (P ≤ 0.07). Similar results were observed in NSW for rump (top butt; gluteus medius) steaks, with favorable tenderness MVP scores associated with more tender (P = 0.006) and acceptable (P = 0.008) beef. Favorable marbling MVP scores were associated with improved (P ≤ 0.021) marbling scores and intramuscular fat (IMF) content in the NSW experiment, despite low variation in marbling in the Brahman cattle. For the WA experiment, however, there were no (P ≥ 0.71) relationships between marbling MVP and marbling scores or IMF content. Although residual (net) feed intake (RFI) was not associated (P = 0.63) with the RFI (feed efficiency) MVP, the RFI MVP was adversely associated with LM tenderness and acceptability of 7-d-aged Achilles-hung carcasses in NSW (P ≤ 0.031) and WA (P ≤ 0.037). Some other relationships and trends were noted between the MVP and the other traits, but few reached statistical significance, and none were evident in both experiments. Results from this study provide evidence to support the use of the tenderness MVP. The value of the marbling MVP, which was associated with marbling in only 1 herd, warrants further evaluation; however, there appears to be no evidence to support use of the RFI MVP in Brahman cattle.
Collapse
Affiliation(s)
- P L Greenwood
- Australian Cooperative Research Centre for Beef Genetic Technologies, University of New England, Armidale, NSW 2351, Australia
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Lu D, Sargolzaei M, Kelly M, Vander Voort G, Wang Z, Mandell I, Moore S, Plastow G, Miller SP. Genome-wide association analyses for carcass quality in crossbred beef cattle. BMC Genet 2013; 14:80. [PMID: 24024930 PMCID: PMC3827924 DOI: 10.1186/1471-2156-14-80] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022] Open
Abstract
Background Genetic improvement of beef quality will benefit both producers and consumers, and can be achieved by selecting animals that carry desired quantitative trait nucleotides (QTN), which result from intensive searches using genetic markers. This paper presents a genome-wide association approach utilizing single nucleotide polymorphisms (SNP) in the Illumina BovineSNP50 BeadChip to seek genomic regions that potentially harbor genes or QTN underlying variation in carcass quality of beef cattle. This study used 747 genotyped animals, mainly crossbred, with phenotypes on twelve carcass quality traits, including hot carcass weight (HCW), back fat thickness (BF), Longissimus dorsi muscle area or ribeye area (REA), marbling scores (MRB), lean yield grade by Beef Improvement Federation formulae (BIFYLD), steak tenderness by Warner-Bratzler shear force 7-day post-mortem (LM7D) as well as body composition as determined by partial rib (IMPS 103) dissection presented as a percentage of total rib weight including body cavity fat (BDFR), lean (LNR), bone (BNR), intermuscular fat (INFR), subcutaneous fat (SQFR), and total fat (TLFR). Results At the genome wide level false discovery rate (FDR < 10%), eight SNP were found significantly associated with HCW. Seven of these SNP were located on Bos taurus autosome (BTA) 6. At a less stringent significance level (P < 0.001), 520 SNP were found significantly associated with mostly individual traits (473 SNP), and multiple traits (47 SNP). Of these significant SNP, 48 were located on BTA6, and 22 of them were in association with hot carcass weight. There were 53 SNP associated with percentage of rib bone, and 12 of them were on BTA20. The rest of the significant SNP were scattered over other chromosomes. They accounted for 1.90 - 5.89% of the phenotypic variance of the traits. A region of approximately 4 Mbp long on BTA6 was found to be a potential area to harbor candidate genes influencing growth. One marker on BTA25 accounting for 2.67% of the variation in LM7D may be worth further investigation for the improvement of beef tenderness. Conclusion This study provides useful information to further assist the identification of chromosome regions and subsequently genes affecting carcass quality traits in beef cattle. It also revealed many SNP that acted pleiotropically to affect carcass quality. This knowledge is important in selecting subsets of SNP to improve the performance of beef cattle.
Collapse
Affiliation(s)
- Duc Lu
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
| | | | | | | | | | | | | | | | | |
Collapse
|