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Abstract
Heat stress is described as the cumulative detrimental effect caused by an imbalance between heat production within the body and heat dissipation. When cattle are exposed to heat stress with skin surface temperatures exceeding 35 °C, gene networks within and across cells respond to environmental heat loads with both intra and extracellular signals that coordinate cellular and whole-animal metabolism changes to store heat and rapidly increase evaporative heat loss. In this study, we examined evidence from genes known to be associated with heat tolerance (Hsp70, HSF1, HspB8, SOD1, PRLH, ATP1A1, MTOR, and EIF2AK4). This information could serve as valuable resource material for breeding programs aimed at increasing the thermotolerance of cattle.
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Affiliation(s)
- LuLan Zeng
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Gerasimov NP, Dzhulamanov KM, Lebedev SV, Kolpakov VI. Effect of IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle. Vet World 2023; 16:1584-1592. [PMID: 37766706 PMCID: PMC10521179 DOI: 10.14202/vetworld.2023.1584-1592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/26/2023] [Indexed: 09/29/2023] Open
Abstract
Background and Aim Improving the feed efficiency of beef cattle is necessary to increase the profitability of meat production. Implementing marker-assisted selection breeding systems can improve the genetic potential of beef cattle for increased productivity. This research aimed to study the effects of insulin-like growth factor (IGF)-1 C472T, growth hormone (GH) C2141G, and GH receptor (GHR) T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle. Materials and Methods Young Kazakh white-headed cattle (n = 50) were grouped after weaning according to sex (28 bulls and 22 heifers) and they were genotyped according to the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms. The test period was conducted from 8 to 15 months of age. The experimental animals were evaluated for live weight (LW) at the beginning and end of the test period. They were also assessed for average daily gain, hip height, metabolic mid-weight (MMWT), actual dry matter intake (DMI), and residual feed intake (RFI). Results Significant differences in MMWT were found between the bulls with the IGF-1TT and IGF-1CT genotypes, which was a 2.2 kg increase in heterozygous cattle (p < 0.05). Heterozygous IGF-1CT bulls differed with a higher DMI of 0.087 kg/day (p < 0.05) compared to IGF-1TT homozygotes. Carriers of the IGF-1TT genotype had the greatest feed efficiency at 0.068 kg/day (p < 0.05). Heifers with the GHCC genotype differed in their maximum DMI with an increase of 1.17%-1.57% (p < 0.05) relative to the other genotypes. The G allele in the GH C2141G polymorphism was associated with better (p < 0.05) feed efficiency in the Kazakh white-headed breed. The minimum DMI and RFI in GHR T914A heterozygous heifers were significantly inferior (p < 0.05) to the other genotypes. Conclusion Association studies of the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms indicate a relationship between growth, development, and feed efficiency with the genetic characteristics of young Kazakh white-headed cattle. A significant (p < 0.05) dominant effect was found in the IGF-1 gene in bulls and in the GHR gene in heifers, which should be considered when breeding with heterogeneous parental pairs. The negative effect of the allele substitution in the IGF-1 C472T polymorphism was observed in the LW of heifers (-3.25 kg) at the age of 8 months and bulls (-6.05 kg) at 15 months. The substitution in the GH C2141G polymorphism was associated with a significant reduction in DMI by 0.036 kg (p < 0.05) and an increase in feed efficiency by 0.023 kg (p < 0.05) during the rearing of heifers. These results can improve the production efficiency of mature herds of Kazakh white-headed cattle.
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Affiliation(s)
- Nikolay P. Gerasimov
- Federal Research Centre of Biological Systems and Agrotechnologies RAS, Orenburg, Russian Federation
| | - K. M. Dzhulamanov
- Federal Research Centre of Biological Systems and Agrotechnologies RAS, Orenburg, Russian Federation
| | - S. V. Lebedev
- Federal Research Centre of Biological Systems and Agrotechnologies RAS, Orenburg, Russian Federation
| | - V. I. Kolpakov
- Federal Research Centre of Biological Systems and Agrotechnologies RAS, Orenburg, Russian Federation
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Buss CE, Afonso J, de Oliveira PSN, Petrini J, Tizioto PC, Cesar ASM, Gustani-Buss EC, Cardoso TF, Rovadoski GA, da Silva Diniz WJ, de Lima AO, Rocha MIP, Andrade BGN, Wolf JB, Coutinho LL, Mourão GB, de Almeida Regitano LC. Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle. Mamm Genome 2023; 34:90-103. [PMID: 36463529 DOI: 10.1007/s00335-022-09969-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2022]
Abstract
Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.
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Affiliation(s)
- Carlos Eduardo Buss
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Mindflow Genomics, Leuven, Flanders, Belgium
| | - Juliana Afonso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Priscila S N de Oliveira
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Emanuele Cristina Gustani-Buss
- Mindflow Genomics, Leuven, Flanders, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tainã Figueiredo Cardoso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Gregori A Rovadoski
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genomics Science, University of Washington, Seattle, WA, USA
| | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
- Department of Computer Science, Munster Technological University/MTU, Cork, Ireland
| | - Jason B Wolf
- Department of Biology & Biochemistry, Milner Centre for Evolution Bath, University of Bath, Bath, BA2 7AY, UK
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups. Animals (Basel) 2023; 13:ani13030359. [PMID: 36766249 PMCID: PMC9913155 DOI: 10.3390/ani13030359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.
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Comparative Analysis of Multiple GWAS Results Identifies Metabolic Pathways Associated with Resistance to A. flavus Infection and Aflatoxin Accumulation in Maize. Toxins (Basel) 2022; 14:toxins14110738. [PMID: 36355988 PMCID: PMC9695789 DOI: 10.3390/toxins14110738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 01/26/2023] Open
Abstract
Aflatoxins are carcinogenic secondary metabolites produced by several species of Aspergillus, including Aspergillus flavus, an important ear rot pathogen in maize. Most commercial corn hybrids are susceptible to infection by A. flavus, and aflatoxin contaminated grain causes economic damage to farmers. The creation of inbred lines resistant to Aspergillus fungal infection or the accumulation of aflatoxins would be aided by knowing the pertinent alleles and metabolites associated with resistance in corn lines. Multiple Quantitative Trait Loci (QTL) and association mapping studies have uncovered several dozen potential genes, but each with a small effect on resistance. Metabolic pathway analysis, using the Pathway Association Study Tool (PAST), was performed on aflatoxin accumulation resistance using data from four Genome-wide Association Studies (GWAS). The present research compares the outputs of these pathway analyses and seeks common metabolic mechanisms underlying each. Genes, pathways, metabolites, and mechanisms highlighted here can contribute to improving phenotypic selection of resistant lines via measurement of more specific and highly heritable resistance-related traits and genetic gain via marker assisted or genomic selection with multiple SNPs linked to resistance-related pathways.
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Identification of Candidate Genes Regulating Carcass Depth and Hind Leg Circumference in Simmental Beef Cattle Using Illumina Bovine Beadchip and Next-Generation Sequencing Analyses. Animals (Basel) 2022; 12:ani12091103. [PMID: 35565529 PMCID: PMC9102740 DOI: 10.3390/ani12091103] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022] Open
Abstract
Genome-wide association studies are a robust means of identifying candidate genes that regulate economically important traits in farm animals. The aim of this study is to identify single-nucleotide polymorphisms (SNPs) and candidate genes potentially related to carcass depth and hind leg circumference in Simmental beef cattle. We performed Illumina Bovine HD Beadchip (~670 k SNPs) and next-generation sequencing (~12 million imputed SNPs) analyses of data from 1252 beef cattle, to which we applied a linear mixed model. Using a statistical threshold (p = 0.05/number of SNPs identified) and adopting a false discovery rate (FDR), we identified many putative SNPs on different bovine chromosomes. We identified 12 candidate genes potentially annotated with the markers identified, including CDKAL1 and E2F3, related to myogenesis and skeletal muscle development. The identification of such genes in Simmental beef cattle will help breeders to understand and improve related traits, such as meat yield.
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Mauki DH, Tijjani A, Ma C, Ng’ang’a SI, Mark AI, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Kazwala RR, Gwakisa PS, Yin TT, Li Y, Peng MS, Adeola AC, Zhang YP. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics 2022; 23:306. [PMID: 35428239 PMCID: PMC9012019 DOI: 10.1186/s12864-022-08512-w] [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: 01/25/2021] [Accepted: 03/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. Results The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. Conclusion The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08512-w.
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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Fonseca PADS, Caldwell T, Mandell I, Wood K, Cánovas A. Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages. Meat Sci 2022; 186:108733. [PMID: 35007800 DOI: 10.1016/j.meatsci.2022.108733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tim Caldwell
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ira Mandell
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Katharine Wood
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Naji MM, Utsunomiya YT, Sölkner J, Rosen BD, Mészáros G. Assessing Bos taurus introgression in the UOA Bos indicus assembly. Genet Sel Evol 2021; 53:96. [PMID: 34922445 PMCID: PMC8684283 DOI: 10.1186/s12711-021-00688-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022] Open
Abstract
Background Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus—B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus—B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. Results The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. Conclusions We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00688-1.
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Affiliation(s)
- Maulana M Naji
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Yuri T Utsunomiya
- AgroPartners Consulting, R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Araçatuba, São Paulo, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, São Paulo, Brazil
| | - Johann Sölkner
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA, ARS, Beltsville, MD, USA.
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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Zhang X, Luan P, Cao D, Hu G. A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp ( Cyprinus carpio). Front Genet 2021; 12:778487. [PMID: 34868267 PMCID: PMC8633483 DOI: 10.3389/fgene.2021.778487] [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: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9-15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.
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Affiliation(s)
- Xiaofeng Zhang
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | | | | | - Guo Hu
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
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Expression of candidate genes for residual feed intake in tropically adapted Bos taurus and Bos indicus bulls under thermoneutral and heat stress environmental conditions. J Therm Biol 2021; 99:102998. [PMID: 34420630 DOI: 10.1016/j.jtherbio.2021.102998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/16/2021] [Indexed: 01/17/2023]
Abstract
The objectives of this study were to measure the relative expression of the ATP1A1, NR3C1, POMC, NPY, and LEP genes in Caracu (Bos taurus) and Nelore (Bos indicus) bulls submitted to feed efficiency tests at high environmental temperatures, and to evaluate differences in adaptability to tropical conditions between breeds. Thirty-five Caracu and 30 Nelore bulls were submitted to a feed efficiency test using automated feeding stations. At the end of the test, the animals were subjected to thermoneutral (TN) and heat stress (HS) conditions. Blood samples were collected after the exposure to the TN and HS conditions and the relative expression of genes was measured by qPCR. The bulls exhibited lower expression of ATP1A1 in the HS condition than in the TN condition (1.98 ± 0.27 and 2.86 ± 0.26, P = 0.02), while the relative expression of NR3C1, POMC, and LEP did not differ (P > 0.05) between climatic conditions. The breed and feed intake influenced NPY and LEP expression levels (P < 0.05). Different climate conditions associated with residual feed intake can modify the gene expression patterns of ATP1A1 and NPY. The association observed among all genes studied shows that they are involved in appetite control. Bos taurus and Bos indicus bulls exhibited similar adaptability to tropical climate conditions.
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Nafikova E, Mironova I, Gazeev I, Blagov D, Nigmatiyanov A. The effect of an energy additive on the metabolism of cattle. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2021; 85:210-217. [PMID: 34248266 PMCID: PMC8243801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 06/13/2023]
Abstract
The objective of this study was to determine the effect of an energy additive on the metabolism of cattle. This article provides information on the analysis of the diet of young cattle calculated for when the animals were both indoors and outdoors. The ration was prepared for 40 heifers, divided into 4 groups consisting of 10 animals in each group. Three of these groups were fed different amounts of a high-energy additive, which was not fed to the control group. The effectiveness of the additive was analyzed according to the balance experiment and by calculating digestibility coefficients. It was determined that the percentage of nitrogen use in young animals was higher in the groups that were fed the additive than in the control group. Increasing the dose of the additive increased the level of nitrogen use. Comparative analysis of live weight indicated intergroup differences in favor of heifers in the groups that were fed the additive of 1.34% to 2.41% at the age of 9 mo; 2.51% to 4.16% at 12 mo; 3.14% to 5.46% at 15 mo; and 3.57% to 6.30% at 18 mo. The average daily growth dynamics indicated a gradual increase in all animals up to 15 mo, with a slight decrease by 18 mo of age. The difference among the groups ranged from 5.08% to 8.85% at 6 to 9 mo of age; 7.08% to 10.79% at 9 to 12 mo; 5.64% to 10.97% at 12 to 15 mo; and 6.05% to 11.11% at 18 mo. It was concluded that feeding the energy additive Tanrem to heifers increased their metabolism so that nitrogen use was improved, and feed was digested more efficiently, which in turn improved the growth of animals. Using an energy additive at the mid-range dose of 500 g a day per animal is recommended, since the effect was similar at the mid-range and maximum dosages.
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Affiliation(s)
- Elina Nafikova
- Department of Technologies of Meat, Dairy Products and Chemistry (Nafikova, Mironova), Department of Life Safety and Process Equipment (Gazeev), and Department of Technology Catering and Processing of Vegetable Raw Materials (Nigmatiyanov), Federal State Budgetary Educational Establishment of Higher Education "Bashkir State Agrarian University," 50-letia Octyabrya Str., 34, Ufa, 450099, Russia; Department for Information Technologies in Agricultural Production, Institute of Technical Support of Agriculture (ITSA) - Branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center (FSAC) VIM," Ryazan, Russia (Blagov)
| | - Irina Mironova
- Department of Technologies of Meat, Dairy Products and Chemistry (Nafikova, Mironova), Department of Life Safety and Process Equipment (Gazeev), and Department of Technology Catering and Processing of Vegetable Raw Materials (Nigmatiyanov), Federal State Budgetary Educational Establishment of Higher Education "Bashkir State Agrarian University," 50-letia Octyabrya Str., 34, Ufa, 450099, Russia; Department for Information Technologies in Agricultural Production, Institute of Technical Support of Agriculture (ITSA) - Branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center (FSAC) VIM," Ryazan, Russia (Blagov)
| | - Igor Gazeev
- Department of Technologies of Meat, Dairy Products and Chemistry (Nafikova, Mironova), Department of Life Safety and Process Equipment (Gazeev), and Department of Technology Catering and Processing of Vegetable Raw Materials (Nigmatiyanov), Federal State Budgetary Educational Establishment of Higher Education "Bashkir State Agrarian University," 50-letia Octyabrya Str., 34, Ufa, 450099, Russia; Department for Information Technologies in Agricultural Production, Institute of Technical Support of Agriculture (ITSA) - Branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center (FSAC) VIM," Ryazan, Russia (Blagov)
| | - Dmitry Blagov
- Department of Technologies of Meat, Dairy Products and Chemistry (Nafikova, Mironova), Department of Life Safety and Process Equipment (Gazeev), and Department of Technology Catering and Processing of Vegetable Raw Materials (Nigmatiyanov), Federal State Budgetary Educational Establishment of Higher Education "Bashkir State Agrarian University," 50-letia Octyabrya Str., 34, Ufa, 450099, Russia; Department for Information Technologies in Agricultural Production, Institute of Technical Support of Agriculture (ITSA) - Branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center (FSAC) VIM," Ryazan, Russia (Blagov)
| | - Azat Nigmatiyanov
- Department of Technologies of Meat, Dairy Products and Chemistry (Nafikova, Mironova), Department of Life Safety and Process Equipment (Gazeev), and Department of Technology Catering and Processing of Vegetable Raw Materials (Nigmatiyanov), Federal State Budgetary Educational Establishment of Higher Education "Bashkir State Agrarian University," 50-letia Octyabrya Str., 34, Ufa, 450099, Russia; Department for Information Technologies in Agricultural Production, Institute of Technical Support of Agriculture (ITSA) - Branch of the Federal State Budgetary Scientific Institution "Federal Scientific Agroengineering Center (FSAC) VIM," Ryazan, Russia (Blagov)
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14
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McKenna C, Keogh K, Porter RK, Waters SM, Cormican P, Kenny DA. An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake. Sci Rep 2021; 11:8942. [PMID: 33903612 PMCID: PMC8076192 DOI: 10.1038/s41598-021-87842-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.
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Affiliation(s)
- Clare McKenna
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland.,School of Biochemistry & Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Kate Keogh
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - Richard K Porter
- School of Biochemistry & Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Sinead M Waters
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - Paul Cormican
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland.
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15
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Parameswari B, Nithya K, Kumar S, Holkar SK, Chabbra ML, Kumar P, Viswanathan R. Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research. INDIAN PHYTOPATHOLOGY 2021. [DOI: 10.1007/s42360-021-00323-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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16
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Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
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17
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Mukiibi R, Johnston D, Vinsky M, Fitzsimmons C, Stothard P, Waters SM, Li C. Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes. Sci Rep 2020; 10:19309. [PMID: 33168877 PMCID: PMC7653039 DOI: 10.1038/s41598-020-73885-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.
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Affiliation(s)
- Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Dayle Johnston
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Michael Vinsky
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada.
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18
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Prakash A, Saxena VK, Ravi Kumar G, Tomar S, Singh MK. Molecular basis of residual feed intake in broilers. WORLD POULTRY SCI J 2020. [DOI: 10.1080/00439339.2020.1789534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Anand Prakash
- Division of Avian Genetics and Breeding, ICAR-Central Avian Research Institute, Izatnagar, India
- Department of Livestock Farm Complex, SVU-GADVASU, Ludhiana, India
| | - Vishesh Kumar Saxena
- Division of Avian Genetics and Breeding, ICAR-Central Avian Research Institute, Izatnagar, India
| | - Gandham Ravi Kumar
- Department of Biotechnology, National Institute of Animal Biotechnology, Hyderabad
| | - Simmi Tomar
- Division of Avian Genetics and Breeding, ICAR-Central Avian Research Institute, Izatnagar, India
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19
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Conditional and unconditional genome-wide association study reveal complicate genetic architecture of human body weight and impacts of smoking. Sci Rep 2020; 10:12136. [PMID: 32699216 PMCID: PMC7376032 DOI: 10.1038/s41598-020-68935-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
To reveal the impacts of smoking on genetic architecture of human body weight, we conducted a genome-wide association study on 5,336 subjects in four ethnic populations from MESA (The Multi-Ethnic Study of Atherosclerosis) data. A full genetic model was applied to association mapping for analyzing genetic effects of additive, dominance, epistasis, and their ethnicity-specific effects. Both the unconditional model (base) and conditional model including smoking as a cofactor were investigated. There were 10 SNPs involved in 96 significant genetic effects detected by the base model, which accounted for a high heritability (61.78%). Gene ontology analysis revealed that a number of genetic factors are related to the metabolic pathway of benzopyrene, a main compound in cigarettes. Smoking may play important roles in genetic effects of dominance, dominance-related epistasis, and gene-ethnicity interactions on human body weight. Gene effect prediction shows that the genetic effects of smoking cessation on body weight vary from different populations.
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20
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Bordbar F, Jensen J, Zhu B, Wang Z, Xu L, Chang T, Xu L, Du M, Zhang L, Gao H, Xu L, Li J. Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing. PLoS One 2019; 14:e0223671. [PMID: 31600309 PMCID: PMC6786524 DOI: 10.1371/journal.pone.0223671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/25/2019] [Indexed: 01/01/2023] Open
Abstract
Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was to detect potential candidate genes associated mainly with muscle development traits related to dimension of hindquarter in cattle. A next generation sequencing (NGS) dataset to imputed to 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were used to search for genes affecting hindquarter traits using a linear, mixed model approach. We also used haplotype and linkage disequilibrium blocks to further support our identifications. We identified 202 significant SNPs in the bovine BTA4 chromosome region associated with width of hind leg, based on a stringent statistical threshold (p = 0.05/ effective number of SNPs identified). After exploring the region around these SNPs, we found candidate genes that were potentially related to the associated markers. More importantly, we identified a region of approximately 280 Kb on the BTA4 chromosome that harbored several muscle specific candidate genes, genes to be in a potential region for muscle development. However, we also found candidate gene SLC13A1 on BTA4, which seems to be associated with bone disorders (such as chondrodysplasia) in Simmental beef cattle.
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Affiliation(s)
- Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Just Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianpeng Chang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Min Du
- Department of Animal Sciences, Washington Center for Muscle Biology, Washington State University, Pullman, Washington, United States of America
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (JYL); (LYX)
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (JYL); (LYX)
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21
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Li B, Fang L, Null DJ, Hutchison JL, Connor EE, VanRaden PM, VandeHaar MJ, Tempelman RJ, Weigel KA, Cole JB. High-density genome-wide association study for residual feed intake in Holstein dairy cattle. J Dairy Sci 2019; 102:11067-11080. [PMID: 31563317 DOI: 10.3168/jds.2019-16645] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/19/2019] [Indexed: 01/27/2023]
Abstract
Improving feed efficiency (FE) of dairy cattle may boost farm profitability and reduce the environmental footprint of the dairy industry. Residual feed intake (RFI), a candidate FE trait in dairy cattle, can be defined to be genetically uncorrelated with major energy sink traits (e.g., milk production, body weight) by including genomic predicted transmitting ability of such traits in genetic analyses for RFI. We examined the genetic basis of RFI through genome-wide association (GWA) analyses and post-GWA enrichment analyses and identified candidate genes and biological pathways associated with RFI in dairy cattle. Data were collected from 4,823 lactations of 3,947 Holstein cows in 9 research herds in the United States. Of these cows, 3,555 were genotyped and were imputed to a high-density list of 312,614 SNP. We used a single-step GWA method to combine information from genotyped and nongenotyped animals with phenotypes as well as their ancestors' information. The estimated genomic breeding values from a single-step genomic BLUP were back-solved to obtain the individual SNP effects for RFI. The proportion of genetic variance explained by each 5-SNP sliding window was also calculated for RFI. Our GWA analyses suggested that RFI is a highly polygenic trait regulated by many genes with small effects. The closest genes to the top SNP and sliding windows were associated with dry matter intake (DMI), RFI, energy homeostasis and energy balance regulation, digestion and metabolism of carbohydrates and proteins, immune regulation, leptin signaling, mitochondrial ATP activities, rumen development, skeletal muscle development, and spermatogenesis. The region of 40.7 to 41.5 Mb on BTA25 (UMD3.1 reference genome) was the top associated region for RFI. The closest genes to this region, CARD11 and EIF3B, were previously shown to be related to RFI of dairy cattle and FE of broilers, respectively. Another candidate region, 57.7 to 58.2 Mb on BTA18, which is associated with DMI and leptin signaling, was also associated with RFI in this study. Post-GWA enrichment analyses used a sum-based marker-set test based on 4 public annotation databases: Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Reactome pathways, and medical subject heading (MeSH) terms. Results of these analyses were consistent with those from the top GWA signals. Across the 4 databases, GWA signals for RFI were highly enriched in the biosynthesis and metabolism of amino acids and proteins, digestion and metabolism of carbohydrates, skeletal development, mitochondrial electron transport, immunity, rumen bacteria activities, and sperm motility. Our findings offer novel insight into the genetic basis of RFI and identify candidate regions and biological pathways associated with RFI in dairy cattle.
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Affiliation(s)
- B Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - L Fang
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350; Department of Animal and Avian Sciences, University of Maryland, College Park 20742; Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - D J Null
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - J L Hutchison
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - E E Connor
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - M J VandeHaar
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - R J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350.
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22
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Carvalho EB, Gionbelli MP, Rodrigues RTS, Bonilha SFM, Newbold CJ, Guimarães SEF, Silva W, Verardo LL, Silva FF, Detmann E, Duarte MS. Differentially expressed mRNAs, proteins and miRNAs associated to energy metabolism in skeletal muscle of beef cattle identified for low and high residual feed intake. BMC Genomics 2019; 20:501. [PMID: 31208329 PMCID: PMC6580615 DOI: 10.1186/s12864-019-5890-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
Background Feed efficiency is one of the most important parameters that affect beef production costs. The energy metabolism of skeletal muscle greatly contributes to variations in feed efficiency. However, information regarding differences in proteins involved in the energy metabolism of the skeletal muscle in beef cattle divergently identified for feed efficiency is scarce. In this study, we aimed to investigate energy metabolism of skeletal muscle of Nellore beef cattle, identified for low and high residual feed intake using a proteomics approach. We further assessed the expression of candidate microRNAs as a one of the possible mechanisms controlling the biosynthesis of the proteins involved in energy metabolism that were differentially abundant between high and low residual feed intake animals. Results A greater abundance of 14–3-3 protein epsilon (P = 0.01) was observed in skeletal muscle of residual feed intake (RFI) high animals (RFI-High). Conversely, a greater abundance of Heat Shock Protein Beta 1 (P < 0.01) was observed in the skeletal muscle of RFI-Low cattle. A greater mRNA expression of YWHAE, which encodes the 14–3-3 protein epsilon, was also observed in the skeletal muscle of RFI-High animals (P = 0.01). A lower mRNA expression of HSPB1, which encodes the Heat Shock Protein Beta 1, was observed in the skeletal muscle of RFI-High animals (P = 0.01). The miR-665 was identified as a potential regulator of the 14–3-3 protein epsilon, and its expression was greater in RFI-Low animals (P < .001). A greater expression of miR-34a (P = 0.01) and miR-2899 (P < .001) was observed in the skeletal muscle of RFI-High animals, as both miRNAs were identified as potential regulators of HSPB1 expression. Conclusion Our results show that Nellore cattle divergently identified for feed efficiency by RFI present changes in the abundance of proteins involved in energy expenditure in skeletal muscle. Moreover, our data point towards that miR-665, miR34a and miR-2899 are likely involved in controlling both 14-3-3 epsilon and HSPB1 proteins identified as differentially abundant in the skeletal muscle of RFI-High and RFI-Low Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-019-5890-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa B Carvalho
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil.,Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Mateus P Gionbelli
- Department of Animal Science, Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Rafael T S Rodrigues
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil.,Department of Veterinary Sciences, Universidade Federal do Vale do São Francisco, Petrolina, PE, Brazil
| | - Sarah F M Bonilha
- Centro APTA Bovinos de Corte, Instituto de Zootecnia, Sertãozinho, SP, Brazil
| | | | - Simone E F Guimarães
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Walmir Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Lucas L Verardo
- Department of Animal Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Fabyano F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Edenio Detmann
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcio S Duarte
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Iqbal N, Liu X, Yang T, Huang Z, Hanif Q, Asif M, Khan QM, Mansoor S. Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan. PLoS One 2019; 14:e0215065. [PMID: 30973947 PMCID: PMC6459497 DOI: 10.1371/journal.pone.0215065] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/26/2019] [Indexed: 12/30/2022] Open
Abstract
The primary goal of cattle genomics is the identification of genome-wide polymorphism associated with economically important traits. The bovine genome sequencing project was completed in 2009. Since then, using massively parallel sequencing technologies, a large number of Bos taurus cattle breeds have been resequenced and scanned for genome-wide polymorphisms. As a result, a substantial number of single nucleotide polymorphisms (SNPs) have been discovered across European Bos taurus genomes, whereas extremely less number of SNPs are cataloged for Bos indicus breeds. In this study, we performed whole-genome resequencing, reference-based mapping, functional annotation and gene enrichment analysis of 20 sires representing eleven important Bos indicus (indicine) breeds of Pakistan. The breeds sequenced here include: Sahiwal, Red Sindhi, Tharparkar and Cholistani (tropically adapted dairy and dual purpose breeds), Achai, Bhagnari, Dajal and Lohani (high altitude adapted dual and drought purpose breeds); Dhanni, Hisar Haryana and Gabrali (dairy and light drought purpose breeds). A total of 17.4 billion QC passed reads were produced using BGISEQ-500 next generation sequencing platform to generate 9 to 27-fold genome coverage (average ~16×) for each of the 20 sequenced sires. A total of 67,303,469 SNPs were identified, of which 3,850,365 were found novel and 1,083,842 insertions-deletions (InDels) were detected across the whole sequenced genomes (491,247 novel). Comparative analysis using coding region SNPs revealed a close relationship between the best milking indicine breeds; Red Sindhi and Sahiwal. On the other hand, Bhagnari and Tharparkar being popular for their adaptation to dry and extremely hot climates were found to share the highest number of SNPs. Functional annotation identified a total of 3,194 high-impact (disruptive) SNPs and 745 disruptive InDels (in 275 genes) that may possibly affect economically important dairy and beef traits. Functional enrichment analysis was performed and revealed that high or moderate impact variants in wingless-related integration site (Wnt) and vascular smooth muscle contraction (VSMC) signaling pathways were significantly over-represented in tropically adapted heat tolerant Pakistani-indicine breeds. On the other hand, vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1 (HIF-1) signaling pathways were found over-represented in highland adapted Pakistani-indicine breeds. Similarly, the ECM-receptor interaction and Jak-STAT signaling pathway were significantly enriched in dairy and beef purpose Pakistani-indicine cattle breeds. The Toll-like receptor signaling pathway was significantly enriched in most of the Pakistani-indicine cattle. Therefore, this study provides baseline data for further research to investigate the molecular mechanisms of major traits and to develop potential genomic markers associated with economically important breeding traits, particularly in indicine cattle.
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Affiliation(s)
- Naveed Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
- Department of Biotechnology & Informatics, Faculty of life Sciences, Baluchistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Baluchistan, Pakistan
| | - Xin Liu
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ting Yang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Ziheng Huang
- Beijing Genomic Institute (BGI), Shenzhen, Guangdong, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Qaiser Mahmood Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, Pakistan
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Muscle transcriptome signature and gene regulatory network analysis in two divergent lines of a hilly bovine species Mithun (Bos frontalis). Genomics 2019; 112:252-262. [PMID: 30822468 DOI: 10.1016/j.ygeno.2019.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 11/23/2022]
Abstract
A massive bovine, Bos frontalis, also known as Mithun or Gayal, found at higher altitude is very promising meat and milk animal. For candidate gene and marker discovery, RNA-seq data was generated from longissimus dorsi muscle tissues with Illumina-HiSeq. Such markers can be used in future for genetic gain of traits like feed conversion efficiency (FCE) and average daily gain (ADG). Analysis revealed 297differentially expressed genes (DEGs) having 173 up and 124 down-regulated unigenes. Extensive conservation was found in genic region while comparing with Bos taurus. Analysis revealed 57 pathways having 112 enzymes, 72 transcriptional factors and cofactors, 212 miRNAs regulating 71 DEGs, 25,855 SSRs, mithun-specific 104,822 variants and 7288 indels, gene regulatory network (GRN) having 24 hub-genes and transcriptional factors regulating cell proliferation, immune tolerance and myogenesis. This is first report of muscle transcriptome depicting candidate genes with GRN controlling FCE and ADG. Reported putative molecular markers, candidate genes and hub proteins can be valuable genomic resources for association studies in genetic improvement programme.
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25
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HONG MINWOOK, CHOI SOYOUNG, SINGH NARESHKUMAR, KIM HUN, YANG SONGYI, KWAK KYEONGROK, KIM JONGBOK, LEE SUNGJIN. Genome-wide association analysis to identify QTL for carcass traits in Hanwoo (Korean native cattle). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2019. [DOI: 10.56093/ijans.v89i1.86384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genome-wide association study (GWAS) was performed to investigate the genetic markers associated with carcass traits of Hanwoo (Bos taurus coreanae) steer in the Gangwon region of Korea. Hanwoo steer (139) from the Gangwon region were genotyped with Bovine SNP50K BeadChip, and 35,769 SNPs were analyzed for five specific carcass traits after applying several filters. A total of seven quantitative trait loci were detected, of which four, one, and 2 SNPs were detected on various B. taurus autosomal chromosomes (BTA) by the respective model. The four significant SNPs associated with backfat thickness were ARS-BFGL-NGS–41475 on BTA 5, ARS-BFGLNGS- 36359 on BTA 19, ARS-BFGL-NGS-56813 on BTA 22, and Hapmap25048-BTA-138242 on BTA 25. Among the detected SNPs, one and two SNPs were associated with marbling score (ARS-BFGL-NGS-110066 on BTA 23) and meat colour (BTB-01920239 on BTA 15 and ARS-BFGL-NGS-24934 on BTA 18). In this GWAS, we identified three positional candidate genes for carcass traits, backfat thickness (Fibulin-2, FBLN2; Sorting nexin 29, SNX29) and meat colour (WW domain containing oxidoreductase, WWOX). Our results suggest that the candidate SNP markers do affect the genomic selection of associated carcass traits for Hanwoo in the Gangwon region.
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Higgins MG, Fitzsimons C, McClure MC, McKenna C, Conroy S, Kenny DA, McGee M, Waters SM, Morris DW. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Sci Rep 2018; 8:14301. [PMID: 30250203 PMCID: PMC6155370 DOI: 10.1038/s41598-018-32374-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
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Affiliation(s)
- Marc G Higgins
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland.,Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Claire Fitzsimons
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.,Department of Agriculture, Fisheries and the Marine, Celbridge, Co. Kildare, Ireland
| | - Matthew C McClure
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland.,ABS-Global, DeForest, WI, USA
| | - Clare McKenna
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Stephen Conroy
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
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27
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Hay EH, Roberts A. Genome-wide association study for carcass traits in a composite beef cattle breed. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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28
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Yi Z, Li X, Luo W, Xu Z, Ji C, Zhang Y, Nie Q, Zhang D, Zhang X. Feed conversion ratio, residual feed intake and cholecystokinin type A receptor gene polymorphisms are associated with feed intake and average daily gain in a Chinese local chicken population. J Anim Sci Biotechnol 2018; 9:50. [PMID: 29942508 PMCID: PMC6000933 DOI: 10.1186/s40104-018-0261-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 04/25/2018] [Indexed: 11/25/2022] Open
Abstract
Background The feed conversion ratio (FCR) and residual feed intake (RFI) are common indexes in measuring feed efficiency for livestock. RFI is a feed intake adjusted for requirements for maintenance and production so these two traits are related. Similarly, FCR is related to feed intake and weight gain because it is their ratio. Cholecystokinin type A receptor (CCKAR) plays an important role in animal digestive process. We examined the interplay of these three parameters in a local Chinese chicken population. Results The feed intake (FI) and body weights (BW) of 1,841 individuals were monitored on a daily basis from 56 to 105 d of age. There was a strong correlation between RFI and average daily feed intake (ADFI) and a negative correlation between the FCR and daily gain (rg = − 0.710). Furthermore, we identified 51 single nucleotide polymorphisms (SNPs) in the CCKAR and 4 of these resulted in amino acid mutations. The C334A mutation was specifically associated with FI and the expected feed intake (EFI) (P < 0.01) and significantly associated with the average daily gain (ADG) (P < 0.05). G1290A was significantly associated with FI and EFI (P < 0.05). Conclusion FCR is apply to weight selecting, and RFI is more appropriate if the breeding focus is feed intake. And C334A and G1290A of the CCKAR gene can be deemed as candidate markers for feed intake and weight gain. Electronic supplementary material The online version of this article (10.1186/s40104-018-0261-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenhua Yi
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China
| | - Xing Li
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China
| | - Wen Luo
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China
| | - Zhenqiang Xu
- Wen's Nanfang Poultry Breeding Co. Ltd, Yunfu, 527400 Guangdong China
| | - Congliang Ji
- Wen's Nanfang Poultry Breeding Co. Ltd, Yunfu, 527400 Guangdong China
| | - Yan Zhang
- Wen's Nanfang Poultry Breeding Co. Ltd, Yunfu, 527400 Guangdong China
| | - Qinghua Nie
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China
| | - Dexiang Zhang
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China.,Wen's Nanfang Poultry Breeding Co. Ltd, Yunfu, 527400 Guangdong China
| | - Xiquan Zhang
- 1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, 510642 Guangdong China.,2Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, 510642 Guangdong China
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29
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Mukiibi R, Vinsky M, Keogh KA, Fitzsimmons C, Stothard P, Waters SM, Li C. Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle. Sci Rep 2018; 8:7303. [PMID: 29740082 PMCID: PMC5940658 DOI: 10.1038/s41598-018-25605-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/12/2018] [Indexed: 11/09/2022] Open
Abstract
The genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds.
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Affiliation(s)
- Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, T4L 1W1, Canada
| | - Kate A Keogh
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, T4L 1W1, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada. .,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, T4L 1W1, Canada.
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30
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Pang M, Luo W, Fu B, Yu X, Zhou Y, Tong J. Transcriptomic Profiles of Brain Provide Insights into Molecular Mechanism of Feed Conversion Efficiency in Crucian Carp (Carassius auratus). Int J Mol Sci 2018. [PMID: 29538345 PMCID: PMC5877719 DOI: 10.3390/ijms19030858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Feed efficiency is an economically crucial trait for cultured animals, however, progress has been scarcely made in the genetic analyses of feed conversion efficiency (FCE) in fish because of the difficulties in measurement of trait phenotypes. In the present investigation, we present the first application of RNA sequencing (RNA-Seq) combined with differentially expressed genes (DEGs) analysis for identification of functional determinants related to FCE at the gene level in an aquaculture fish, crucian carp (Carassius auratus). Brain tissues of six crucian carp with extreme FCE performances were subjected to transcriptome analysis. A total of 544,612 unigenes with a mean size of 644.38 bp were obtained from Low- and High-FCE groups, and 246 DEGs that may be involved in FCE traits were identified in these two groups. qPCR confirmed that genes previously identified as up- or down-regulated by RNA-Seq were effectively up- or down-regulated under the studied conditions. Thirteen key genes, whose functions are associated with metabolism (Dgkk, Mgst3 and Guk1b), signal transduction (Vdnccsa1b, Tgfα, Nr4a1 and Tacr2) and growth (Endog, Crebrtc2, Myh7, Myh1,Myh14 and Igfbp7) were identified according to GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotations. Our novel findings provide useful pathway information and candidate genes for future studies of genetic mechanisms underlying FCE in crucian carp.
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Affiliation(s)
- Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Weiwei Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
| | - Ying Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China.
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31
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Pang M, Fu B, Yu X, Liu H, Wang X, Yin Z, Xie S, Tong J. Quantitative trait loci mapping for feed conversion efficiency in crucian carp (Carassius auratus). Sci Rep 2017; 7:16971. [PMID: 29209087 PMCID: PMC5717303 DOI: 10.1038/s41598-017-17269-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/21/2017] [Indexed: 11/29/2022] Open
Abstract
QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98.76% of the crucian carp genome. 35 chromosome-wide QTL affecting feed conversion efficiency (FCE, 8 QTL), relative growth rate (RGR, 9 QTL), average daily gain (ADG, 13 QTL) and average daily feed intake (ADFI, 5 QTL) were detected on 14 LGs, explaining 14.0–20.9% of the phenotypic variations. In LGs of LG16, LG25, LG36 and LG49, several QTL affecting different traits clustered together at the identical or close regions of the same linkage group. Seven candidate genes, whose biological functions may involve in the energy metabolism, digestion, biosynthesis and signal transduction, were identified from these QTL intervals by comparative genomics analysis. These results provide a basis for elucidating genetic mechanism of feed efficiency and potential marker-assisted selection in crucian carp.
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Affiliation(s)
- Meixia Pang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Beide Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiaomu Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Haiyang Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xinhua Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhan Yin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shouqi Xie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Jingou Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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32
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Viana JMS, Mundim GB, Pereira HD, Andrade ACB, e Silva FF. Efficiency of genome-wide association studies in random cross populations. MOLECULAR BREEDING 2017; 37:102. [PMID: 0 DOI: 10.1007/s11032-017-0703-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle. BMC Genomics 2017; 18:386. [PMID: 28521758 PMCID: PMC5437562 DOI: 10.1186/s12864-017-3754-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
Background Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations. Results Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE ≥ 1.0%) and a nominal P-value threshold (P ≤ 5e-05). Lead SNPs with PVE ≥ 2.0% were considered putative evidence of large-effect QTL (n = 52), whereas those with PVE ≥ 1.0% but < 2.0% were considered putative evidence for moderate-effect QTL (n = 35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained). Conclusions Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs ≤ 3Mb) to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3754-y) contains supplementary material, which is available to authorized users.
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34
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Gondret F, Vincent A, Houée-Bigot M, Siegel A, Lagarrigue S, Causeur D, Gilbert H, Louveau I. A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs. BMC Genomics 2017; 18:244. [PMID: 28327084 PMCID: PMC5361837 DOI: 10.1186/s12864-017-3639-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/17/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). RESULTS Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines. CONCLUSIONS Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.
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Affiliation(s)
| | - Annie Vincent
- Pegase, Agrocampus Ouest, INRA, 35590, Saint-Gilles, France
| | - Magalie Houée-Bigot
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, 35000, Rennes, France
| | - Anne Siegel
- IRISA, CNRS, Université Rennes-1, INRIA, 35042, Rennes cedex, France
| | | | - David Causeur
- Laboratoire de Mathématiques Appliquées, IRMAR, Agrocampus Ouest, 35000, Rennes, France
| | - Hélène Gilbert
- GenPhySE, INRA, ENVT, Université de Toulouse, 31326, Castanet-Tolosan cedex, France
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Brito LF, Kijas JW, Ventura RV, Sargolzaei M, Porto-Neto LR, Cánovas A, Feng Z, Jafarikia M, Schenkel FS. Genetic diversity and signatures of selection in various goat breeds revealed by genome-wide SNP markers. BMC Genomics 2017; 18:229. [PMID: 28288562 PMCID: PMC5348779 DOI: 10.1186/s12864-017-3610-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/07/2017] [Indexed: 01/08/2023] Open
Abstract
Background The detection of signatures of selection has the potential to elucidate the identities of genes and mutations associated with phenotypic traits important for livestock species. It is also very relevant to investigate the levels of genetic diversity of a population, as genetic diversity represents the raw material essential for breeding and has practical implications for implementation of genomic selection. A total of 1151 animals from nine goat populations selected for different breeding goals and genotyped with the Illumina Goat 50K single nucleotide polymorphisms (SNP) Beadchip were included in this investigation. Results The proportion of polymorphic SNPs ranged from 0.902 (Nubian) to 0.995 (Rangeland). The overall mean HO and HE was 0.374 ± 0.021 and 0.369 ± 0.023, respectively. The average pairwise genetic distance (D) ranged from 0.263 (Toggenburg) to 0.323 (Rangeland). The overall average for the inbreeding measures FEH, FVR, FLEUT, FROH and FPED was 0.129, −0.012, −0.010, 0.038 and 0.030, respectively. Several regions located on 19 chromosomes were potentially under selection in at least one of the goat breeds. The genomic population tree constructed using all SNPs differentiated breeds based on selection purpose, while genomic population tree built using only SNPs in the most significant region showed a great differentiation between LaMancha and the other breeds. We hypothesized that this region is related to ear morphogenesis. Furthermore, we identified genes potentially related to reproduction traits, adult body mass, efficiency of food conversion, abdominal fat deposition, conformation traits, liver fat metabolism, milk fatty acids, somatic cells score, milk protein, thermo-tolerance and ear morphogenesis. Conclusions In general, moderate to high levels of genetic variability were observed for all the breeds and a characterization of runs of homozygosity gave insights into the breeds’ development history. The information reported here will be useful for the implementation of genomic selection and other genomic studies in goats. We also identified various genome regions under positive selection using smoothed FST and hapFLK statistics and suggested genes, which are potentially under selection. These results can now provide a foundation to formulate biological hypotheses related to selection processes in goats. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3610-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luiz F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.
| | - James W Kijas
- CSIRO Agriculture & Food, Brisbane, Queensland, Australia
| | - Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Beef Improvement Opportunities, Guelph, Ontario, Canada
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,The Semex Alliance, Guelph, Ontario, Canada
| | | | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Zeny Feng
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada.,Canadian Centre for Swine Improvement Inc., Ottawa, Ontario, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
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Tizioto PC, Coutinho LL, Oliveira PSN, Cesar ASM, Diniz WJS, Lima AO, Rocha MI, Decker JE, Schnabel RD, Mourão GB, Tullio RR, Zerlotini A, Taylor JF, Regitano LCA. Gene expression differences in Longissimus muscle of Nelore steers genetically divergent for residual feed intake. Sci Rep 2016; 6:39493. [PMID: 28004777 PMCID: PMC5177880 DOI: 10.1038/srep39493] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/24/2016] [Indexed: 12/18/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes.
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Affiliation(s)
- Polyana C Tizioto
- Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Andressa O Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marina I Rocha
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA.,Informatics Institute, University of Missouri, Columbia, Missouri, 65211, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | | | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri Columbia, Columbia, MO, USA
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37
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Sahoo SS, Mishra C, Rout M, Nayak G, Mohanty ST, Panigrahy KK. Comparative in silico and protein-protein interaction network analysis of ATP1A1 gene. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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38
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Andreassen R, Rangnes F, Sivertsen M, Chiang M, Tran M, Worren MM. Discovery of miRNAs and Their Corresponding miRNA Genes in Atlantic Cod (Gadus morhua): Use of Stable miRNAs as Reference Genes Reveals Subgroups of miRNAs That Are Highly Expressed in Particular Organs. PLoS One 2016; 11:e0153324. [PMID: 27128807 PMCID: PMC4851352 DOI: 10.1371/journal.pone.0153324] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background Atlantic cod (Gadus morhua) is among the economically most important species in the northern Atlantic Ocean and a model species for studying development of the immune system in vertebrates. MicroRNAs (miRNAs) are an abundant class of small RNA molecules that regulate fundamental biological processes at the post-transcriptional level. Detailed knowledge about a species miRNA repertoire is necessary to study how the miRNA transcriptome modulate gene expression. We have therefore discovered and characterized mature miRNAs and their corresponding miRNA genes in Atlantic cod. We have also performed a validation study to identify suitable reference genes for RT-qPCR analysis of miRNA expression in Atlantic cod. Finally, we utilized the newly characterized miRNA repertoire and the dedicated RT-qPCR method to reveal miRNAs that are highly expressed in certain organs. Results The discovery analysis revealed 490 mature miRNAs (401 unique sequences) along with precursor sequences and genomic location of the miRNA genes. Twenty six of these were novel miRNA genes. Validation studies ranked gmo-miR-17-1—5p or the two-gene combination gmo-miR25-3p and gmo-miR210-5p as most suitable qPCR reference genes. Analysis by RT-qPCR revealed 45 miRNAs with significantly higher expression in tissues from one or a few organs. Comparisons to other vertebrates indicate that some of these miRNAs may regulate processes like growth, lipid metabolism, immune response to microbial infections and scar damage repair. Three teleost-specific and three novel Atlantic cod miRNAs were among the differentially expressed miRNAs. Conclusions The number of known mature miRNAs was considerably increased by our identification of miRNAs and miRNA genes in Atlantic cod. This will benefit further functional studies of miRNA expression using deep sequencing methods. The validation study showed that stable miRNAs are suitable reference genes for RT-qPCR analysis of miRNA expression. Applying RT-qPCR we have identified several miRNAs likely to have important regulatory functions in particular organs.
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Affiliation(s)
- Rune Andreassen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
- * E-mail:
| | - Fredrik Rangnes
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Maria Sivertsen
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Chiang
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Michelle Tran
- Department of Pharmacy and Biomedical Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Oslo, Norway
| | - Merete Molton Worren
- Bioinformatics Core Facility, Institute for Medical Informatics, Oslo University Hospital, Oslo, Norway
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39
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de Almeida Santana MH, Junior GAO, Cesar ASM, Freua MC, da Costa Gomes R, da Luz E Silva S, Leme PR, Fukumasu H, Carvalho ME, Ventura RV, Coutinho LL, Kadarmideen HN, Ferraz JBS. Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. J Appl Genet 2016; 57:495-504. [PMID: 27001052 DOI: 10.1007/s13353-016-0344-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/20/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
Abstract
The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.
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Affiliation(s)
- Miguel Henrique de Almeida Santana
- Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark.,Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | | | | | - Mateus Castelani Freua
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Rodrigo da Costa Gomes
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, BR 262 km 4, 79002-970, Campo Grande, Brazil
| | - Saulo da Luz E Silva
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Paulo Roberto Leme
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Minos Esperândio Carvalho
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.,University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Luiz Lehmann Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, 13418-900, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
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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.
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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
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Kashyap N, Kumar P, Deshmukh B, Bhat S, Kumar A, Chauhan A, Bhushan B, Singh G, Sharma D. Association of ATP1A1 gene polymorphism with thermotolerance in Tharparkar and Vrindavani cattle. Vet World 2015; 8:892-7. [PMID: 27047171 PMCID: PMC4774683 DOI: 10.14202/vetworld.2015.892-897] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/13/2015] [Accepted: 06/20/2015] [Indexed: 11/24/2022] Open
Abstract
Aim: One of the major biochemical aspects of thermoregulation is equilibrium of ion gradient across biological membranes. Na+/K+-ATPase, a member of P type-ATPase family, is a major contributor to the mechanism that actively controls cross-membrane ion gradient. Thus, we examined ATP1A1 gene that encodes alpha-1 chain of Na+/K+-ATPase, for genetic polymorphisms. Materials and Methods: A total of 100 Vrindavani (composite cross strain of Hariana x Holstein-Friesian/Brown Swiss/Jersey) and 64 Tharparkar (indigenous) cattle were screened for genetic polymorphism in ATP1A1 gene, using polymerase chain reaction single-strand conformation polymorphism and DNA sequencing. For association studies, rectal temperature (RT) and respiration rate (RR) of all animals were recorded twice daily for 3 seasons. Results: A SNP (C2789A) was identified in exon 17 of ATP1A1 gene. Three genotypes namely CC, CA, and AA were observed in both, Vrindavani and Tharparkar cattle. The gene frequencies in Tharparkar and Vrindavani for allele A were 0.51 and 0.48, and for allele C were 0.49 and 0.52, respectively, which remained at intermediate range. Association study of genotypes with RT and RR in both cattle population revealed that the animals with genotype CC exhibited significantly lower RT and higher heat tolerance coefficient than CA and AA genotypes. Conclusion: Differential thermoregulation between different genotypes of ATP1A1 gene indicate that the ATP1A1 gene could be potentially contributing to thermotolerance in both, Tharparkar, an indigenous breed and Vrindavani, a composite crossbred cattle.
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Affiliation(s)
- Neeraj Kashyap
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Pushpendra Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Bharti Deshmukh
- Department of Animal Genetics and Breeding, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Sandip Bhat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Anuj Chauhan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Gyanendra Singh
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
| | - Deepak Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, India
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Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs. Sci Rep 2015; 5:11953. [PMID: 26150313 PMCID: PMC4493709 DOI: 10.1038/srep11953] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 06/10/2015] [Indexed: 11/08/2022] Open
Abstract
Feed efficiency (FE) can be measured by feed conversion ratio (FCR) or residual feed intake (RFI). In this study, we measured the FE related phenotypes of 236 castrated purebred Yorkshire boars, and selected 10 extreme individuals with high and low RFI for transcriptome analysis. We used RNA-seq analyses to determine the differential expression of genes and miRNAs in skeletal muscle. There were 99 differentially expressed genes identified (q ≤ 0.05). The down-regulated genes were mainly involved in mitochondrial energy metabolism, including FABP3, RCAN, PPARGC1 (PGC-1A), HK2 and PRKAG2. The up-regulated genes were mainly involved in skeletal muscle differentiation and proliferation, including IGF2, PDE7A, CEBPD, PIK3R1 and MYH6. Moreover, 15 differentially expressed miRNAs (|log2FC| ≥ 1, total reads count ≥ 20, p ≤ 0.05) were identified. Among them, miR-136, miR-30e-5p, miR-1, miR-208b, miR-199a, miR-101 and miR-29c were up-regulated, while miR-215, miR-365-5p, miR-486, miR-1271, miR-145, miR-99b, miR-191 and miR-10b were down-regulated in low RFI pigs. We conclude that decreasing mitochondrial energy metabolism, possibly through AMPK - PGC-1A pathways, and increasing muscle growth, through IGF-1/2 and TGF-β signaling pathways, are potential strategies for the improvement of FE in pigs (and possibly other livestock). This study provides new insights into the molecular mechanisms that determine RFI and FE in pigs.
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Zhao F, McParland S, Kearney F, Du L, Berry DP. Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genet Sel Evol 2015; 47:49. [PMID: 26089079 PMCID: PMC4472243 DOI: 10.1186/s12711-015-0127-3] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/19/2015] [Indexed: 01/05/2023] Open
Abstract
Background Artificial selection for economically important traits in cattle is expected to have left distinctive selection signatures on the genome. Access to high-density genotypes facilitates the accurate identification of genomic regions that have undergone positive selection. These findings help to better elucidate the mechanisms of selection and to identify candidate genes of interest to breeding programs. Results Information on 705 243 autosomal single nucleotide polymorphisms (SNPs) in 3122 dairy and beef male animals from seven cattle breeds (Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental) were used to detect selection signatures by applying two complementary methods, integrated haplotype score (iHS) and global fixation index (FST). To control for false positive results, we used false discovery rate (FDR) adjustment to calculate adjusted iHS within each breed and the genome-wide significance level was about 0.003. Using the iHS method, 83, 92, 91, 101, 85, 101 and 86 significant genomic regions were detected for Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental cattle, respectively. None of these regions was common to all seven breeds. Using the FST approach, 704 individual SNPs were detected across breeds. Annotation of the regions of the genome that showed selection signatures revealed several interesting candidate genes i.e. DGAT1, ABCG2, MSTN, CAPN3, FABP3, CHCHD7, PLAG1, JAZF1, PRKG2, ACTC1, TBC1D1, GHR, BMP2, TSG1, LYN, KIT and MC1R that play a role in milk production, reproduction, body size, muscle formation or coat color. Fifty-seven common candidate genes were found by both the iHS and global FST methods across the seven breeds. Moreover, many novel genomic regions and genes were detected within the regions that showed selection signatures; for some candidate genes, signatures of positive selection exist in the human genome. Multilevel bioinformatic analyses of the detected candidate genes suggested that the PPAR pathway may have been subjected to positive selection. Conclusions This study provides a high-resolution bovine genomic map of positive selection signatures that are either specific to one breed or common to a subset of the seven breeds analyzed. Our results will contribute to the detection of functional candidate genes that have undergone positive selection in future studies. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0127-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fuping Zhao
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Sinead McParland
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorpark, Co., Cork, Ireland.
| | - Francis Kearney
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co., Cork, Ireland.
| | - Lixin Du
- National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorpark, Co., Cork, Ireland.
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Widmann P, Reverter A, Weikard R, Suhre K, Hammon HM, Albrecht E, Kuehn C. Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG) and cellular maintenance processes as major contributors to genetic variability in bovine feed efficiency. PLoS One 2015; 10:e0124574. [PMID: 25875852 PMCID: PMC4398489 DOI: 10.1371/journal.pone.0124574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 03/11/2015] [Indexed: 12/24/2022] Open
Abstract
Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53) and Transforming Growth Factor beta 1 (TGFB1) genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG) I442M (rs109570900) and the Growth /differentiation factor 8 (GDF8) Q204X (rs110344317) loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily energy intake as observed in our study.
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Affiliation(s)
- Philipp Widmann
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
| | | | - Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
| | - Karsten Suhre
- Weill Cornell Medical College in Qatar, Doha, State of Qatar
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Harald M. Hammon
- Leibniz Institute for Farm Animal Biology, Institute for Nutritional Physiology “Oskar Kellner”, Dummerstorf, Germany
| | - Elke Albrecht
- Leibniz Institute for Farm Animal Biology, Institute for Muscle Biology and Growth, Dummerstorf, Germany
| | - Christa Kuehn
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Genome Physiology Unit, Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
- * E-mail:
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Bolormaa S, Pryce JE, Zhang Y, Reverter A, Barendse W, Hayes BJ, Goddard ME. Non-additive genetic variation in growth, carcass and fertility traits of beef cattle. Genet Sel Evol 2015; 47:26. [PMID: 25880217 PMCID: PMC4382858 DOI: 10.1186/s12711-015-0114-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 03/20/2015] [Indexed: 12/25/2022] Open
Abstract
Background A better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of individuals. Genome-wide panels of single nucleotide polymorphisms (SNPs) have been mainly used to map additive effects for quantitative traits, but they can also be used to investigate non-additive effects. We estimated dominance and epistatic effects of SNPs on various traits in beef cattle and the variance explained by dominance, and quantified the increase in accuracy of phenotype prediction by including dominance deviations in its estimation. Methods Genotype data (729 068 real or imputed SNPs) and phenotypes on up to 16 traits of 10 191 individuals from Bos taurus, Bos indicus and composite breeds were used. A genome-wide association study was performed by fitting the additive and dominance effects of single SNPs. The dominance variance was estimated by fitting a dominance relationship matrix constructed from the 729 068 SNPs. The accuracy of predicted phenotypic values was evaluated by best linear unbiased prediction using the additive and dominance relationship matrices. Epistatic interactions (additive × additive) were tested between each of the 28 SNPs that are known to have additive effects on multiple traits, and each of the other remaining 729 067 SNPs. Results The number of significant dominance effects was greater than expected by chance and most of them were in the direction that is presumed to increase fitness and in the opposite direction to inbreeding depression. Estimates of dominance variance explained by SNPs varied widely between traits, but had large standard errors. The median dominance variance across the 16 traits was equal to 5% of the phenotypic variance. Including a dominance deviation in the prediction did not significantly increase its accuracy for any of the phenotypes. The number of additive × additive epistatic effects that were statistically significant was greater than expected by chance. Conclusions Significant dominance and epistatic effects occur for growth, carcass and fertility traits in beef cattle but they are difficult to estimate precisely and including them in phenotype prediction does not increase its accuracy.
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Affiliation(s)
- Sunduimijid Bolormaa
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.
| | - Jennie E Pryce
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.
| | - Yuandan Zhang
- Animal Genetics and Breeding Unit, UNE, Armidale, NSW, 2351, Australia.
| | - Antonio Reverter
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, QLD, 4067, Australia.
| | - William Barendse
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, QLD, 4067, Australia.
| | - Ben J Hayes
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia.
| | - Michael E Goddard
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia. .,School of Land and Environment, University of Melbourne, Parkville, VIC, 3010, Australia.
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Luo C, Sun L, Ma J, Wang J, Qu H, Shu D. Association of single nucleotide polymorphisms in the microRNA miR-1596 locus with residual feed intake in chickens. Anim Genet 2015; 46:265-71. [PMID: 25818998 DOI: 10.1111/age.12284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2015] [Indexed: 02/04/2023]
Abstract
MicroRNAs are an abundant class of small non-coding RNAs that regulate gene expression. Genetic variations in microRNA sequences may be associated with phenotype differences by influencing the expression of microRNAs and/or their targets. This study identified two single nucleotide polymorphisms (SNPs) in the genomic region of the microRNA miR-1596 locus of chicken. Of the two SNPs, one was 95 bp upstream of miR-1596 (g.5678784A>T) and the other was in the middle of the sequence producing the mature microRNA gga-miR-1596-3p (g.5678944A>G). Genotypic distribution of the two SNPs had large differences among 12 chicken breeds (lines), especially between the fast-growing commercial lines and the slow-growing Chinese indigenous breeds for the g.5678784A>T SNP. Only the g.5678784A>T SNP was significantly associated with residual feed intake (RFI) in the F2 population derived from a fast-growing and a slow-growing broiler as well as in the pure Huiyang bearded chicken. The birds with the AA genotype of the g.5678784A>T SNP had lower RFI and higher expression of the mature gga-miR-1596-3p microRNA of miR-1596 than did those with the other genotypes of the same SNP. We also found that the expression of the mature gga-miR-1596-3p microRNA of miR-1596 was significantly associated with RFI. These findings suggest that miR-1596 can become a candidate gene related to RFI, and its genetic variation may contribute to changes in RFI by altering expression levels of the mature gga-miR-1596-3p microRNA in chicken.
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Affiliation(s)
- C Luo
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China; State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, 510640, China
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Samayoa LF, Malvar RA, Olukolu BA, Holland JB, Butrón A. Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel. BMC PLANT BIOLOGY 2015; 15:35. [PMID: 25652257 PMCID: PMC4340109 DOI: 10.1186/s12870-014-0403-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/22/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs. RESULTS Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r(2) < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations. CONCLUSIONS Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.
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Affiliation(s)
- Luis Fernando Samayoa
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
| | - Rosa Ana Malvar
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
| | - Bode A Olukolu
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, 27695, USA.
| | - James B Holland
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, 27695, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Plant Science Research Unit, Raleigh, North Carolina, 27695, USA.
| | - Ana Butrón
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.
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Invited review: Improving feed efficiency in dairy production: challenges and possibilities. Animal 2015; 9:395-408. [DOI: 10.1017/s1751731114002997] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Porto-Neto LR, Reverter A, Prayaga KC, Chan EKF, Johnston DJ, Hawken RJ, Fordyce G, Garcia JF, Sonstegard TS, Bolormaa S, Goddard ME, Burrow HM, Henshall JM, Lehnert SA, Barendse W. The genetic architecture of climatic adaptation of tropical cattle. PLoS One 2014; 9:e113284. [PMID: 25419663 PMCID: PMC4242650 DOI: 10.1371/journal.pone.0113284] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
Adaptation of global food systems to climate change is essential to feed the world. Tropical cattle production, a mainstay of profitability for farmers in the developing world, is dominated by heat, lack of water, poor quality feedstuffs, parasites, and tropical diseases. In these systems European cattle suffer significant stock loss, and the cross breeding of taurine x indicine cattle is unpredictable due to the dilution of adaptation to heat and tropical diseases. We explored the genetic architecture of ten traits of tropical cattle production using genome wide association studies of 4,662 animals varying from 0% to 100% indicine. We show that nine of the ten have genetic architectures that include genes of major effect, and in one case, a single location that accounted for more than 71% of the genetic variation. One genetic region in particular had effects on parasite resistance, yearling weight, body condition score, coat colour and penile sheath score. This region, extending 20 Mb on BTA5, appeared to be under genetic selection possibly through maintenance of haplotypes by breeders. We found that the amount of genetic variation and the genetic correlations between traits did not depend upon the degree of indicine content in the animals. Climate change is expected to expand some conditions of the tropics to more temperate environments, which may impact negatively on global livestock health and production. Our results point to several important genes that have large effects on adaptation that could be introduced into more temperate cattle without detrimental effects on productivity.
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Affiliation(s)
- Laercio R. Porto-Neto
- CSIRO Food Futures Flagship, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Antonio Reverter
- CSIRO Food Futures Flagship, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | | | - Eva K. F. Chan
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia
| | - David J. Johnston
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW, Australia
| | - Rachel J. Hawken
- Cobb-Vantress Inc., Siloam Springs, Arizona, United States of America
| | - Geoffry Fordyce
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Jose Fernando Garcia
- Faculdade de Medicina Veterinaria de Araçatuba, (UNESP) Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - Tad S. Sonstegard
- United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
| | | | | | - Heather M. Burrow
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - John M. Henshall
- CSIRO Food Futures Flagship, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Sigrid A. Lehnert
- CSIRO Food Futures Flagship, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - William Barendse
- CSIRO Animal, Food and Health Science, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
- * E-mail:
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QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies. BMC Genomics 2014; 15:1004. [PMID: 25410110 PMCID: PMC4253998 DOI: 10.1186/1471-2164-15-1004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/31/2014] [Indexed: 11/21/2022] Open
Abstract
Background The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. Results A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value <0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. Conclusions This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.
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