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George L, Alex R, Gowane G, Vohra V, Joshi P, Kumar R, Verma A. Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes. Anim Biotechnol 2024; 35:2319622. [PMID: 38437001 DOI: 10.1080/10495398.2024.2319622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
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Affiliation(s)
- Linda George
- National Dairy Research Institute, Karnal, India
| | - Rani Alex
- National Dairy Research Institute, Karnal, India
| | - Gopal Gowane
- National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- National Dairy Research Institute, Karnal, India
| | - Pooja Joshi
- National Dairy Research Institute, Karnal, India
| | - Ravi Kumar
- National Dairy Research Institute, Karnal, India
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Igoshin AV, Romashov GA, Yurchenko AA, Yudin NS, Larkin DM. Scans for Signatures of Selection in Genomes of Wagyu and Buryat Cattle Breeds Reveal Candidate Genes and Genetic Variants for Adaptive Phenotypes and Production Traits. Animals (Basel) 2024; 14:2059. [PMID: 39061521 PMCID: PMC11274160 DOI: 10.3390/ani14142059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and FST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds.
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Affiliation(s)
- Alexander V. Igoshin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Grigorii A. Romashov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Andrey A. Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, 94800 Villejuif, France
| | - Nikolay S. Yudin
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia; (A.V.I.)
| | - Denis M. Larkin
- Royal Veterinary College, University of London, London NW1 0TU, UK
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Zhou X, Shen K, Cao S, Li P, Xiao J, Dong J, Cheng Q, Hu L, Xu Z, Yang L. Polymorphism rs2327430 in TCF21 predicts the risk and prognosis of gastric cancer by affecting the binding between TFAP2A and TCF21. Cancer Cell Int 2024; 24:159. [PMID: 38714991 PMCID: PMC11075239 DOI: 10.1186/s12935-024-03343-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Single nuclear polymorphisms (SNPs) have been published to be correlated with multiple diseases. Transcription Factor 21 (TCF21) is a critical transcription factor involved in various types of cancers. However, the association of TCF21 genetic polymorphisms with gastric cancer (GC) susceptibility and prognosis remains unclear. METHODS A case-control study comprising 890 patients diagnosed with GC and an equal number of cancer-free controls was conducted. After rigorous statistical analysis, molecular experiments were carried out to elucidate the functional significance of the SNPs in the context of GC. RESULTS TCF21 rs2327430 (OR = 0.78, P = 0.026) provides protection against GC, while rs4896011 (OR = 1.39, P = 0.005) exhibit significant associations with GC risk. Furthermore, patients with the (TC + CC) genotype of rs2327430 demonstrate a relatively favorable prognosis (OR = 0.47, P = 0.012). Mechanistically, chromatin immunoprecipitation assay and luciferase reporter assay revealed that the C allele of rs2327430 disrupts the binding of Transcription Factor AP-2 Alpha (TFAP2A) to the promoter region of TCF21, resulting in increased expression of TCF21 and inhibition of malignant behaviors in GC cells. CONCLUSION Our findings highlight the significant role of TCF21 SNPs in both the risk and prognosis of GC and provide valuable insights into the underlying molecular mechanisms. Specifically, the disruptive effect of rs2327430 on TCF21 expression and its ability to modulate malignant cell behaviors suggest that rs2327430 may serve as a potential predictive marker for GC risk and prognosis.
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Affiliation(s)
- Xinyi Zhou
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Kuan Shen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Shuqing Cao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Pengyu Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Jian Xiao
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Jiacheng Dong
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Quan Cheng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Li Hu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu, 210029, China.
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Zayas GA, Rodriguez EE, Hernandez AS, Rezende FM, Mateescu RG. Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation. J Appl Genet 2024; 65:383-394. [PMID: 38528244 DOI: 10.1007/s13353-024-00859-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits.
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Affiliation(s)
- Gabriel A Zayas
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA.
| | | | - Aakilah S Hernandez
- Department of Animal Science, North Carolina States University, Raleigh, NC, USA
| | - Fernanda M Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
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Rowan TN, Schnabel RD, Decker JE. Uncovering the architecture of selection in two Bos taurus cattle breeds. Evol Appl 2024; 17:e13666. [PMID: 38405336 PMCID: PMC10883790 DOI: 10.1111/eva.13666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/27/2024] Open
Abstract
Directional selection alters the genome via hard sweeps, soft sweeps, and polygenic selection. However, mapping polygenic selection is difficult because it does not leave clear signatures on the genome like a selective sweep. In populations with temporally stratified genotypes, the Generation Proxy Selection Mapping (GPSM) method identifies variants associated with generation number (or appropriate proxy) and thus variants undergoing directional allele frequency changes. Here, we use GPSM on two large datasets of beef cattle to detect associations between an animal's generation and 11 million imputed SNPs. Using these datasets with high power and dense mapping resolution, GPSM detected a total of 294 unique loci actively under selection in two cattle breeds. We observed that GPSM has a high power to detect selection in the very recent past (<10 years), even when allele frequency changes are small. Variants identified by GPSM reside in genomic regions associated with known breed-specific selection objectives, such as fertility and maternal ability in Red Angus, and carcass merit and coat color in Simmental. Over 60% of the selected loci reside in or near (<50 kb) annotated genes. Using haplotype-based and composite selective sweep statistics, we identify hundreds of putative selective sweeps that likely occurred earlier in the evolution of these breeds; however, these sweeps have little overlap with recent polygenic selection. This makes GPSM a complementary approach to sweep detection methods when temporal genotype data are available. The selected loci that we identify across methods demonstrate the complex architecture of selection in domesticated cattle.
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Affiliation(s)
- Troy N. Rowan
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Department of Animal ScienceUniversity of Tennessee Institute of AgricultureKnoxvilleTennesseeUSA
- Department of Large Animal Clinical Sciences, College of Veterinary MedicineUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Robert D. Schnabel
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Institute for Data Science and InformaticsUniversity of MissouriColumbiaMissouriUSA
| | - Jared E. Decker
- Division of Animal SciencesUniversity of MissouriColumbiaMissouriUSA
- Genetics Area ProgramUniversity of MissouriColumbiaMissouriUSA
- Institute for Data Science and InformaticsUniversity of MissouriColumbiaMissouriUSA
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Sanchez MP, Tribout T, Kadri NK, Chitneedi PK, Maak S, Hozé C, Boussaha M, Croiseau P, Philippe R, Spengeler M, Kühn C, Wang Y, Li C, Plastow G, Pausch H, Boichard D. Sequence-based GWAS meta-analyses for beef production traits. Genet Sel Evol 2023; 55:70. [PMID: 37828440 PMCID: PMC10568825 DOI: 10.1186/s12711-023-00848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. As part of the H2020 BovReg project, we performed sequence-level MA for beef production traits. Five partners from France, Switzerland, Germany, and Canada contributed summary statistics from sequence-based GWAS conducted with 54,782 animals from 15 purebred or crossbred populations. We combined the summary statistics for four growth, nine morphology, and 15 carcass traits into 16 MA, using both fixed effects and z-score methods. RESULTS The fixed-effects method was generally more informative to provide indication on potentially causal variants, although we combined substantially different traits in each MA. In comparison with within-population GWAS, this approach highlighted (i) a larger number of quantitative trait loci (QTL), (ii) QTL more frequently located in genomic regions known for their effects on growth and meat/carcass traits, (iii) a smaller number of genomic variants within the QTL, and (iv) candidate variants that were more frequently located in genes. MA pinpointed variants in genes, including MSTN, LCORL, and PLAG1 that have been previously associated with morphology and carcass traits. We also identified dozens of other variants located in genes associated with growth and carcass traits, or with a function that may be related to meat production (e.g., HS6ST1, HERC2, WDR75, COL3A1, SLIT2, MED28, and ANKAR). Some of these variants overlapped with expression or splicing QTL reported in the cattle Genotype-Tissue Expression atlas (CattleGTEx) and could therefore regulate gene expression. CONCLUSIONS By identifying candidate genes and potential causal variants associated with beef production traits in cattle, MA demonstrates great potential for investigating the biological mechanisms underlying these traits. As a complement to within-population GWAS, this approach can provide deeper insights into the genetic architecture of complex traits in beef cattle.
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Affiliation(s)
- Marie-Pierre Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Thierry Tribout
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Praveen K Chitneedi
- Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Steffen Maak
- Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
| | - Chris Hozé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- Eliance, 75595, Paris, France
| | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Pascal Croiseau
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Romain Philippe
- INRAE, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | | | - Christa Kühn
- Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany
- Agricultural and Environmental faculty, University Rostock, 18059, Rostock, Germany
- Friedrich-Loeffler-Institut (FLI), 17493, Greifswald, Insel Riems, Germany
| | - Yining Wang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, T4L 1W1, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, T4L 1W1, Canada
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, AB, T6G 2HI, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, AB, T6G 2HI, Canada
| | - Hubert Pausch
- Animal Genomics, ETH Zurich, 8092, Zurich, Switzerland
| | - Didier Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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Yang C, Huang Z, Pan C, Wang S. Characterization of feed efficiency-related key signatures molecular in different cattle breeds. PLoS One 2023; 18:e0289939. [PMID: 37756351 PMCID: PMC10529570 DOI: 10.1371/journal.pone.0289939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/30/2023] [Indexed: 09/29/2023] Open
Abstract
Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.
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Affiliation(s)
- Chaoyun Yang
- College of Animal Science, Xichang University, Xichang City, Sichuan Province, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Zengwen Huang
- College of Animal Science, Xichang University, Xichang City, Sichuan Province, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
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Cai W, Zhang Y, Chang T, Wang Z, Zhu B, Chen Y, Gao X, Xu L, Zhang L, Gao H, Song J, Li J. The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle. J Anim Sci Biotechnol 2023; 14:78. [PMID: 37165455 PMCID: PMC10173583 DOI: 10.1186/s40104-023-00876-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/05/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit in beef cattle. To prioritize the putative variants and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle. Then, we applied expression quantitative trait loci (eQTL) mapping between the genotype variants and transcriptome of three tissues (longissimus dorsi muscle, backfat, and liver) in 120 cattle. RESULTS We identified 1,580 association signals for 21 beef agronomic traits using GWAS. We then illuminated 854,498 cis-eQTLs for 6,017 genes and 46,970 trans-eQTLs for 1,903 genes in three tissues and built a synergistic network by integrating transcriptomics with agronomic traits. These cis-eQTLs were preferentially close to the transcription start site and enriched in functional regulatory regions. We observed an average of 43.5% improvement in cis-eQTL discovery using multi-tissue eQTL mapping. Fine-mapping analysis revealed that 111, 192, and 194 variants were most likely to be causative to regulate gene expression in backfat, liver, and muscle, respectively. The transcriptome-wide association studies identified 722 genes significantly associated with 11 agronomic traits. Via the colocalization and Mendelian randomization analyses, we found that eQTLs of several genes were associated with the GWAS signals of agronomic traits in three tissues, which included genes, such as NADSYN1, NDUFS3, LTF and KIFC2 in liver, GRAMD1C, TMTC2 and ZNF613 in backfat, as well as TIGAR, NDUFS3 and L3HYPDH in muscle that could serve as the candidate genes for economic traits. CONCLUSIONS The extensive atlas of GWAS, eQTL, fine-mapping, and transcriptome-wide association studies aid in the suggestion of potentially functional variants and genes in cattle agronomic traits and will be an invaluable source for genomics and breeding in beef cattle.
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Affiliation(s)
- Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yapeng Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, 20742, USA.
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Shen K, Zhou X, Hu L, Xiao J, Cheng Q, Wang Y, Liu K, Fan H, Xu Z, Yang L. Rs15285, a functional polymorphism located in lipoprotein lipase, predicts the risk and prognosis of gastric cancer. Appl Microbiol Biotechnol 2023; 107:3243-3256. [PMID: 37036527 DOI: 10.1007/s00253-023-12505-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/23/2023] [Accepted: 03/28/2023] [Indexed: 04/11/2023]
Abstract
Lipoprotein lipase (LPL), a crucial gene in lipid metabolism, has a significant role in the progression of malignant tumors. The purpose of this research was to investigate the impact of rs15285 found in the LPL gene's 3'UTR region on the risk, biological behavior, and gastric cancer (GC) prognosis as well as to examine its potential function. Genotyping of rs15285 in 888 GC cases and 874 controls was conducted by SNaPshot technology. We used bioinformatics analysis and in vitro experiments to study the role of rs15285. First, this study revealed for the first time that polymorphism rs15285 increases the risk of GC (OR = 1.48, 95%CI = 1.16-1.89, P = 0.002). Although no relationship was found between rs12585 and the pathological features of GC, the prognosis of individuals with the rs12585 TT genotype was poorer than that of patients with the CC or CC+CT genotype (HR = 2.39 for TT vs. CC, P = 0.025; HR = 2.38 for TT vs. CC+CT, P = 0.025). In addition, bioinformatics analysis showed rs12585 may affect the binding of miRNAs to LPL, resulting in an increase of LPL expression to promote cancer progression. Ultimately, in vitro tests revealed that the rs15285 T allele increased LPL expression on the mRNA as well as the protein levels, promoting GC cell proliferation, invasion, and metastasis. The LPL rs12528 TT genotype increased the risk of GC and predicted a poor prognosis. Mechanistically, the rs15285 T allele could improve the expression of LPL, and thus promotes the malignant phenotype of GC. Therefore, our study may provide new biological predictors and a theoretical basis for the prognosis and customized therapy of stomach cancer patients. KEY POINTS: • Rs15285 polymorphism is a risk factor for GC. • Rs12585 TT genotype predicts a bad outcome in GC individuals. • Rs15285 T allele enhances GC cells malignant biological behavior.
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Affiliation(s)
- Kuan Shen
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Xinyi Zhou
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Li Hu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Jian Xiao
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Quan Cheng
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Yuanhang Wang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Kanghui Liu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Hao Fan
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Zekuan Xu
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Li Yang
- Department of General Surgery, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China.
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Heidaritabar M, Bink MCAM, Dervishi E, Charagu P, Huisman A, Plastow GS. Genome-wide association studies for additive and dominance effects for body composition traits in commercial crossbred Piétrain pigs. J Anim Breed Genet 2023. [PMID: 36883263 DOI: 10.1111/jbg.12768] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/18/2023] [Indexed: 03/09/2023]
Abstract
Fat depth (FD) and muscle depth (MD) are economically important traits and used to estimate carcass lean content (LMP), which is one of the main breeding objectives in pig breeding programmes. We assessed the genetic architectures of body composition traits for additive and dominance effects in commercial crossbred Piétrain pigs using both 50 K array and sequence genotypes. We first performed a genome-wide association study (GWAS) using single-marker association analysis with a false discovery rate of 0.1. Then, we estimated the additive and dominance effects of the most significant variant in the quantitative trait loci (QTL) regions. It was investigated whether the use of whole-genome sequence (WGS) will improve the QTL detection (both additive and dominance) with a higher power compared with lower density SNP arrays. Our results showed that more QTL regions were detected by WGS compared with 50 K array (n = 54 vs. n = 17). Of the novel associated regions associated with FD and LMP and detected by WGS, the most pronounced peak was on SSC13, situated at ~116-118, 121-127 and 129-134 Mbp. Additionally, we found that only additive effects contributed to the genetic architecture of the analysed traits and no significant dominance effects were found for the tested SNPs at QTL regions, regardless of panel density. The associated SNPs are located in or near several relevant candidate genes. Of these genes, GABRR2, GALR1, RNGTT, CDH20 and MC4R have been previously reported as being associated with fat deposition traits. However, the genes on SSC1 (ZNF292, ORC3, CNR1, SRSF12, MDN1, TSHZ1, RELCH and RNF152) and SSC18 (TTC26 and KIAA1549) have not been reported previously to our best knowledge. Our current findings provide insights into the genomic regions influencing composition traits in Piétrain pigs.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Marco C A M Bink
- Hendrix Genetics Research, Technology & Services B.V., Boxmeer, the Netherlands
| | - Elda Dervishi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick Charagu
- Hendrix Genetics, Swine Business Unit, Regina, Saskatchewan, Canada
| | - Abe Huisman
- Hendrix Genetics Research, Technology & Services B.V., Boxmeer, the Netherlands
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
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11
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Lin C, Wang W, Zhang D, Huang K, Li X, Zhang Y, Zhao Y, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhao L, Ma Z, Yang X, Huang Y, Cui P, Liu J, Zeng X, Zhai R, Sun L, Weng X, Wu W, Zhang X, Zheng W. Polymorphisms in SHISA3 and RFC3 genes and their association with feed conversion ratio in Hu sheep. Front Vet Sci 2023; 9:1010045. [PMID: 36686193 PMCID: PMC9850526 DOI: 10.3389/fvets.2022.1010045] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023] Open
Abstract
In animal husbandry, feed efficiency is a crucial economic trait. In this study, the general linear model was used to perform association analysis for various genotypes and feed conversion ratio (FCR)-related traits. Reverse transcription-quantitative PCR (RT-qPCR) was used to detect the expression of SHISA3 and RFC3 mRNA levels in 10 tissues from 6 sheep. The results showed that SNPs in the NC_040257.1:c.625 T > C and NC_040261.1:g.9905 T > C were analyzed whether they were associated to feed efficiency parameters in Hu sheep (body weight, feed intake, average daily growth, and feed conversion ratio). NC_040257.1:c.625 T > C was shown to be significantly associated with body weight at 80, 100, and 120 days as well as feed conversion ratio (P < 0.05), whereas NC_040261.1:g.9905 T > C was found to be significantly associated with average daily weight gain from 80-140 days (ADG80-140) and FCR (P < 0.05). In Hu sheep, the CC genotypes of SHISA3 and RFC3 were the most common genotypes related to feed efficiency traits. Furthermore, the feed conversion ratio of the combined genotypes TT SHISA3-CC RFC3, TT SHISA3-CT RFC3, TT SHISA3-TT RFC3, CT SHISA3-CC RFC3 and CT SHISA3-CT RFC3 was significantly better than the FCR of CC SHISA3-TT RFC3. RT-qPCR results showed that the expression levels of SHISA3 were lower in the lung than in spleen, kidney, muscle and lymph (P < 0.05), and RFC3 was the lung had a highly significant higher expression level than the heart, liver, spleen, and muscle (P < 0.01). In conclusion, SHISA3 and RFC3 polymorphisms can be used as genetic markers for improving feed conversion efficiency in Hu sheep.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Landi Sun
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuxiu Weng
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Weiwei Wu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China,*Correspondence: Xiaoxue Zhang ✉
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China,Wenxin Zheng ✉
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12
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Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [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: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
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Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
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13
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Russell CA, Kuehn LA, Snelling WM, Kachman SD, Spangler ML. Variance component estimates for growth traits in beef cattle using selected variants from imputed low-pass sequence data. J Anim Sci 2023; 101:skad274. [PMID: 37585275 PMCID: PMC10464510 DOI: 10.1093/jas/skad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023] Open
Abstract
A beef cattle population (n = 2,343) was used to assess the impact of variants identified from the imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post-weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (low, modifier, moderate, high) based on predicted functional impact and re-partitioned based on the consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models. Multiple analyses were conducted to compare the proportion of additive genetic variation explained by the different subsets individually and collectively, and these estimates were benchmarked against all LPS variants in a single GRM and array (e.g., GeneSeek Genomic Profiler 100K) genotypes. When all variants were included in a single GRM, heritability estimates for BWT and PWG were 0.43 ± 0.05 and 0.38 ± 0.05, respectively. Heritability estimates for BWT ranged from 0.10 to 0.42 dependent on which variant subsets were included. Similarly, estimates for PWG ranged from 0.05 to 0.38. Results showed that variants in the subsets modifier and G1 (untranslated region) yielded the highest heritability estimates and were similar to the inclusion of all variants, while estimates from GRM containing only variants in the categories High, G4 (non-coding transcript exon), and G6 (start and stop loss/gain) were the lowest. All variants combined provided similar heritability estimates to chip genotypes and provided minimal to no additional information when combined with chip data. This suggests that the chip single nucleotide polymorphisms and the variants from LPS predicted to be less consequential are in relatively high linkage disequilibrium with the underlying causal variants as a whole and sufficiently spread throughout the genome to capture larger proportions of additive genetic variation.
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Affiliation(s)
- Chad A Russell
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583, USA
| | - Larry A Kuehn
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Warren M Snelling
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Stephen D Kachman
- Department of Statistics, University of Nebraska, Lincoln, NE 68583, USA
| | - Matthew L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583, USA
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14
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Yang C, Ding Y, Dan X, Shi Y, Kang X. Multi-transcriptomics reveals RLMF axis-mediated signaling molecules associated with bovine feed efficiency. Front Vet Sci 2023; 10:1090517. [PMID: 37035824 PMCID: PMC10073569 DOI: 10.3389/fvets.2023.1090517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
The regulatory axis plays a vital role in interpreting the information exchange and interactions among mammal organs. In this study on feed efficiency, it was hypothesized that a rumen-liver-muscle-fat (RLMF) regulatory axis exists and scrutinized the flow of energy along the RLMF axis employing consensus network analysis from a spatial transcriptomic standpoint. Based on enrichment analysis and protein-protein interaction analysis of the consensus network and tissue-specific genes, it was discovered that carbohydrate metabolism, energy metabolism, immune and inflammatory responses were likely to be the biological processes that contribute most to feed efficiency variation on the RLMF regulatory axis. In addition, clusters of genes related to the electron respiratory chain, including ND (2,3,4,4L,5,6), NDUF (A13, A7, S6, B3, B6), COX (1,3), CYTB, UQCR11, ATP (6,8), clusters of genes related to fatty acid metabolism including APO (A1, A2, A4, B, C3), ALB, FG (A, G), as well as clusters of the ribosomal-related gene including RPL (8,18A,18,15,13, P1), the RPS (23,27A,3A,4X), and the PSM (A1-A7, B6, C1, C3, D2-D4, D8 D9, E1) could be the primary effector genes responsible for feed efficiency variation. The findings demonstrate that high feed efficiency cattle, through the synergistic action of the regulatory axis RLMF, may improve the efficiency of biological processes (carbohydrate metabolism, protein ubiquitination, and energy metabolism). Meanwhile, high feed efficiency cattle might enhance the ability to respond to immunity and inflammation, allowing nutrients to be efficiently distributed across these organs associated with digestion and absorption, energy-producing, and energy-storing organs. Elucidating the distribution of nutrients on the RLMF regulatory axis could facilitate an understanding of feed efficiency variation and achieve the study on its molecular regulation.
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15
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Heidaritabar M, Huisman A, Krivushin K, Stothard P, Dervishi E, Charagu P, Bink MCAM, Plastow GS. Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs. Front Genet 2022; 13:1022681. [PMID: 36303553 PMCID: PMC9593086 DOI: 10.3389/fgene.2022.1022681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Imputed whole-genome sequence (WGS) has been proposed to improve genome-wide association studies (GWAS), since all causative mutations responsible for phenotypic variation are expected to be present in the data. This approach was applied on a large number of purebred (PB) and crossbred (CB) pigs for 18 pork color traits to evaluate the impact of using imputed WGS relative to medium-density marker panels. The traits included Minolta A*, B*, and L* for fat (FCOL), quadriceps femoris muscle (QFCOL), thawed loin muscle (TMCOL), fresh ham gluteus medius (GMCOL), ham iliopsoas muscle (ICOL), and longissimus dorsi muscle on the fresh loin (FMCOL). Sequence variants were imputed from a medium-density marker panel (61K for CBs and 50K for PBs) in all genotyped pigs using BeagleV5.0. We obtained high imputation accuracy (average of 0.97 for PBs and 0.91 for CBs). GWAS were conducted for three datasets: 954 CBs and 891 PBs, and the combined CBs and PBs. For most traits, no significant associations were detected, regardless of panel density or population type. However, quantitative trait loci (QTL) regions were only found for a few traits including TMCOL Minolta A* and GMCOL Minolta B* (CBs), FMCOL Minolta B*, FMCOL Minolta L*, and ICOL Minolta B* (PBs) and FMCOL Minolta A*, FMCOL Minolta B*, GMCOL Minolta B*, and ICOL Minolta B* (Combined dataset). More QTL regions were identified with WGS (n = 58) relative to medium-density marker panels (n = 22). Most of the QTL were linked to previously reported QTLs or candidate genes that have been previously reported to be associated with meat quality, pH and pork color; e.g., VIL1, PRKAG3, TTLL4, and SLC11A1, USP37. CTDSP1 gene on SSC15 has not been previously associated with meat color traits in pigs. The findings suggest any added value of WGS was only for detecting novel QTL regions when the sample size is sufficiently large as with the Combined dataset in this study. The percentage of phenotypic variance explained by the most significant SNPs also increased with WGS compared with medium-density panels. The results provide additional insights into identification of a number of candidate regions and genes for pork color traits in different pig populations.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Marzieh Heidaritabar,
| | - Abe Huisman
- Hendrix Genetics Research, Boxmeer, Netherlands
| | - Kirill Krivushin
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Elda Dervishi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | | | - Graham S. Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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16
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Smith JL, Wilson ML, Nilson SM, Rowan TN, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle. BMC Genomics 2022; 23:517. [PMID: 35842584 PMCID: PMC9287884 DOI: 10.1186/s12864-022-08667-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus beef cattle distributed across the continental U.S. and a union set of 836,118 imputed SNPs to conduct genome-wide association analyses (GWAA) for growth traits using univariate linear mixed models (LMM); including birth weight, weaning weight, and yearling weight. Genomic relationship matrix heritability estimates were produced for all growth traits, and genotype-by-environment (GxE) interactions were investigated. Results Moderate to high heritabilities with small standard errors were estimated for birth weight (0.51 ± 0.01), weaning weight (0.25 ± 0.01), and yearling weight (0.42 ± 0.01). GWAA revealed 12 pleiotropic QTL (BTA6, BTA14, BTA20) influencing Red Angus birth weight, weaning weight, and yearling weight which met a nominal significance threshold (P ≤ 1e-05) for polygenic traits using 836K imputed SNPs. Moreover, positional candidate genes associated with Red Angus growth traits in this study (i.e., LCORL, LOC782905, NCAPG, HERC6, FAM184B, SLIT2, MMRN1, KCNIP4, CCSER1, GRID2, ARRDC3, PLAG1, IMPAD1, NSMAF, PENK, LOC112449660, MOS, SH3PXD2B, STC2, CPEB4) were also previously associated with feed efficiency, growth, and carcass traits in beef cattle. Collectively, 14 significant GxE interactions were also detected, but were less consistent among the investigated traits at a nominal significance threshold (P ≤ 1e-05); with one pleiotropic GxE interaction detected on BTA28 (24 Mb) for Red Angus weaning weight and yearling weight. Conclusions Sixteen well-supported QTL regions detected from the GWAA and GxE GWAA for growth traits (birth weight, weaning weight, yearling weight) in U.S. Red Angus cattle were found to be pleiotropic. Twelve of these pleiotropic QTL were also identified in previous studies focusing on feed efficiency and growth traits in multiple beef breeds and/or their composites. In agreement with other beef cattle GxE studies our results implicate the role of vasodilation, metabolism, and the nervous system in the genetic sensitivity to environmental stress. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08667-6.
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Affiliation(s)
- Johanna L Smith
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Miranda L Wilson
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA
| | - Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
| | - Troy N Rowan
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.,Genetics Area Program, University of Missouri, Columbia, 65211, USA.,Informatics Institute, University of Missouri, Columbia, 65211, USA
| | - Christopher M Seabury
- Department of Veterinary Pathobiology, Texas A&M University, College Station, 77843, USA.
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17
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Mota LFM, Santos SWB, Júnior GAF, Bresolin T, Mercadante MEZ, Silva JAV, Cyrillo JNSG, Monteiro FM, Carvalheiro R, Albuquerque LG. Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits. BMC Genomics 2022; 23:424. [PMID: 35672696 PMCID: PMC9172108 DOI: 10.1186/s12864-022-08671-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08671-w.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Tiago Bresolin
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Josineudson A V Silva
- National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.,School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu - SP, 18618-681, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Fábio M Monteiro
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil. .,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.
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18
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Rare and population-specific functional variation across pig lines. Genet Sel Evol 2022; 54:39. [PMID: 35659233 PMCID: PMC9164375 DOI: 10.1186/s12711-022-00732-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/17/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in commercial livestock populations, in particular regarding population-specific variation and how it can affect applications such as across-breed genomic prediction. METHODS We re-sequenced the whole genome of 7848 individuals from nine commercial pig lines (average sequencing coverage: 4.1×) and imputed whole-genome genotypes for 440,610 pedigree-related individuals. The called variants were categorized according to predicted functional annotation (from LOF to intergenic) and prevalence level (number of lines in which the variant segregated; from private to widespread). Variants in each category were examined in terms of their distribution along the genome, alternative allele frequency, per-site Wright's fixation index (FST), individual load, and association to production traits. RESULTS Of the 46 million called variants, 28% were private (called in only one line) and 21% were widespread (called in all nine lines). Genomic regions with a low recombination rate were enriched with private variants. Low-prevalence variants (called in one or a few lines only) were enriched for lower allele frequencies, lower FST, and putatively functional and regulatory roles (including LOF and deleterious missense variants). On average, individuals carried fewer private deleterious missense alleles than expected compared to alleles with other predicted consequences. Only a small subset of the low-prevalence variants had intermediate allele frequencies and explained small fractions of phenotypic variance (up to 3.2%) of production traits. The significant low-prevalence variants had higher per-site FST than the non-significant ones. These associated low-prevalence variants were tagged by other more widespread variants in high linkage disequilibrium, including intergenic variants. CONCLUSIONS Most low-prevalence variants have low minor allele frequencies and only a small subset of low-prevalence variants contributed detectable fractions of phenotypic variance of production traits. Accounting for low-prevalence variants is therefore unlikely to noticeably benefit across-breed analyses, such as the prediction of genomic breeding values in a population using reference populations of a different genetic background.
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19
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Zhou M, Zhu Z, Sun HZ, Zhao K, Dugan MER, Bruce H, Fitzsimmons C, Li C, Guan LL. Breed dependent regulatory mechanisms of beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue in cattle with divergent feed efficiency. Sci Rep 2022; 12:4612. [PMID: 35301378 PMCID: PMC8931072 DOI: 10.1038/s41598-022-08572-8] [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: 08/17/2021] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
The current study aimed to determine whether breed and feed efficiency affect the molecular mechanisms regulating beneficial and non-beneficial fatty acid profiles in subcutaneous adipose tissue of beef steers. Fatty acid profiling and RNA-Seq based transcriptome analysis were performed on subcutaneous adipose tissues collected from beef steers with three divergent breeds (Angus, ANG, n = 47; Charolais, CHAR, n = 48; Kinsella Composite, KC, n = 48) and different residual feed intake (RFI, a measure of feed efficiency). The comparison of fatty acid profiles showed that KC had higher beneficial FAs compared to the other two breeds. Distinct FA profiles between H-RFIfat and L-RFIfat steers was more obvious for KC steers, where H-RFIfat steers tended to have higher proportion of healthy FAs and lower proportion of the unhealthy FAs. A higher number of differentially expressed (DE) genes were observed for KC steers, whereas ANG and CHAR steers had a lower number of DE genes between H- and L-RFIfat steers. The association analyses of the gene expressions and FA profiles showed that 10 FA metabolism-associated genes together with the one upstream regulator (SREBF1) were associated with the proportion of C18:2n-6, total n-6, PUFA and PUFA/SFA for KC steers but not the other two breeds. Subcutaneous adipose tissue FA profiles and healthy FA index differed in cattle with divergent feed efficiency and such variation was unique for the three examined cattle breeds. Key FA metabolism-associated genes together with SREBF1 which is the upstream regulator of a set of genes involved in lipid metabolism may be of importance for genetic selection of meat with higher healthy FA index in beef cattle.
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Affiliation(s)
- Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Zhi Zhu
- College of Animal Science and Technology, Southwest University, Chongqing, 402460, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ke Zhao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi, 710119, China
| | - Mike E R Dugan
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Heather Bruce
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.,Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.,Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB, T4L 1W1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
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20
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Li J, Wang Y, Mukiibi R, Karisa B, Plastow GS, Li C. Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle. Sci Rep 2022; 12:3389. [PMID: 35232965 PMCID: PMC8888742 DOI: 10.1038/s41598-022-06567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, L-glutamine, succinic acid, pyruvic acid, L-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, D-glucose, and glycerol), 2 (L-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10-5), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits.
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Affiliation(s)
- Jiyuan Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yining Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Brian Karisa
- Results Driven Agriculture Research, Edmonton, AB, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. .,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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21
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Halli K, Bohlouli M, Schulz L, Sundrum A, König S. Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed. Transl Anim Sci 2022; 6:txac022. [PMID: 35308836 PMCID: PMC8925308 DOI: 10.1093/tas/txac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 12/03/2022] Open
Abstract
With regard to potential applications of genomic selection in small numbered breeds, we evaluated genomic models and focused on potential candidate gene annotations for weight and meat quality traits in the local Rotes Höhenvieh (RHV) breed. Traits included 6,003 birth weights (BWT), 5,719 200 d-weights (200dw), 4,594 365 d-weights (365dw), and 547 records for intramuscular fat content (IMF). A total of 581,304 SNP from 370 genotyped cattle with phenotypic records were included in genomic analyses. Model evaluations focused on single- and multiple-trait models with direct and with direct and maternal genetic effects. Genetic relationship matrices were based on pedigree (A-matrix), SNP markers (G-matrix), or both (H-matrix). Genome-wide association studies (GWASs) were carried out using linear mixed models to identify potential candidate genes for the traits of interest. De-regressed proofs (DRP) for direct and maternal genetic components were used as pseudo-phenotypes in the GWAS. Accuracies of direct breeding values were higher from models based on G or on H compared to A. Highest accuracies (> 0.89) were obtained for IMF with multiple-trait models using the G-matrix. Direct heritabilities with maternal genetic effects ranged from 0.62 to 0.66 for BWT, from 0.45 to 0.55 for 200dW, from 0.40 to 0.44 for 365dW, and from 0.48 to 0.75 for IMF. Maternal heritabilities for BWT, 200dW, and 365dW were in a narrow range from 0.21 to 0.24, 0.24 to 0.27, and 0.21 to 0.25, respectively, and from 0.25 to 0.65 for IMF. Direct genetic correlations among body weight traits were positive and favorable, and very similar from different models but showed a stronger variation with 0.31 (A), −0.13 (G), and 0.45 (H) between BWT and IMF. In gene annotations, we identified 6, 3, 1, and 6 potential candidate genes for direct genetic effect on BWT, 200dW, 365dW, and IMF traits, respectively. Regarding maternal genetic effects, four (SHROOM3, ZNF609, PECAM1, and TEX2) and two (TMEM182 and SEC11A) genes were detected as potential candidate genes for BWT and 365dW, respectively. Potential candidate genes for maternal effect on IMF were GRHL2, FGA, FGB, and CTNNA3. As the most important finding from a practical breeding perspective, a small number of genotyped RHV cattle enabled accurate breeding values for high heritability IMF.
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Affiliation(s)
- K Halli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - M Bohlouli
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
| | - L Schulz
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - A Sundrum
- Department of Animal Nutrition and Animal Health, Kassel University, Witzenhausen, Germany
| | - S König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University, Giessen, Germany
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22
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Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Gao X, Chen Y, Zhang L, Gao H, Li J, Xu L. Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle. Front Genet 2021; 12:750746. [PMID: 34912371 PMCID: PMC8667311 DOI: 10.3389/fgene.2021.750746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.
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Affiliation(s)
- Qunhao Niu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianliu Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianzhen Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zezhao Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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23
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Li J, Mukiibi R, Wang Y, Plastow GS, Li C. Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle. BMC Genomics 2021; 22:823. [PMID: 34781903 PMCID: PMC8591823 DOI: 10.1186/s12864-021-08064-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. RESULTS Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10-5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. CONCLUSIONS This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.
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Affiliation(s)
- Jiyuan Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Yining Wang
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada
| | - Graham S Plastow
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
| | - Changxi Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada.
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24
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Exploring the size of reference population for expected accuracy of genomic prediction using simulated and real data in Japanese Black cattle. BMC Genomics 2021; 22:799. [PMID: 34742249 PMCID: PMC8572443 DOI: 10.1186/s12864-021-08121-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Background Size of reference population is a crucial factor affecting the accuracy of prediction of the genomic estimated breeding value (GEBV). There are few studies in beef cattle that have compared accuracies achieved using real data to that achieved with simulated data and deterministic predictions. Thus, extent to which traits of interest affect accuracy of genomic prediction in Japanese Black cattle remains obscure. This study aimed to explore the size of reference population for expected accuracy of genomic prediction for simulated and carcass traits in Japanese Black cattle using a large amount of samples. Results A simulation analysis showed that heritability and size of reference population substantially impacted the accuracy of GEBV, whereas the number of quantitative trait loci did not. The estimated numbers of independent chromosome segments (Me) and the related weighting factor (w) derived from simulation results and a maximum likelihood (ML) approach were 1900–3900 and 1, respectively. The expected accuracy for trait with heritability of 0.1–0.5 fitted well with empirical values when the reference population comprised > 5000 animals. The heritability for carcass traits was estimated to be 0.29–0.41 and the accuracy of GEBVs was relatively consistent with simulation results. When the reference population comprised 7000–11,000 animals, the accuracy of GEBV for carcass traits can range 0.73–0.79, which is comparable to estimated breeding value obtained in the progeny test. Conclusion Our simulation analysis demonstrated that the expected accuracy of GEBV for a polygenic trait with low-to-moderate heritability could be practical in Japanese Black cattle population. For carcass traits, a total of 7000–11,000 animals can be a sufficient size of reference population for genomic prediction. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08121-z.
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25
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Wang M, Bissonnette N, Dudemaine PL, Zhao X, Ibeagha-Awemu EM. Whole Genome DNA Methylation Variations in Mammary Gland Tissues from Holstein Cattle Producing Milk with Various Fat and Protein Contents. Genes (Basel) 2021; 12:1727. [PMID: 34828333 PMCID: PMC8618717 DOI: 10.3390/genes12111727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/20/2022] Open
Abstract
Milk fat and protein contents are among key elements of milk quality, and they are attracting more attention in response to consumers' demand for high-quality dairy products. To investigate the potential regulatory roles of DNA methylation underlying milk component yield, whole genome bisulfite sequencing was employed to profile the global DNA methylation patterns of mammary gland tissues from 17 Canada Holstein cows with various milk fat and protein contents. A total of 706, 2420 and 1645 differentially methylated CpG sites (DMCs) were found between high vs. low milk fat (HMF vs. LMF), high vs. low milk protein (HMP vs. LMP), and high vs. low milk fat and protein (HMFP vs. LMFP) groups, respectively (q value < 0.1). Twenty-seven, 56 and 67 genes harboring DMCs in gene regions (denoted DMC genes) were identified for HMF vs. LMF, HMP vs. LMP and HMFP vs. LMFP, respectively. DMC genes from HMP vs. LMP and HMFP vs. LMFP comparisons were significantly overrepresented in GO terms related to aerobic electron transport chain and/or mitochondrial ATP (adenosine triphosphate) synthesis coupled electron transport. A total of 83 (HMF vs. LMF), 708 (HMP vs. LMP) and 408 (HMFP vs. LMFP) DMCs were co-located with 87, 147 and 158 quantitative trait loci (QTL) for milk component and yield traits, respectively. In conclusion, the identified methylation changes are potentially involved in the regulation of milk fat and protein yields, as well as the variation in reported co-located QTLs.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC H9X 3V9, Canada;
| | - Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC J1M 0C8, Canada; (M.W.); (N.B.); (P.-L.D.)
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26
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Manca E, Cesarani A, Falchi L, Atzori AS, Gaspa G, Rossoni A, Macciotta NPP, Dimauro C. Genome-wide association study for residual concentrate intake using different approaches in Italian Brown Swiss. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1963864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- E. Manca
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - L. Falchi
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. S. Atzori
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - G. Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, University of Torino, Grugliasco, Italy
| | - A. Rossoni
- Associazione Nazionale degli Allevatori di Razza Bruna (ANARB), Verona, Italy
| | | | - C. Dimauro
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
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27
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Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Zhang L, Gao H, Song J, Li J, Xu L. Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle. Genomics 2021; 113:3325-3336. [PMID: 34314829 DOI: 10.1016/j.ygeno.2021.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/05/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022]
Abstract
Carcass merits are widely considered as economically important traits affecting beef production in the beef cattle industry. However, the genetic basis of carcass traits remains to be well understood. Here, we applied multiple methods, including the Composite of Likelihood Ratio (CLR) and Genome-wide Association Study (GWAS), to explore the selection signatures and candidate variants affecting carcass traits. We identified 11,600 selected regions overlapping with 2214 candidate genes, and most of those were enriched in binding and gene regulation. Notably, we identified 66 and 110 potential variants significantly associated with carcass traits using single-trait and multi-traits analyses, respectively. By integrating selection signatures with single and multi-traits associations, we identified 12 and 27 putative genes, respectively. Several highly conserved missense variants were identified in OR5M13D, NCAPG, and TEX2. Our study supported polygenic genetic architecture of carcass traits and provided novel insights into the genetic basis of complex traits in beef cattle.
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Affiliation(s)
- Qunhao Niu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianliu Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ling Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianzhen Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zezhao Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Zhu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, USA
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Bai X, Yang T, Putz AM, Wang Z, Li C, Fortin F, Harding JCS, Dyck MK, Dekkers JCM, Field CJ, Plastow GS. Investigating the genetic architecture of disease resilience in pigs by genome-wide association studies of complete blood count traits collected from a natural disease challenge model. BMC Genomics 2021; 22:535. [PMID: 34256695 PMCID: PMC8278769 DOI: 10.1186/s12864-021-07835-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Genetic improvement for disease resilience is anticipated to be a practical method to improve efficiency and profitability of the pig industry, as resilient pigs maintain a relatively undepressed level of performance in the face of infection. However, multiple biological functions are known to be involved in disease resilience and this complexity means that the genetic architecture of disease resilience remains largely unknown. Here, we conducted genome-wide association studies (GWAS) of 465,910 autosomal SNPs for complete blood count (CBC) traits that are important in an animal’s disease response. The aim was to identify the genetic control of disease resilience. Results Univariate and multivariate single-step GWAS were performed on 15 CBC traits measured from the blood samples of 2743 crossbred (Landrace × Yorkshire) barrows drawn at 2-weeks before, and at 2 and 6-weeks after exposure to a polymicrobial infectious challenge. Overall, at a genome-wise false discovery rate of 0.05, five genomic regions located on Sus scrofa chromosome (SSC) 2, SSC4, SSC9, SSC10, and SSC12, were significantly associated with white blood cell traits in response to the polymicrobial challenge, and nine genomic regions on multiple chromosomes (SSC1, SSC4, SSC5, SSC6, SSC8, SSC9, SSC11, SSC12, SSC17) were significantly associated with red blood cell and platelet traits collected before and after exposure to the challenge. By functional enrichment analyses using Ingenuity Pathway Analysis (IPA) and literature review of previous CBC studies, candidate genes located nearby significant single-nucleotide polymorphisms were found to be involved in immune response, hematopoiesis, red blood cell morphology, and platelet aggregation. Conclusions This study helps to improve our understanding of the genetic basis of CBC traits collected before and after exposure to a polymicrobial infectious challenge and provides a step forward to improve disease resilience. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07835-4.
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Affiliation(s)
- Xuechun Bai
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Tianfu Yang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Current: ST Genetics, Navasota, TX, USA
| | - Austin M Putz
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Frédéric Fortin
- Centre de Développement du Porc du Québec, Inc., Quebec City, QC, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael K Dyck
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | | | - Catherine J Field
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
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Eydivandi S, Roudbar MA, Karimi MO, Sahana G. Genomic scans for selective sweeps through haplotype homozygosity and allelic fixation in 14 indigenous sheep breeds from Middle East and South Asia. Sci Rep 2021; 11:2834. [PMID: 33531649 PMCID: PMC7854752 DOI: 10.1038/s41598-021-82625-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/22/2021] [Indexed: 01/30/2023] Open
Abstract
The performance and productivity of livestock have consistently improved by natural and artificial selection over the centuries. Both these selections are expected to leave patterns on the genome and lead to changes in allele frequencies, but natural selection has played the major role among indigenous populations. Detecting selective sweeps in livestock may assist in understanding the processes involved in domestication, genome evolution and discovery of genomic regions associated with economically important traits. We investigated population genetic diversity and selection signals in this study using SNP genotype data of 14 indigenous sheep breeds from Middle East and South Asia, including six breeds from Iran, namely Iranian Balochi, Afshari, Moghani, Qezel, Zel, and Lori-Bakhtiari, three breeds from Afghanistan, namely Afghan Balochi, Arabi, and Gadik, three breeds from India, namely Indian Garole, Changthangi, and Deccani, and two breeds from Bangladesh, namely Bangladeshi Garole and Bangladesh East. The SNP genotype data were generated by the Illumina OvineSNP50 Genotyping BeadChip array. To detect genetic diversity and population structure, we used principal component analysis (PCA), admixture, phylogenetic analyses, and Runs of homozygosity. We applied four complementary statistical tests, FST (fixation index), xp-EHH (cross-population extended haplotype homozygosity), Rsb (extended haplotype homozygosity between-populations), and FLK (the extension of the Lewontin and Krakauer) to detect selective sweeps. Our results not only confirm the previous studies but also provide a suite of novel candidate genes involved in different traits in sheep. On average, FST, xp-EHH, Rsb, and FLK detected 128, 207, 222, and 252 genomic regions as candidates for selective sweeps, respectively. Furthermore, nine overlapping candidate genes were detected by these four tests, especially TNIK, DOCK1, USH2A, and TYW1B which associate with resistance to diseases and climate adaptation. Knowledge of candidate genomic regions in sheep populations may facilitate the identification and potential exploitation of the underlying genes in sheep breeding.
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Affiliation(s)
- Sirous Eydivandi
- Department of Animal Science, Behbahan Branch, Islamic Azad University, Behbahan, Iran.
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark.
| | - Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Dezful, Iran
| | - Mohammad Osman Karimi
- Department of Animal Science, Faculty of Agriculture, Herat University, Herat, Afghanistan
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, 8830, Tjele, Denmark
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Stegemiller MR, Murdoch GK, Rowan TN, Davenport KM, Becker GM, Hall JB, Murdoch BM. Genome-Wide Association Analyses of Fertility Traits in Beef Heifers. Genes (Basel) 2021; 12:genes12020217. [PMID: 33540904 PMCID: PMC7913221 DOI: 10.3390/genes12020217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
The ability of livestock to reproduce efficiently is critical to the sustainability of animal agriculture. Antral follicle count (AFC) and reproductive tract scores (RTS) can be used to estimate fertility in beef heifers, but the genetic mechanisms influencing variation in these measures are not well understood. Two genome-wide association studies (GWAS) were conducted to identify the significant loci associated with these traits. In total, 293 crossbred beef heifers were genotyped on the Bovine GGP 50K chip and genotypes were imputed to 836,121 markers. A GWAS was performed with the AFC phenotype for 217 heifers with a multi-locus mixed model, conducted using the year, age at time of sampling and principal component analysis groupings as the covariates. The RTS GWAS was performed with 289 heifers using an additive correlation/trend test comparing prepubertal to pubertal heifers. The loci on chromosomes 2, 3 and 23 were significant in the AFC GWAS and the loci on chromosomes 2, 8, 10 and 11 were significant in the RTS GWAS. The significant region on chromosome 2 was similar between both analyses. These regions contained genes associated with cell proliferation, transcription, apoptosis and development. This study proposes candidate genes for beef cattle fertility, although future research is needed to elucidate the precise mechanisms.
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Affiliation(s)
- Morgan R. Stegemiller
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
| | - Gordon K. Murdoch
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
- Department of Animal Sciences, Washington State University, Pullman, WA 99164, USA
| | - Troy N. Rowan
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Kimberly M. Davenport
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
| | - Gabrielle M. Becker
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
| | - John B. Hall
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
- Nancy M. Cummings Research, Education, and Extension Center, University of Idaho, Carmen, ID 83462, USA
- Correspondence: (J.B.H.); (B.M.M.); Tel.: +1-208-756-2749 (J.B.H.); +1-208-885-2088 (B.M.M.)
| | - Brenda M. Murdoch
- Department of Animal, Veterinary & Food Sciences, University of Idaho, Moscow, ID 83843, USA; (M.R.S.); (G.K.M.); (K.M.D.); (G.M.B.)
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
- Correspondence: (J.B.H.); (B.M.M.); Tel.: +1-208-756-2749 (J.B.H.); +1-208-885-2088 (B.M.M.)
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Brunes LC, Baldi F, Lopes FB, Lobo RB, Espigolan R, Costa MFO, Magnabosco CU. Selection criteria for feed efficiency-related traits and their association with growth, reproductive and carcass traits in Nelore cattle. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Context
Livestock feed costs have a higher impact on the profitability of beef production systems and are directly related to feed efficiency. However, these traits are hard and have high costs to measure, reducing the availability of phenotypic records and reliability of genetic evaluations. Thus, the use of genomic information can increase the robustness of genetic studies that address them.
Aims
The aim of the present study was to estimate genetic parameters for feed efficiency, growth, reproductive and carcass traits in Nelore cattle and the correlated response among them, using genomic information.
Methods
Residual feed intake (RFI), dry-matter intake, feed conversion ratio, feed efficiency (FE), residual average daily gain (RG), residual feed intake and average daily gain (RIG), birthweight, weight at 120, 240, 365 and 450 days of age, scrotal circumference at 365 and 450 days of age, rib-eye area, backfat thickness and rump fat thickness were evaluated. The genetic parameters were estimated using the single-step genomic best linear unbiased prediction approach.
Key results
The FE-related traits showed low to moderate heritability ranging from 0.07 to 0.23. Feed efficiency-related traits showed low genetic correlations with reproductive (–0.24 to 0.27), carcass (–0.17 to 0.27) and growth (–0.19 to 0.24) traits, except for growth with dry-matter intake (0.32–0.56) and weight at 365 days of age with FE (–0.40).
Conclusions
The selection to improve growth, reproductive and carcass traits would not change RFI, RG and RIG. The choice of the most adequate selection criterion depends on the production system, that is, RFI might be used for low-input beef cattle systems, and RIG would be used for more intensive and without-any-dietary-restrictions beef cattle systems.
Implications
The estimates of heritability and genetic correlations suggest that genetic selection for feed efficiency using RFI, RG and RIG in Nellore cattle leads to higher genetic gain than does that using FE and feed conversion ratio without affecting other profitability traits.
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Lee SH, Lee D, Lee M, Ryoo SH, Seo S, Choi I. Analysis of single nucleotide polymorphisms related to heifer fertility in Hanwoo (Korean cattle). Anim Biotechnol 2020; 33:964-969. [PMID: 33287639 DOI: 10.1080/10495398.2020.1856124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Genome-wide association studies (GWAS) have accelerated the identification of functional trait loci in cattle and identified single nucleotide polymorphisms (SNPs) in candidate genes associated with fertility and production traits in high milk yield dairy cattle. The fertility of Hanwoo (Korean native beef cattle) has declined after the adaptation of a selection program for high quantity and quality meat. However, there are few GWAS studies of fertility in beef cattle. We performed a genome-wide association study of 40 Korean native beef cattle heifers with imputed 770 K genotype and identified 12 significant SNPs within seven regions on three chromosomes (BTA 8, BTA 16 and BTA 24) associated with services per conception (SPC). Five SNPs were located in the ABCA1, BRINP3 and ESRRG genes, which are involved in early embryo development. In addition, 27 proximal genes were identified within 1 Mb of the candidate SNPs, which are involved in muscle cell differentiation and muscle structure development. However, we did not find any previously reported SNPs related to fertility in Holstein cows. Taken together, we identified SNPs associated with SPC and their proximal genes using gene-based analysis and the candidates were different from SNPs associated with subfertility of dairy cattle.
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Affiliation(s)
- Seung-Hwan Lee
- Division of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Dooho Lee
- Division of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Mingyung Lee
- Division of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Seung-Heui Ryoo
- Livestock Experiment Institute, Government of Chungcheongnam-do, Chungcheongnam-do, Republic of Korea
| | - Seongwon Seo
- Division of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Inchul Choi
- Division of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
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33
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Li J, Akanno EC, Valente TS, Abo-Ismail M, Karisa BK, Wang Z, Plastow GS. Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle. Front Genet 2020; 11:538600. [PMID: 33193612 PMCID: PMC7542097 DOI: 10.3389/fgene.2020.538600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolites, substrates or products of metabolic processes, are involved in many biological functions, such as energy metabolism, signaling, stimulatory and inhibitory effects on enzymes and immunological defense. Metabolomic phenotypes are influenced by combination of genetic and environmental effects allowing for metabolome-genome-wide association studies (mGWAS) as a powerful tool to investigate the relationship between these phenotypes and genetic variants. The objectives of this study were to estimate genomic heritability and perform mGWAS and in silico functional enrichment analyses for a set of plasma metabolites in Canadian crossbred beef cattle. Thirty-three plasma metabolites and 45,266 single nucleotide polymorphisms (SNPs) were available for 475 animals. Genomic heritability for all metabolites was estimated using genomic best linear unbiased prediction (GBLUP) including genomic breed composition as covariates in the model. A single-step GBLUP implemented in BLUPF90 programs was used to determine SNP P values and the proportion of genetic variance explained by SNP windows containing 10 consecutive SNPs. The top 10 SNP windows that explained the largest genetic variation for each metabolite were identified and mapped to detect corresponding candidate genes. Functional enrichment analyses were performed on metabolites and their candidate genes using the Ingenuity Pathway Analysis software. Eleven metabolites showed low to moderate heritability that ranged from 0.09 ± 0.15 to 0.36 ± 0.15, while heritability estimates for 22 metabolites were zero or negligible. This result indicates that while variations in 11 metabolites were due to genetic variants, the majority are largely influenced by environment. Three significant SNP associations were detected for betaine (rs109862186), L-alanine (rs81117935), and L-lactic acid (rs42009425) based on Bonferroni correction for multiple testing (family wise error rate <0.05). The SNP rs81117935 was found to be located within the Catenin Alpha 2 gene (CTNNA2) showing a possible association with the regulation of L-alanine concentration. Other candidate genes were identified based on additive genetic variance explained by SNP windows of 10 consecutive SNPs. The observed heritability estimates and the candidate genes and networks identified in this study will serve as baseline information for research into the utilization of plasma metabolites for genetic improvement of crossbred beef cattle.
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Affiliation(s)
- Jiyuan Li
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Everestus C Akanno
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tiago S Valente
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, Ethology and Animal Ecology Research Group, São Paulo State University, Jaboticabal, Brazil
| | - Mohammed Abo-Ismail
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, College of Agriculture, Food and Environmental Sciences, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Brian K Karisa
- Ministry of Agriculture and Forestry, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
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Laghouaouta H, Sosa-Madrid BS, Zubiri-Gaitán A, Hernández P, Blasco A. Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits. Animals (Basel) 2020; 10:ani10112090. [PMID: 33187110 PMCID: PMC7697864 DOI: 10.3390/ani10112090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0-37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0-48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.
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35
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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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Liu L, Zhou J, Chen CJ, Zhang J, Wen W, Tian J, Zhang Z, Gu Y. GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle. Animals (Basel) 2020; 10:E2048. [PMID: 33167458 PMCID: PMC7694478 DOI: 10.3390/ani10112048] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10-7), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.
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Affiliation(s)
- Liyuan Liu
- School of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; (L.L.); (J.Z.); (J.Z.)
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USA;
| | - Jinghang Zhou
- School of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; (L.L.); (J.Z.); (J.Z.)
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USA;
| | - Chunpeng James Chen
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USA;
| | - Juan Zhang
- School of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; (L.L.); (J.Z.); (J.Z.)
| | - Wan Wen
- Animal Husbandry Workstation, Yinchuan 750001, Ningxia, China; (W.W.); (J.T.)
| | - Jia Tian
- Animal Husbandry Workstation, Yinchuan 750001, Ningxia, China; (W.W.); (J.T.)
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, DC 99164, USA;
| | - Yaling Gu
- School of Agriculture, Ningxia University, Yinchuan 750021, Ningxia, China; (L.L.); (J.Z.); (J.Z.)
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Wang Y, Zhang F, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits. BMC Genomics 2020; 21:38. [PMID: 31931697 PMCID: PMC6958779 DOI: 10.1186/s12864-019-6273-1] [Citation(s) in RCA: 21] [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] [Received: 06/26/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated. RESULTS The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits. CONCLUSIONS The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.
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Affiliation(s)
- Yining Wang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Feng Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi China
- Present Address: Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi China
| | - Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Liuhong Chen
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - John Basarab
- Alberta Agriculture and Forestry, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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