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Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. J Anim Sci Biotechnol 2023; 14:131. [PMID: 37817239 PMCID: PMC10565993 DOI: 10.1186/s40104-023-00931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. RESULTS Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. CONCLUSIONS In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.
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Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - In-Sul Hwang
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032 USA
| | - Mi-Ryung Park
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
| | - Seongsoo Hwang
- Animal Welfare Research Team, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Jeollabuk-do, 55365 Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
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Bennett GL, Tait RG, Shackelford SD, Wheeler TL, King DA, Casas E, Smith TPL. Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and µ-calpain genes. J Anim Sci 2019; 97:569-577. [PMID: 30476168 DOI: 10.1093/jas/sky451] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/21/2018] [Indexed: 01/20/2023] Open
Abstract
The objective of this study was to enhance estimates of additive, dominance, and epistatic effects of marker polymorphisms on beef carcass and quality traits. Myostatin (MSTN) F94L SNP and the µ-calpain (CAPN1) 316 and 4751 SNP haplotype have previously been associated with fat and muscle traits in beef cattle. Multiyear selection in a composite population segregating these polymorphisms increased minor allele (F94L L) and chosen haplotype (CAPN1 CC and GT) frequencies to intermediate levels resulting in more precise estimates of additive and nonadditive genetic effects. During the 3 yr after selection, 176 steers were evaluated for growth, carcass, meat quality, tenderness (n = 103), and meat color traits. The statistical model included year, age of dam, age of the steer, and genotype in a random animal model. The 9 genotypes (3 CAPN1 diplotypes × 3 F94L genotypes) affected marbling score, ribeye area, adjusted fat thickness, vision yield grade (all P < 0.001), slice shear force (P = 0.03), and CIE L* reflectance (P = 0.01). Linear contrasts of the 9 genotypes estimated additive, recessive, and epistatic genetic effects. Significant additive effects of the F94L L allele decreased marbling score, adjusted fat thickness, vision yield grade, and slice shear force; and increased ribeye area and CIE L* reflectance. The homozygous F94L FF and LL genotypes differed by 1.3 to 1.9 phenotypic SD for most carcass traits and by 0.8 to 0.9 SD for slice shear force and CIE L* reflectance but carcass weight differed by only 3 kg (0.1 SD). The L allele was partially recessive to F for ribeye area (P = 0.02) and the heterozygous FL means tended to be closer to the FF genotype than the LL genotype for other carcass traits but differences from additive were not significant. The CAPN1 additive × F94L additive effect on slice shear force was the only significant epistatic estimate. The F94L L allele is prevalent in Limousin but nearly absent in other U.S. purebreds. This allele had about half of the effects on birth weight, muscle, and fat traits reported for severe MSTN mutations in Belgian Blue and Piedmontese breeds. The interaction between MSTN and CAPN1 genotypes may reflect the strong additive effects of MSTN F94L L allele on fat and muscle traits interfering with the phenotypic effect of CAPN1 genotype on meat tenderness.
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Affiliation(s)
- Gary L Bennett
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Richard G Tait
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Steven D Shackelford
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Tommy L Wheeler
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - David A King
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Eduardo Casas
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
| | - Timothy P L Smith
- USDA, Agricultural Research Service, Roman L. Hruska US Meat Animal Research Center, Clay Center, NE
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Sumreddee P, Toghiani S, Hay EH, Roberts A, Agrrey SE, Rekaya R. Inbreeding depression in line 1 Hereford cattle population using pedigree and genomic information. J Anim Sci 2019; 97:1-18. [PMID: 30304409 DOI: 10.1093/jas/sky385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 11/14/2022] Open
Abstract
This study aimed at assessing inbreeding and its effect on growth and fertility traits using the longtime closed line 1 Hereford cattle population. Inbreeding was estimated based on pedigree (FPED) and genomic information. For the latter, three estimates were derived based on the diagonal elements of the genomic relationship matrix using estimated (FGRM) or fixed (FGRM0.5) minor allele frequencies or runs of homozygosity (ROH) (FROH). A pedigree containing 10,186 animals was used to calculate FPED. Genomic inbreeding was evaluated using 785 animals genotyped for 30,810 SNP. Traits analyzed were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), ADG, and age at first calving (AFC). The number of ROH per animal ranged between 6 and 119 segments with an average of 83. The shortest and longest segments were 1.36 and 64.86 Mb long, respectively, reflecting both ancient and recent inbreeding occurring in the last 30 to 40 generations. The average inbreeding was 29.2%, 16.1%, 30.2%, and 22.9% for FPED, FGRM, FGRM0.5, and FROH, respectively. FROH provided the highest correlations with FPED (r = 0.66). Across paternal half-sib families, with minimal variation in FPED, there were substantial variations in their genomic inbreeding. Inbreeding depression analyses showed that a 1% increase in an animal's FPED resulted in a decrease of 1.20 kg, 2.03 kg, and 0.004 kg/d in WWT, YWT, and ADG, respectively. Maternal inbreeding showed significantly negative effects on progeny growth performance. AFC increased by 1.4 and 0.8 d for each 1% increase in FPED of the cow and her dam, respectively. Using genomic inbreeding, similar impact on growth traits was observed although the magnitude of the effect varied between methods. Across all genomic measures, WWT, YWT, and ADG decreased by 0.21 to 0.53 kg, 0.46 to 1.13 kg, and 0.002 to 0.006 kg/d for each 1% increase in genomic inbreeding, respectively. Four chromosomes (9, 12, 17, and 27) were identified to have a significant association between their homozygosity (FROH-CHR) and growth traits. Variability in genomic inbreeding could be useful when deciding between full and half-sib selection candidates. Despite the high level of inbreeding in this study, its negative impact on growth performance was not as severe as expected, which may be attributed to the purging of the deleterious alleles due to natural or artificial selection over time.
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Affiliation(s)
| | - Sajjad Toghiani
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT
| | - Samuel E Agrrey
- Department of Poultry Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA.,Institute of Bioinformatics, The University of Georgia, Athens, GA.,Department of Statistics, The University of Georgia, Athens, GA
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Buzanskas ME, Grossi DA, Ventura RV, Schenkel FS, Sargolzaei M, Meirelles SLC, Mokry FB, Higa RH, Mudadu MA, da Silva MVGB, Niciura SCM, Júnior RAAT, Alencar MM, Regitano LCA, Munari DP. Genome-wide association for growth traits in Canchim beef cattle. PLoS One 2014; 9:e94802. [PMID: 24733441 PMCID: PMC3986245 DOI: 10.1371/journal.pone.0094802] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/20/2014] [Indexed: 12/01/2022] Open
Abstract
Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.
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Affiliation(s)
- Marcos E. Buzanskas
- Departamento de Ciências Exatas, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Daniela A. Grossi
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
| | - Ricardo V. Ventura
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
- Beef Improvement Opportunities (BIO), Guelph, Ontario, Canada
| | - Flávio S. Schenkel
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Department of Animal and Poultry Science, University of Guelph, Centre for Genetic Improvement of Livestock (CGIL), Guelph, Ontario, Canada
- The Semex Alliance, Guelph, Ontario, Canada
| | - Sarah L. C. Meirelles
- Department of Animal Science, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil
| | - Fabiana B. Mokry
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil
| | - Roberto H. Higa
- Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | | | | | | | | | | | | | - Danísio P. Munari
- Departamento de Ciências Exatas, UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
- * E-mail:
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Lu D, Sargolzaei M, Li C, Abo-Ismail M, Vander Voort G, Wang Z, Plastow G, Moore S, Miller SP. Association analysis for feed efficiency traits in beef cattle using preserved haplotypes. Genome 2013; 56:586-91. [DOI: 10.1139/gen-2013-0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. The study used data from 597 Angus, 450 Charolais, and 616 crossbred beef cattle, and the Illumina Bovine SNP50 beadchip. Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. Such regions in the crossbreds were tested for association with ADG, DMI, and RFI. At false discovery rates of 5% and 10%, there were six and eight chromosome regions showing significant associations with the traits, respectively. At nominal significance levels (at least P < 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. The proportion of phenotypic variance explained by these 23 regions varied depending on the trait; the highest proportion for ADG, DMI, and RFI was 13.50%, 9.92%, and 2.64%, respectively. Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. Thirty-six quantitative trait loci for 16 production traits, from the current literature, covered fully or in part the 23 chromosome regions. The findings from this study might be an important contribution to the current knowledge of the beef cattle genome and to the effective identification of causative genes associated with important traits in cattle.
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Affiliation(s)
- Duc Lu
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Lacombe, AB T4L 1W1, Canada
| | - Mohammed Abo-Ismail
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
- Department of Animal and Poultry Science, Damanhour University, Damanhour, Elbeheira, Egypt
| | - Gordon Vander Voort
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Zhiquan Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Stephen Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia 4072, Australia
| | - Stephen P. Miller
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
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7
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McClure MC, Morsci NS, Schnabel RD, Kim JW, Yao P, Rolf MM, McKay SD, Gregg SJ, Chapple RH, Northcutt SL, Taylor JF. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim Genet 2011; 41:597-607. [PMID: 20477797 DOI: 10.1111/j.1365-2052.2010.02063.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.
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Affiliation(s)
- M C McClure
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H. A genome-wide scan for signatures of recent selection in Holstein cattle. Anim Genet 2010; 41:377-89. [PMID: 20096028 DOI: 10.1111/j.1365-2052.2009.02016.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.
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Affiliation(s)
- S Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August University, 37075 Göttingen, Germany.
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Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds. Animal 2010; 4:530-4. [DOI: 10.1017/s175173110999139x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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MacNeil MD, Nkrumah JD, Woodward BW, Northcutt SL. Genetic evaluation of Angus cattle for carcass marbling using ultrasound and genomic indicators. J Anim Sci 2009; 88:517-22. [PMID: 19897629 DOI: 10.2527/jas.2009-2022] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The objectives were to estimate genetic parameters needed to elucidate the relationships of a molecular breeding value (MBV) for marbling, intramuscular fat (IMF) of yearling bulls measured with ultrasound, and marbling score (MRB) of slaughtered steers, and to assess the utility of MBV and IMF in predicting the breeding value for MRB. Records for MRB (n = 38,296) and IMF (n = 6,594) were from the American Angus Association database used for national cattle evaluation. A total of 1,006 records of MBV were used in this study. (Co)variance components were estimated with ASREML, fitting an animal model with fixed contemporary groups for MRB and IMF similar to those used in the Angus national genetic evaluation. The overall mean was the only fixed effect included in the model for MBV. Heritability estimates for carcass measures were 0.48 +/- 0.03, 0.31 +/- 0.03, and 0.98 +/- 0.05 for MRB, IMF, and MBV, respectively. Genetic correlations of IMF and MBV with MRB were 0.56 +/- 0.09 and 0.38 +/- 0.10, respectively. The genetic correlation between IMF and MBV was 0.80 +/- 0.22. These results indicate the MBV evaluated may yield a greater genetic advance of approximately 20% when used as an indicator trait for genetic prediction of MRB compared with IMF. However, neither of these indicators alone provides sufficient information to produce highly accurate prediction of breeding value for the economically relevant trait MRB. Given that the goal is a highly accurate prediction of true breeding value for MRB, results of this work point to the need to 1) continue progeny testing, and 2) continue increasing the genetic correlation between the MBV and MRB.
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Márquez GC, Enns RM, Grosz MD, Alexander LJ, MacNeil MD. Quantitative trait loci with effects on feed efficiency traits in Hereford × composite double backcross populations. Anim Genet 2009; 40:986-8. [DOI: 10.1111/j.1365-2052.2009.01946.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jiang Z, Michal JJ, Chen J, Daniels TF, Kunej T, Garcia MD, Gaskins CT, Busboom JR, Alexander LJ, Wright RW, Macneil MD. Discovery of novel genetic networks associated with 19 economically important traits in beef cattle. Int J Biol Sci 2009; 5:528-42. [PMID: 19727437 PMCID: PMC2726579 DOI: 10.7150/ijbs.5.528] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 07/16/2009] [Indexed: 11/20/2022] Open
Abstract
Quantitative or complex traits are determined by the combined effects of many loci, and are
affected by genetic networks or molecular pathways. In the present study, we genotyped a total
of 138 mutations, mainly single nucleotide polymorphisms derived from 71 functional genes on a
Wagyu x Limousin reference population. Two hundred forty six F2 animals were
measured for 5 carcass, 6 eating quality and 8 fatty acid composition traits. A total of 2,280
single marker-trait association runs with 120 tagged mutations selected based on the HAPLOVIEW
analysis revealed 144 significant associations (P < 0.05), but 50 of them were removed
from the analysis due to the small number of animals (≤ 9) in one genotype group or
absence of one genotype among three genotypes. The remaining 94 single-trait associations were
then placed into three groups of quantitative trait modes (QTMs) with additive, dominant and
overdominant effects. All significant markers and their QTMs associated with each of these 19
traits were involved in a linear regression model analysis, which confirmed single-gene
associations for 4 traits, but revealed two-gene networks for 8 traits and three-gene networks
for 5 traits. Such genetic networks involving both genotypes and QTMs resulted in high
correlations between predicted and actual values of performance, thus providing evidence that
the classical Mendelian principles of inheritance can be applied in understanding genetic
complexity of complex phenotypes. Our present study also indicated that carcass, eating quality
and fatty acid composition traits rarely share genetic networks. Therefore, marker-assisted
selection for improvement of one category of these traits would not interfere with improvement
of another.
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Affiliation(s)
- Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA.
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Alexander LJ, Kuehn LA, Smith TPL, Matukumalli LK, Mote B, Koltes JE, Reecy J, Geary TW, Rule DC, MacNeil MD. A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wagyu-Limousin F2 population1,2. J Anim Sci 2009; 87:1576-81. [DOI: 10.2527/jas.2008-1531] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abe T, Saburi J, Hasebe H, Nakagawa T, Kawamura T, Saito K, Nade T, Misumi S, Okumura T, Kuchida K, Hayashi T, Nakane S, Mitsuhasi T, Nirasawa K, Sugimoto Y, Kobayashi E. Bovine quantitative trait loci analysis for growth, carcass, and meat quality traits in an F2 population from a cross between Japanese Black and Limousin. J Anim Sci 2008; 86:2821-32. [PMID: 18599673 DOI: 10.2527/jas.2007-0676] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- T Abe
- National Livestock Breeding Center, Nishigo, Fukushima 961-8511, Japan.
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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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