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Fu X, Li C, Liu Q, McMillin KW. GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: The regulation of beef quality by resident progenitor cells1. J Anim Sci 2019; 97:2658-2673. [PMID: 30982893 PMCID: PMC6541817 DOI: 10.1093/jas/skz111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
The intramuscular adipose tissue deposition in the skeletal muscle of beef cattle is a highly desired trait essential for high-quality beef. In contrast, the excessive accumulation of crosslinked collagen in intramuscular connective tissue contributes to beef toughness. Recent studies revealed that adipose tissue and connective tissue share an embryonic origin in mice and may be derived from a common immediate bipotent precursor in mice and humans. Having the same linkages in the development of adipose tissue and connective tissue in beef, the lineage commitment and differentiation of progenitor cells giving rise to these tissues may directly affect beef quality. It has been shown that these processes are regulated by some key transcription regulators and are subjective to epigenetic modifications such as DNA methylation, histone modifications, and microRNAs. Continued exploration of relevant regulatory pathways is very important for the identification of mechanisms influencing meat quality and the development of proper management strategies for beef quality improvement.
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Affiliation(s)
- Xing Fu
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Chaoyang Li
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Qianglin Liu
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Kenneth W McMillin
- School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA
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Dang CG, Cho SH, Sharma A, Kim HC, Jeon GJ, Yeon SH, Hong SK, Park BY, Kang HS, Lee SH. Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:1328-35. [PMID: 25178377 PMCID: PMC4150200 DOI: 10.5713/ajas.2013.13690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/02/2014] [Accepted: 04/11/2014] [Indexed: 01/23/2023]
Abstract
Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10−6) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.
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Affiliation(s)
- C G Dang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Cho
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - A Sharma
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H C Kim
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - G J Jeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Yeon
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S K Hong
- National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - B Y Park
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - H S Kang
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
| | - S H Lee
- Animal Product Research and Development Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea
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Gonzalez JM, Johnson DD, Elzo MA, White MC, Stelzleni AM, Johnson SE. Effect of Brahman Genetic Influence on Collagen Enzymatic Crosslinking Gene Expression and Meat Tenderness. Anim Biotechnol 2014; 25:165-78. [PMID: 24669867 DOI: 10.1080/10495398.2013.846862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Choi JW, Chung WH, Lee KT, Choi JW, Jung KS, Cho Y, Kim N, Kim TH. Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery. Korean J Food Sci Anim Resour 2013. [DOI: 10.5851/kosfa.2013.33.6.715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Chang LY, Pitchford WS, Bottema CDK. Modeling tenderness for genetic and quantitative trait loci analyses. J Anim Sci 2013; 92:39-47. [PMID: 24249798 DOI: 10.2527/jas.2013-6696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tenderness is the one of the most important attributes of beef with regards to the intent of consumers to repurchase. Beef tenderness is frequently measured objectively as Warner-Bratzler shear force. However, to better understand the genetics underlying tenderness, better descriptors were derived herein. Two traits, adjusted shear force and aging rate, were calculated to incorporate measures of Warner-Bratzler shear force repeated over aging time of 2 muscles, longissimus dorsi (LD) and semitendinosus (ST). Analysis of these traits indicated that the shear forces of the 2 muscles are lowly correlated and aging rate, as calculated, was not correlated with adjusted shear force. Breed, SNP, and QTL effects were analyzed for the 4 traits (2 traits × 2 muscles). For adjusted shear force, the QTL were located on cattle chromosomes BTA 5, 18, 25, and 29. With the exception of the QTL on BTA 5, the adjusted shear force QTL were observed for either the LD or the ST but not both muscles. The QTL for aging rate were located on BTA 1, 4, 7, 11, 13, 19, and 20.
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Affiliation(s)
- L Y Chang
- Cooperative Research Centre for Beef Genetic Technologies, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, South Australia, 5371 Australia
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Esmailizadeh AK, Morris CA, Cullen NG, Kruk ZA, Lines DS, Hickey SM, Dobbie PM, Bottema CDK, Pitchford WS. Genetic mapping of quantitative trait loci for meat quality and muscle metabolic traits in cattle. Anim Genet 2011; 42:592-9. [PMID: 22035000 DOI: 10.1111/j.1365-2052.2011.02197.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A whole-genome scan was carried out in New Zealand and Australia to detect quantitative trait loci (QTL) for live animal and carcass composition traits and meat quality attributes in cattle. Backcross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. This paper reports on meat quality traits (tenderness measured as shear force at 4-5 ages on two muscles as well as associated traits of meat colour, pH and cooking loss) and a number of metabolic traits. For meat quality traits, 18 significant QTL (P < 0.05), located in nine linkage groups, were detected on a genome-wise basis, in combined-sire (seven QTL) or within-sire analyses (11 QTL). For metabolic traits, 11 significant QTL (P < 0.05), located in eight linkage groups, were detected on a genome-wise basis, in combined-sire (five QTL) or within-sire analyses (six QTL). BTA2 and BTA3 had QTL for both metabolic traits and meat quality traits. Six significant QTL for meat quality and metabolic traits were found at the proximal end of chromosome 2. BTA2 and BTA29 were the most common chromosomes harbouring QTL for meat quality traits; QTL for improved tenderness were associated with Limousin-derived and Jersey-derived alleles on these two chromosomes, respectively.
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Affiliation(s)
- A K Esmailizadeh
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Roseworthy, SA 5371, Australia.
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Bolormaa S, Neto LRP, Zhang YD, Bunch RJ, Harrison BE, Goddard ME, Barendse W. A genome-wide association study of meat and carcass traits in Australian cattle. J Anim Sci 2011; 89:2297-309. [PMID: 21421834 DOI: 10.2527/jas.2010-3138] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromosomal regions containing DNA variation affecting the traits intramuscular fat percentage (IMF), meat tenderness measured as peak force to shear the LM (LLPF), and rump fat measured at the sacro-iliac crest in the chiller (CHILLP8) were identified using a set of 53,798 SNP genotyped on 940 taurine and indicine cattle sampled from a large progeny test experiment. Of these SNP, 87, 64, and 63 were significantly (P < 0.001) associated with the traits IMF, LLPF, and CHILLP8, respectively. A second, nonoverlapping sample of 1,338 taurine and indicine cattle from the same large progeny test experiment genotyped for 335 SNP, including as a positive control the calpastatin (CAST) c.2832A > G SNP, was used to confirm these locations. In total, 37 SNP were significantly (P < 0.05) associated with the same trait and with the same favorable homozygote in both data sets, representing 27 chromosomal regions. For the trait IMF, the effect of SNP in the confirmation data set was predicted from the discovery set by multiplying the estimated allele effect of each SNP in the discovery set by the number of copies of the reference allele of each SNP in the confirmation set. These weighted effects were then summed over all SNP to generate a molecular breeding value (MBV) for each animal in the confirmation data set. Using a bivariate analysis of MBV and IMF phenotypes of animals in the confirmation set, a panel of 14 SNP explained 5.6 and 15.6% of the phenotypic and genetic variance of IMF, respectively, in the confirmation data set. The amount of variation did not increase as more SNP were added to the MBV and instead decreased to 1.2 and 3.8% of the phenotypic and genetic variance of IMF, respectively, when 329 SNP were included in the analysis.
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Affiliation(s)
- S Bolormaa
- Cooperative Research Centre for Beef Genetic Technologies, Armidale, New South Wales 2351, Australia
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Johnston DJ, Graser HU. Estimated gene frequencies of GeneSTAR markers and their size of effects on meat tenderness, marbling, and feed efficiency in temperate and tropical beef cattle breeds across a range of production systems1. J Anim Sci 2010; 88:1917-35. [DOI: 10.2527/jas.2009-2305] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Genetic Variability and Linkage Disequilibrium Patterns in the Bovine DNAJA1 Gene. Mol Biotechnol 2009; 44:190-7. [DOI: 10.1007/s12033-009-9228-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Allan MF, Smith TPL. Present and future applications of DNA technologies to improve beef production. Meat Sci 2008; 80:79-85. [PMID: 22063172 DOI: 10.1016/j.meatsci.2008.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 05/16/2008] [Accepted: 05/20/2008] [Indexed: 12/19/2022]
Abstract
Substantial improvements in production efficiency and quality of beef and dairy products have been made possible through manipulation of bovine genetics. The advent of modern breeds in the last two centuries, the institution of phenotypic selection practices and quantitative genetics, even the process of domestication in the distant past, have all represented means to make use of naturally occurring variation in the genome to tailor the animal for a desired outcome. We discuss the history of genome research in cattle and recent technological advances that promise a leap forward in the use of DNA sequence to facilitate selection, in which a detailed genome-level view for individual animals may provide comprehensive and relatively accurate assessment of the consequences, both desired and unintended, of genetic selection for livestock production.
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Affiliation(s)
- M F Allan
- USDA, ARS, US Meat Animal Research Center, PO Box 166, State Spur 18D, Clay Center, NE 68933-0166, United States
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Davis GP, Moore SS, Drinkwater RD, Shorthose WR, Loxton ID, Barendse W, Hetzel DJS. QTL for meat tenderness in the M. longissimus lumborum of cattle. Anim Genet 2008; 39:40-5. [DOI: 10.1111/j.1365-2052.2007.01677.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Analysis of SNPs in Bovine CSRP3, APOBEC2 and Caveolin Gene Family. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2007. [DOI: 10.5187/jast.2007.49.6.719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Barendse W, Harrison BE, Hawken RJ, Ferguson DM, Thompson JM, Thomas MB, Bunch RJ. Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle. Genetics 2007; 176:2601-10. [PMID: 17603104 PMCID: PMC1950658 DOI: 10.1534/genetics.107.074328] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The calpain gene family and its inhibitors have diverse effects, many related to protein turnover, which appear to affect a range of phenotypes such as diabetes, exercise-induced muscle injury, and pathological events associated with degenerative neural diseases in humans, fertility, longevity, and postmortem effects on meat tenderness in livestock species. The calpains are inhibited by calpastatin, which binds directly to calpain. Here we report the direct measurement of epistatic interactions of causative mutations for quantitative trait loci (QTL) at calpain 1 (CAPN1), located on chromosome 29, with causative mutations for QTL variation at calpastatin (CAST), located on chromosome 7, in cattle. First we identified potential causative mutations at CAST and then genotyped these along with putative causative mutations at CAPN1 in >1500 cattle of seven breeds. The maximum allele substitution effect on the phenotype of the CAPN1:c.947G>C single nucleotide polymorphism (SNP) was 0.14 sigma(p) (P = 0.0003) and of the CAST:c.155C>T SNP was also 0.14 sigma(p) (P = 0.0011) when measured across breeds. We found significant epistasis between SNPs at CAPN1 and CAST in both taurine and zebu derived breeds. There were more additive x dominance components of epistasis than additive x additive and dominance x dominance components combined. A minority of breed comparisons did not show epistasis, suggesting that genetic variation at other genes may influence the degree of epistasis found in this system.
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Affiliation(s)
- W Barendse
- Commonwealth Scientific and Industrial Research Organization Livestock Industries, Queensland Bioscience Project, 306 Carmody Road, St. Lucia 4067, Queensland, Australia.
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Recent advances in cattle functional genomics and their application to beef quality. Animal 2007; 1:159-73. [DOI: 10.1017/s1751731107658042] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Barendse W, Bunch RJ, Kijas JW, Thomas MB. The effect of genetic variation of the retinoic acid receptor-related orphan receptor C gene on fatness in cattle. Genetics 2006; 175:843-53. [PMID: 17151246 PMCID: PMC1800623 DOI: 10.1534/genetics.106.064535] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genotypes at the retinoic acid receptor-related orphan receptor C (RORC) gene were associated with fatness in 1750 cattle. Ten SNPs were genotyped in RORC and the adjacent gene leucine-rich repeat neuronal 6D (LRRN6D) to map the QTL, 7 of which are in a 4.2-kb sequence around the ligand-binding domain of the RORC gene. Of the 29 inferred haplotypes for these SNPs, 2 have a combined frequency of 54.6% while the top 5 haplotypes have a combined frequency of 85.3%. The average D' value of linkage disequilibrium was 0.92 although the average r2 was a low 0.18. The RORC:g.3290T>G SNP had the strongest association with marbling. The inferred haplotypes were significantly associated with marbling and the difference between the most divergent haplotypes was 0.35 sigma(p) of marbling and 0.28 sigma(p) of rump fat, explaining the previously reported QTL effect. cDNA for RORC were sequenced and 2 new alternative transcripts were found. Fetal tissue shows 40 times greater transcription of RORC than adult tissue. The highest expression in fetal tissue was found in liver and kidney, but in adults the longissimus muscle had the greatest expression of the tissues tested.
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Affiliation(s)
- W Barendse
- CSIRO Livestock Industries, Queensland Bioscience Precinct, Saint Lucia, Queensland 4067, Australia.
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