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Thieffry S, Aubert J, Devers-Lamrani M, Martin-Laurent F, Romdhane S, Rouard N, Siol M, Spor A. Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134454. [PMID: 38688223 DOI: 10.1016/j.jhazmat.2024.134454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/09/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 - between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.
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Affiliation(s)
- Sylvia Thieffry
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France.
| | - Julie Aubert
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120 Palaiseau, France
| | - Marion Devers-Lamrani
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Fabrice Martin-Laurent
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Sana Romdhane
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Nadine Rouard
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Mathieu Siol
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France
| | - Aymé Spor
- INRAE, Institut Agro, Université de Bourgogne, Université de Bourgogne Franche-Comté, Agroécologie,21000 Dijon, France.
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Yin ZT, Li XQ, Sun YX, Smith J, Hincke M, Yang N, Hou ZC. Selection on the promoter regions plays an important role in complex traits during duck domestication. BMC Biol 2023; 21:303. [PMID: 38129834 PMCID: PMC10740227 DOI: 10.1186/s12915-023-01801-0] [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: 02/01/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Identifying the key factors that underlie complex traits during domestication is a great challenge for evolutionary and biological studies. In addition to the protein-coding region differences caused by variants, a large number of variants are located in the noncoding regions containing multiple types of regulatory elements. However, the roles of accumulated variants in gene regulatory elements during duck domestication and economic trait improvement are poorly understood. RESULTS We constructed a genomics, transcriptomics, and epigenomics map of the duck genome and assessed the evolutionary forces that have been in play across the whole genome during domestication. In total, 304 (42.94%) gene promoters have been specifically selected in Pekin duck among all selected genes. Joint multi-omics analysis reveals that 218 genes (72.01%) with selected promoters are located in open and active chromatin, and 267 genes (87.83%) with selected promoters were highly and differentially expressed in domestic trait-related tissues. One important candidate gene ELOVL3, with a strong signature of differentiation on the core promoter region, is known to regulate fatty acid elongation. Functional experiments showed that the nearly fixed variants in the top selected ELOVL3 promoter in Pekin duck decreased binding ability with HLF and increased gene expression, with the overexpression of ELOVL3 able to increase lipid deposition and unsaturated fatty acid enrichment. CONCLUSIONS This study presents genome resequencing, RNA-Seq, Hi-C, and ATAC-Seq data of mallard and Pekin duck, showing that selection of the gene promoter region plays an important role in gene expression and phenotypic changes during domestication and highlights that the variants of the ELOVL3 promoter may have multiple effects on fat and long-chain fatty acid content in ducks.
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Affiliation(s)
- Zhong-Tao Yin
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Xiao-Qin Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yun-Xiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Maxwell Hincke
- Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, MARA, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, China.
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Li S, Zhang X, Dong X, Guo R, Nan J, Yuan J, Schlebusch CM, Sheng Z. Genetic structure and characteristics of Tibetan chickens. Poult Sci 2023; 102:102767. [PMID: 37321029 PMCID: PMC10404676 DOI: 10.1016/j.psj.2023.102767] [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: 12/06/2022] [Revised: 04/21/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.
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Affiliation(s)
- Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinyu Dong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiyang Guo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiuhong Nan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Zheya Sheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education; College of Animal Science and Technology and College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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Yang L, Li X, Zhuang Z, Zhou S, Wu J, Xu C, Ruan D, Qiu Y, Zhao H, Zheng E, Cai G, Wu Z, Yang J. Genome-Wide Association Study Identifies the Crucial Candidate Genes for Teat Number in Crossbred Commercial Pigs. Animals (Basel) 2023; 13:1880. [PMID: 37889833 PMCID: PMC10251818 DOI: 10.3390/ani13111880] [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: 04/19/2023] [Revised: 05/27/2023] [Accepted: 06/03/2023] [Indexed: 10/29/2023] Open
Abstract
The number of teats is a crucial reproductive trait with significant economic implications on maternal capacity and litter size. Consequently, improving this trait is essential to facilitate genetic selection for increased litter size. In this study, we performed a genome-wide association study (GWAS) of the number of teats in a three-way crossbred commercial Duroc × (Landrace × Yorkshire) (DLY) pig population comprising 1518 animals genotyped with the 50K BeadChip. Our analysis identified crucial quantitative trait loci (QTL) for the number of teats, containing the ABCD4 and VRTN genes on porcine chromosome 7. Our results establish SNP variants of ABCD4 and VRTN as new molecular markers for improving the number of teats in DLY pigs. Furthermore, the most significant noteworthy single nucleotide polymorphism (SNP) (7_97568284) was identified within the ABCD4 gene, exhibiting a significant association with the total teat number traits. This SNP accounted for a substantial proportion of the genetic variance, explaining 6.64% of the observed variation. These findings reveal a novel gene on SSC7 for the number of teats and provide a deeper understanding of the genetic mechanisms underlying reproductive traits.
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Affiliation(s)
- Lijuan Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Xuehua Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Yibin Qiu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Hua Zhao
- National S&T Innovation Center for Modern Agricultural Industry, Guangzhou 510642, China;
- Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu 527400, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642, China; (L.Y.); (X.L.); (Z.Z.); (S.Z.); (J.W.); (C.X.); (D.R.); (Y.Q.); (E.Z.); (G.C.)
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
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Nan J, Yang S, Zhang X, Leng T, Zhuoma J, Zhuoma R, Yuan J, Pi J, Sheng Z, Li S. Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis. Anim Genet 2023; 54:55-67. [PMID: 36305422 DOI: 10.1111/age.13268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 01/07/2023]
Abstract
Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted pre-analysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways. Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to a hypoxic environment. We also found that STX2 was significantly selected in the highland group, thus potentially reducing the oxidative stress caused by hypoxia, and that STX2 exhibited the opposite effects on highland adaptation and reproductive traits. Our findings advance our understanding of extreme environment adaptation of highland chickens, and provide some variants and genes beneficial to TBC genetic breeding improvement.
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Affiliation(s)
- Jiuhong Nan
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sendong Yang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaojian Zhang
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianze Leng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Marine Ecosystem Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Joan Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Neighborhood Committee Office, Xigaze City, China
| | - Rensang Zhuoma
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Luomai Township People's Government of Seni District, Naqu City, China
| | - Jingwei Yuan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan, China
| | - Zheya Sheng
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shijun Li
- State Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
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Abdalla EAE, Makanjuola BO, Wood BJ, Baes CF. Genome-wide association study reveals candidate genes relevant to body weight in female turkeys (Meleagris gallopavo). PLoS One 2022; 17:e0264838. [PMID: 35271651 PMCID: PMC8912253 DOI: 10.1371/journal.pone.0264838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/17/2022] [Indexed: 11/18/2022] Open
Abstract
The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Genome-wide association studies (GWAS) is a powerful approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with 18-week body weight in a turkey population. The data included body weight observations for 24,989 female turkeys genotyped based on a 65K SNP panel. The analysis was carried out using a univariate mixed linear model with hatch-week-year and the 2 top principal components fitted as fixed effects and the accumulated polygenic effect of all markers captured by the genomic relationship matrix as random. Thirty-three significant markers were observed on 1, 2, 3, 4, 7 and 12 chromosomes, while 26 showed strong linkage disequilibrium extending up to 410 kb. These significant markers were mapped to 37 genes, of which 13 were novel. Interestingly, many of the investigated genes are known to be involved in growth and body weight. For instance, genes AKR1D1, PARP12, BOC, NCOA1, ADCY3 and CHCHD7 regulate growth, body weight, metabolism, digestion, bile acid biosynthetic and development of muscle cells. In summary, the results of our study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program and adapted in fine mapping of quantitative trait loci to enhance genetic improvement in this species.
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Affiliation(s)
- Emhimad A. E. Abdalla
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
| | - Bayode O. Makanjuola
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
| | - Benjamin J. Wood
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
- School of Veterinary Science, University of Queensland, Gatton, Queensland, Australia
- Hybrid Turkeys, C-650 Riverbend Drive, Suite C, Kitchener, Canada
| | - Christine F. Baes
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario, Canada
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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7
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Meta-analysis of genome-wide association studies and gene networks analysis for milk production traits in Holstein cows. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lee YL, Takeda H, Costa Monteiro Moreira G, Karim L, Mullaart E, Coppieters W, Appeltant R, Veerkamp RF, Groenen MAM, Georges M, Bosse M, Druet T, Bouwman AC, Charlier C. A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle. PLoS Genet 2021; 17:e1009331. [PMID: 34288907 PMCID: PMC8328317 DOI: 10.1371/journal.pgen.1009331] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/02/2021] [Accepted: 06/08/2021] [Indexed: 12/24/2022] Open
Abstract
Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.
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Affiliation(s)
- Young-Lim Lee
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | | | - Latifa Karim
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
- GIGA Genomics Platform, GIGA Institute, University of Liège, Liège, Belgium
| | | | - Ruth Appeltant
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Roel F. Veerkamp
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Martien A. M. Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Aniek C. Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, the Netherlands
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Li F, Liu J, Liu W, Gao J, Lei Q, Han H, Yang J, Li H, Cao D, Zhou Y. Genome-wide association study of body size traits in Wenshang Barred chickens based on the specific-locus amplified fragment sequencing technology. Anim Sci J 2021; 92:e13506. [PMID: 33398896 DOI: 10.1111/asj.13506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
Chicken body size (BS) is an economically important trait, which has been assessed in many studies for genetic selection. However, previous reports detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) of purebred Wenshang Barred chickens. A total of 250 one-day-old male chickens were assessed in this study. Body size in individual birds was measured at 56 days. SLAF-seq was used to genotype and GWAS analysis was carried out using the general linear model (GLM) of the TASSEL program. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, of which 175,211 were tested as candidate SNPs for genome-wide association analysis using the TASSEL general linear model. Three SNPs markers reached genome-wide significance. Of these, chrZ:81729634, chrZ:81841715, and chrZ:81954149 at 81,729,634, 81,841,715, and 81,954,149 bp of GGA Z were significantly associated with body diagonal length at 56 days (BDL56); and tibia length at 56 days (TL56). These SNPs were close to three genes, including ZCCHC7, PAX5, and MELK. These results open new horizons for studies on BS and should promote the use of Chinese chickens, especially Wenshang Barred chickens.
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Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jingchao Yang
- Shandong Animal Husbandry General Station, Ji'nan, P. R. China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
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10
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Li W, Jing Z, Cheng Y, Wang X, Li D, Han R, Li W, Li G, Sun G, Tian Y, Liu X, Kang X, Li Z. Analysis of four complete linkage sequence variants within a novel lncRNA located in a growth QTL on chromosome 1 related to growth traits in chickens. J Anim Sci 2020; 98:5822640. [PMID: 32309860 DOI: 10.1093/jas/skaa122] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
An increasing number of studies have shown that quantitative trait loci (QTLs) at the end of chromosome 1 identified in different chicken breeds and populations exert significant effects on growth traits in chickens. Nevertheless, the causal genes underlying the QTL effect remain poorly understood. Using an updated gene database, a novel lncRNA (named LncFAM) was found at the end of chromosome 1 and located in a growth and digestion QTL. This study showed that the expression level of LncFAM in pancreas tissues with a high weight was significantly higher than that in pancreas tissues with a low weight, which indicates that the expression level of LncFAM was positively correlated with various growth phenotype indexes, such as growth speed and body weight. A polymorphism screening identified four polymorphisms with strong linkage disequilibrium in LncFAM: a 5-bp indel in the second exon, an A/G base mutation, and 7-bp and 97-bp indels in the second intron. A study of a 97-bp insertion in the second intron using an F2 chicken resource population produced by Anka and Gushi chickens showed that the mutant individuals with genotype II had the highest values for body weight (BW) at 0 days and 2, 4, 6, 8, 10 and 12 weeks, shank girth (SG) at 4, 8 and 12 weeks, chest width (CW) at 4, 8 and 12 weeks, body slant length (BSL) at 8 and 12 weeks, and pelvic width (PW) at 4, 8 and 12 weeks, followed by ID and DD genotypes. The amplification and typing of 2,716 chickens from ten different breeds, namely, the F2 chicken resource population, dual-type chickens, including Xichuan black-bone chickens, Lushi green-shell layers, Dongxiang green-shell layers, Changshun green-shell layers, and Gushi chickens, and commercial broilers, including Ross 308, AA, Cobb and Hubbard broilers, revealed that II was the dominant genotype. Interestingly, only genotype II existed among the tested populations of commercial broilers. Moreover, the expression level in the pancreas tissue of Ross 308 chickens was significantly higher than that in the pancreas tissue of Gushi chickens (P < 0.001), which might be related to the conversion rates among different chickens. The prediction and verification of the target gene of LncFAM showed that LncFAM might regulate the expression of its target gene FAM48A through cis-expression. Our results provide useful information on the mutation of LncFAM, which can be used as a potential molecular breeding marker.
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Affiliation(s)
- Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Zhenzhu Jing
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Yingying Cheng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangnan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou
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11
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Rizwan M, Liang P, Ali H, Li Z, Nie H, Ahmed Saqib HS, Fiaz S, Raza MF, Hassanyar AK, Niu Q, Su S. Population genomics of honey bees reveals a selection signature indispensable for royal jelly production. Mol Cell Probes 2020; 52:101542. [PMID: 32105702 DOI: 10.1016/j.mcp.2020.101542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 02/23/2020] [Accepted: 02/23/2020] [Indexed: 02/03/2023]
Abstract
In order to interpret the molecular mechanisms that modulating the organism variations and selection signatures to drive adaptive evolutionary changes are indispensable goals in the new evolutionary ecological genetics. Here, we identified the gene locus associated to royal jelly production through whole-genome sequencing of the DNA from eight populations of honeybees. The analysis of the samples was composed of 120 individuals and each pointed extremely opposite trait values for a given phenotype. We identified functional single nucleotide polymorphisms (SNPs) candidate that might be essential in regulating the phenotypic traits of honeybee populations. Moreover, selection signatures were investigated using pooling sequencing of eight distinct honeybee populations, and the results provided the evidence of signatures of recent selection among populations under different selection objectives. Furthermore, gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that selected genes were potentially involved in several biological processes and molecular functioning, which could directly or indirectly influence the production of royal jelly. Our findings can be used to understand the genomic signatures, as well as implicate a profound glance on genomic regions that control the production trait of royal jelly in honey bees.
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Affiliation(s)
- Muhammad Rizwan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361005, China
| | - Pingping Liang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Habib Ali
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiguo Li
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hongyi Nie
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hafiz Sohaib Ahmed Saqib
- Department of Plant Breeding and Genetics, University of Haripur, Khyber Pkhtunkhwa, Pakistan; Apiculture Science Institute of Jilin Province, Jilin, 132108, China
| | - Sajid Fiaz
- Department of Entomology, University of Agriculture Faisalabad, Depalpur Campus, Okara, Pakistan
| | - Muhammad Fahad Raza
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Aqai Kalan Hassanyar
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qingsheng Niu
- Apiculture Science Institute of Jilin Province, Jilin, 132108, China
| | - Songkun Su
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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12
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Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet 2019; 20:83. [PMID: 31694549 PMCID: PMC6836328 DOI: 10.1186/s12863-019-0783-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. RESULTS Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1-4, 6-7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. CONCLUSIONS The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
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Affiliation(s)
| | - Mirele Daiana Poleti
- University of São Paulo (USP) / College of Animal Science and Food Engineering (FZEA), Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - James M. Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Dorian J. Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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13
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Cho IC, Park HB, Ahn JS, Han SH, Lee JB, Lim HT, Yoo CK, Jung EJ, Kim DH, Sun WS, Ramayo-Caldas Y, Kim SG, Kang YJ, Kim YK, Shin HS, Seong PN, Hwang IS, Park BY, Hwang S, Lee SS, Ryu YC, Lee JH, Ko MS, Lee K, Andersson G, Pérez-Enciso M, Lee JW. A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs. PLoS Genet 2019; 15:e1008279. [PMID: 31603892 PMCID: PMC6788688 DOI: 10.1371/journal.pgen.1008279] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/01/2019] [Indexed: 11/18/2022] Open
Abstract
Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5'-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs.
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Affiliation(s)
- In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
- * E-mail: (I-CC); (J-WL)
| | - Hee-Bok Park
- Department of Animal Resources Science, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jin Seop Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Hyun-Tae Lim
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Eun-Ji Jung
- Bio-Medical Science Co., Ltd., Gimpo, Republic of Korea
| | - Dong-Hwan Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Wu-Sheng Sun
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yuliaxis Ramayo-Caldas
- Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Sang-Geum Kim
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Yong-Jun Kang
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Yoo-Kyung Kim
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Hyun-Sook Shin
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Pil-Nam Seong
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - In-Sul Hwang
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Beom-Young Park
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Seongsoo Hwang
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Sung-Soo Lee
- National Institute of Animal Science, Rural Development Administration, Namwon, Republic of Korea
| | - Youn-Chul Ryu
- Division of Biotechnology, SARI, Jeju National University, Jeju, Republic of Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Deajeon, Republic of Korea
| | - Moon-Suck Ko
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
- ICREA, Carrer de Lluís Companys, Barcelona, Spain
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (I-CC); (J-WL)
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14
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Abstract
Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species loaded into the same well. However, shift assays can access only a subset of reaction possibilities that could be otherwise seen if separate bands of reagent species might instead be collisionally reacted. Here, we adapt gel electrophoresis by fabricating two or more wells in the same lane, loading these wells with different reagent species, and applying an electric field, thereby producing collisional reactions between propagating pulse-like bands of these species, which we image optically. For certain pairs of anionic and cationic dyes, propagating bands pass through each other unperturbed; yet, for other pairs, we observe complexing and precipitation reactions, indicating strong attractive interactions. We generalize this band-collision gel electrophoresis (BCGE) approach to other reaction types, including acid-base, ligand exchange, and redox, as well as to colloidal species in passivated large-pore gels. Electrophoretic mobility shift assays are widely used in gel electrophoresis to study binding interactions between different molecular species, but these assays access only a subset of reaction possibilities. Here, the authors develop a band-collision gel electrophoresis (BCGE) approach that demonstrates a much wider variety of reaction types.
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15
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Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Pértille F, Ledur MC, Moura ASAMT, Garrick DJ, Coutinho LL. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. Sci Rep 2018; 8:16222. [PMID: 30385857 PMCID: PMC6212401 DOI: 10.1038/s41598-018-34364-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.
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Affiliation(s)
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
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16
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Li F, Han H, Lei Q, Gao J, Liu J, Liu W, Zhou Y, Li H, Cao D. Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology. J Appl Genet 2018; 59:305-312. [PMID: 29946990 DOI: 10.1007/s13353-018-0452-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022]
Abstract
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached "suggestive" genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.
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Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China. .,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China.
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17
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Analysis of single nucleotide polymorphisms variation associated with important economic and computed tomography measured traits in Texel sheep. Animal 2018; 12:915-922. [DOI: 10.1017/s1751731117002488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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18
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Weller JI, Ezra E, Ron M. Invited review: A perspective on the future of genomic selection in dairy cattle. J Dairy Sci 2017; 100:8633-8644. [PMID: 28843692 DOI: 10.3168/jds.2017-12879] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022]
Abstract
Genomic evaluation has been successfully implemented in the United States, Canada, Great Britain, Ireland, New Zealand, Australia, France, the Netherlands, Germany, and the Scandinavian countries. Adoption of this technology in the major dairy producing countries has led to significant changes in the worldwide dairy industry. Gradual elimination of the progeny test system has led to a reduction in the number of sires with daughter records and fewer genetic ties between years. As genotyping costs decrease, the number of cows genotyped will continue to increase, and these records will become the basic data used to compute genomic evaluations, most likely via application of "single-step" methodologies. Although genomic selection has been successful in increasing rates of genetic gain, we still know very little about the genetic architecture of quantitative variation. Apparently, a very large number of genes affect nearly all economic traits, in accordance with the infinitesimal model for quantitative traits. Less emphasis in selection goals will be placed on milk production traits, and more on health, reproduction, and efficiency traits and on environmentally friendly production with reduced waste and gas emission. Genetic variance for economic traits is maintained by the increase in frequency of rare alleles, new mutations, and changes in selection goals and management. Thus, it is unlikely that a selection plateau will be reached in the near future.
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Affiliation(s)
- J I Weller
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel.
| | - E Ezra
- Israeli Cattle Breeders Association, Caesarea Industrial Park 3088900, Israel
| | - M Ron
- Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
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19
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Genome-wide association study for sow lifetime productivity related traits in a Landrace purebred population. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Charlier C, Li W, Harland C, Littlejohn M, Coppieters W, Creagh F, Davis S, Druet T, Faux P, Guillaume F, Karim L, Keehan M, Kadri NK, Tamma N, Spelman R, Georges M. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res 2016; 26:1333-1341. [PMID: 27646536 PMCID: PMC5052051 DOI: 10.1101/gr.207076.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/19/2016] [Indexed: 01/20/2023]
Abstract
We herein report the result of a large-scale, next generation sequencing (NGS)-based screen for embryonic lethal (EL) mutations in Belgian beef and New Zealand dairy cattle. We estimated by simulation that cattle might carry, on average, ∼0.5 recessive EL mutations. We mined exome sequence data from >600 animals, and identified 1377 stop-gain, 3139 frame-shift, 1341 splice-site, 22,939 disruptive missense, 62,399 benign missense, and 92,163 synonymous variants. We show that cattle have a comparable load of loss-of-function (LoF) variants (defined as stop-gain, frame-shift, or splice-site variants) as humans despite having a more variable exome. We genotyped >40,000 animals for up to 296 LoF and 3483 disruptive missense, breed-specific variants. We identified candidate EL mutations based on the observation of a significant depletion in homozygotes. We estimated the proportion of EL mutations at 15% of tested LoF and 6% of tested disruptive missense variants. We confirmed the EL nature of nine candidate variants by genotyping 200 carrier × carrier trios, and demonstrating the absence of homozygous offspring. The nine identified EL mutations segregate at frequencies ranging from 1.2% to 6.6% in the studied populations and collectively account for the mortality of ∼0.6% of conceptuses. We show that EL mutations preferentially affect gene products fulfilling basic cellular functions. The resulting information will be useful to avoid at-risk matings, thereby improving fertility.
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Affiliation(s)
- Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Wanbo Li
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, P.R. China
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Mathew Littlejohn
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Wouter Coppieters
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Frances Creagh
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Steve Davis
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - François Guillaume
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Latifa Karim
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium; Genomics Platform, GIGA, University of Liège (B34), 4000-Liège, Belgium
| | - Mike Keehan
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Nico Tamma
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
| | - Richard Spelman
- Livestock Improvement Corporation, Newstead, Hamilton 3240, New Zealand
| | - Michel Georges
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège (B34), 4000-Liège, Belgium
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21
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Fine mapping QTL for resistance to VNN disease using a high-density linkage map in Asian seabass. Sci Rep 2016; 6:32122. [PMID: 27555039 PMCID: PMC4995370 DOI: 10.1038/srep32122] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/02/2016] [Indexed: 12/30/2022] Open
Abstract
Asian seabass has suffered from viral nervous necrosis (VNN) disease. Our previous study has mapped quantitative trait loci (QTL) for resistance to VNN disease. To fine map these QTL and identify causative genes, we identified 6425 single nucleotide polymorphisms (SNPs) from 85 dead and 94 surviving individuals. Combined with 155 microsatellites, we constructed a genetic map consisting of 24 linkage groups (LGs) containing 3000 markers, with an average interval of 1.27 cM. We mapped one significant and three suggestive QTL with phenotypic variation explained (PVE) of 8.3 to 11.0%, two significant and two suggestive QTL with PVE of 7.8 to 10.9%, for resistance in three LGs and survival time in four LGs, respectively. Further analysis one QTL with the largest effect identified protocadherin alpha-C 2-like (Pcdhac2) as the possible candidate gene. Association study in 43 families with 1127 individuals revealed a 6 bp insertion-deletion was significantly associated with disease resistance. qRT-PCR showed the expression of Pcdhac2 was significantly induced in the brain, muscle and skin after nervous necrosis virus (NNV) infection. Our results could facilitate marker-assisted selection (MAS) for resistance to NNV in Asian seabass and set up the basis for functional analysis of the potential causative gene for resistance.
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22
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Noce A, Pazzola M, Dettori ML, Amills M, Castelló A, Cecchinato A, Bittante G, Vacca GM. Variations at regulatory regions of the milk protein genes are associated with milk traits and coagulation properties in the Sarda sheep. Anim Genet 2016; 47:717-726. [PMID: 27435993 DOI: 10.1111/age.12474] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2016] [Indexed: 01/17/2023]
Abstract
Regulatory variation at the ovine casein genes could have important effects on the composition and coagulation properties of milk. Herewith, we have partially resequenced the promoters and the 3'-UTR of the four casein genes in 25 Sarda sheep. Alignment of these sequences allowed us to identify a total of 29 SNPs. This level of polymorphism (one SNP every 250 bp) is remarkably high if compared with SNP densities estimated in human genic regions (approximately one SNP per bp). The 29 SNPs identified in our resequencing experiment, plus three previously reported SNPs mapping to the lactalbumin, alpha (LALBA) and β-lactoglobulin (BLG, also known as progestagen-associated endometrial protein, PAEP) genes, were genotyped with a multiplex TaqMan Open Array Real-Time PCR assay in 760 Sarda sheep with records for milk composition and coagulation properties. Association analysis revealed the existence of significant associations of CSN1S2 and CSN3 genotypes with milk protein and casein contents. Moreover, genotypes at CSN1S1 were significantly associated with rennet coagulation time, curd firming time and curd firmness, whereas CSN2 was associated with curd firming time. These results suggest that SNPs mapping to the promoters and 3'-UTRs of ovine casein genes may exert regulatory effects on gene expression and that they could be used for improving sheep milk quality and technological traits at the population level through marker assisted selection.
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Affiliation(s)
- A Noce
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.,Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Pazzola
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy.
| | - M L Dettori
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - A Castelló
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - A Cecchinato
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - G Bittante
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - G M Vacca
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy
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23
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Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly. Sci Rep 2016; 6:27168. [PMID: 27255426 PMCID: PMC4891733 DOI: 10.1038/srep27168] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 05/13/2016] [Indexed: 01/14/2023] Open
Abstract
Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.
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24
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Yaro M, Munyard KA, Stear MJ, Groth DM. Combatting African Animal Trypanosomiasis (AAT) in livestock: The potential role of trypanotolerance. Vet Parasitol 2016; 225:43-52. [PMID: 27369574 DOI: 10.1016/j.vetpar.2016.05.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/29/2016] [Accepted: 05/01/2016] [Indexed: 01/09/2023]
Abstract
African Animal Trypanosomiasis (AAT) is endemic in at least 37 of the 54 countries in Africa. It is estimated to cause direct and indirect losses to the livestock production industry in excess of US$ 4.5 billion per annum. A century of intervention has yielded limited success, owing largely to the extraordinary complexity of the host-parasite interaction. Trypanotolerance, which refers to the inherent ability of some African livestock breeds, notably Djallonke sheep, N'Dama cattle and West African Dwarf goats, to withstand a trypanosomiasis challenge and still remain productive without any form of therapy, is an economically sustainable option for combatting this disease. Yet trypanotolerance has not been adequately exploited in the fight against AAT. In this review, we describe new insights into the genetic basis of trypanotolerance and discuss the potential of exploring this phenomenon as an integral part of the solution for AAT, particularly, in the context of African animal production systems.
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Affiliation(s)
- M Yaro
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - K A Munyard
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - M J Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow University, Garscube Estate, Bearsden Road, Glasgow G61 1QH, UK
| | - D M Groth
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
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25
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Liu P, Wang L, Wan ZY, Ye BQ, Huang S, Wong SM, Yue GH. Mapping QTL for Resistance Against Viral Nervous Necrosis Disease in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:107-116. [PMID: 26475147 DOI: 10.1007/s10126-015-9672-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
Viral nervous necrosis disease (VNN), caused by nervous necrosis virus (NNV), leads to mass mortality in mariculture. However, phenotypic selection for resistance against VNN is very difficult. To facilitate marker-assisted selection (MAS) for resistance against VNN and understanding of the genetic architecture underlying the resistance against this disease, we mapped quantitative trait loci (QTL) for resistance against VNN in Asian seabass. We challenged fingerlings at 37 days post-hatching (dph), from a single back-cross family, with NNV at a concentration of 9 × 10(6) TCID50/ml for 2 h. Daily mortalities were recorded and collected. A panel of 330 mortalities and 190 surviving fingerlings was genotyped using 149 microsatellites with 145 successfully mapped markers covering 24 linkage groups (LGs). Analysis of QTL for both resistance against VNN and survival time was conducted using interval mapping. Five significant QTL located in four LGs and eight suggestive QTL in seven LGs were identified for resistance. Another five significant QTL in three LGs and five suggestive QTL in three LGs were detected for survival time. One significant QTL, spanning 3 cM in LG20, was identified for both resistance and survival time. These QTL explained 2.2-4.1% of the phenotypic variance for resistance and 2.2-3.3% of the phenotypic variance for survival time, respectively. Our results suggest that VNN resistance in Asian seabass is controlled by many loci with small effects. Our data provide information for fine mapping of QTL and identification of candidate genes for a better understanding of the mechanism of disease resistance.
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26
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Targeted Exome Sequencing of Deafness Genes After Failure of Auditory Phenotype-Driven Candidate Gene Screening. Otol Neurotol 2016; 36:1096-102. [PMID: 25830873 DOI: 10.1097/mao.0000000000000747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To demonstrate the efficacy and advantages of targeted exome sequencing (TES) of known deafness genes in cases with failed or misleading auditory phenotype-driven candidate gene screening. STUDY DESIGN Prospective cohort survey. SETTING Otolaryngology department of a tertiary referral hospital. PATIENTS Six hearing-impaired probands with seemingly non-syndromic features from six deaf families were enrolled in this study after failure of genetic diagnosis using auditory phenotype-driven candidate gene screening. INTERVENTION TES of known deafness genes was performed in the six probands, and a final causative variant was pursued using subsequent filtering steps. MAIN OUTCOME MEASURE Potential causative variants determined using TES were confirmed by previously introduced filtering steps. RESULTS We detected causative variants in three (50%) of six families, and these variants were in the COCH, PAX3, and GJB2 genes. Additionally, we also recapitulated the recent finding from other report arguing for the non-pathogenic potential of MYO1A variant. CONCLUSIONS TES of a deafness panel provides a comprehensive genetic screening tool that can be implemented without being misled by the audiogram configuration information and can complement incomplete clinical physical examinations. In addition, the secondary incidental finding obtained by TES contributes useful information regarding the deafness field.
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27
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Shin D, Lee C, Park KD, Kim H, Cho KH. Genome-association analysis of Korean Holstein milk traits using genomic estimated breeding value. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 30:309-319. [PMID: 26954162 PMCID: PMC5337909 DOI: 10.5713/ajas.15.0608] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 08/31/2015] [Accepted: 10/03/2015] [Indexed: 01/29/2023]
Abstract
Objective Holsteins are known as the world’s highest-milk producing dairy cattle. The purpose of this study was to identify genetic regions strongly associated with milk traits (milk production, fat, and protein) using Korean Holstein data. Methods This study was performed using single nucleotide polymorphism (SNP) chip data (Illumina BovineSNP50 Beadchip) of 911 Korean Holstein individuals. We inferred each genomic estimated breeding values based on best linear unbiased prediction (BLUP) and ridge regression using BLUPF90 and R. We then performed a genome-wide association study and identified genetic regions related to milk traits. Results We identified 9, 6, and 17 significant genetic regions related to milk production, fat and protein, respectively. These genes are newly reported in the genetic association with milk traits of Holstein. Conclusion This study complements a recent Holstein genome-wide association studies that identified other SNPs and genes as the most significant variants. These results will help to expand the knowledge of the polygenic nature of milk production in Holsteins.
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Affiliation(s)
- Donghyun Shin
- Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | - Chul Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-921, Korea
| | - Kyoung-Do Park
- The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju 561-756, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-921, Korea
| | - Kwang-Hyeon Cho
- Division of Animal Breeding and Genetics, National Institute of Animal Science, Rural Development Administration, Cheonan 331-801, Korea
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28
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Wu X, Lund MS, Sahana G, Guldbrandtsen B, Sun D, Zhang Q, Su G. Association analysis for udder health based on SNP-panel and sequence data in Danish Holsteins. Genet Sel Evol 2015; 47:50. [PMID: 26087655 PMCID: PMC4472403 DOI: 10.1186/s12711-015-0129-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 05/21/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The sensitivity of genome-wide association studies for the detection of quantitative trait loci (QTL) depends on the density of markers examined and the statistical models used. This study compares the performance of three marker densities to refine six previously detected QTL regions for mastitis traits: 54 k markers of a medium-density SNP (single nucleotide polymorphism) chip (MD), imputed 777 k markers of a high-density SNP chip (HD), and imputed whole-genome sequencing data (SEQ). Each dataset contained data for 4496 Danish Holstein cattle. Comparisons were performed using a linear mixed model (LM) and a Bayesian variable selection model (BVS). RESULTS After quality control, 587, 7825, and 78 856 SNPs in the six targeted regions remained for MD, HD, and SEQ data, respectively. In general, the association patterns between SNPs and traits were similar for the three marker densities when tested using the same statistical model. With the LM model, 120 (MD), 967 (HD), and 7209 (SEQ) SNPs were significantly associated with mastitis, whereas with the BVS model, 43 (MD), 131 (HD), and 1052 (SEQ) significant SNPs (Bayes factor > 3.2) were observed. A total of 26 (MD), 75 (HD), and 465 (SEQ) significant SNPs were identified by both models. In addition, one, 16, and 33 QTL peaks for MD, HD, and SEQ data were detected according to the QTL intensity profile of SNP bins by post-analysis of the BVS model. CONCLUSIONS The power to detect significant associations increased with increasing marker density. The BVS model resulted in clearer boundaries between linked QTL than the LM model. Using SEQ data, the six targeted regions were refined to 33 candidate QTL regions for udder health. The comparison between these candidate QTL regions and known genes suggested that NPFFR2, SLC4A4, DCK, LIFR, and EDN3 may be considered as candidate genes for mastitis susceptibility.
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Affiliation(s)
- Xiaoping Wu
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark. .,Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Mogens S Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
| | - Dongxiao Sun
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Qin Zhang
- Key Laboratory of Animal Genetics and Breeding of Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, DK-8830, Tjele, Denmark.
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29
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Upadhyay MR, Patel AB, Subramanian RB, Shah TM, Jakhesara SJ, Bhatt VD, Koringa PG, Rank DN, Joshi CG. Single nucleotide variant detection in Jaffrabadi buffalo (Bubalus bubalis) using high-throughput targeted sequencing. FRONTIERS IN LIFE SCIENCE 2015. [DOI: 10.1080/21553769.2015.1031915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Yi G, Qu L, Chen S, Xu G, Yang N. Genome-wide copy number profiling using high-density SNP array in chickens. Anim Genet 2015; 46:148-57. [PMID: 25662183 DOI: 10.1111/age.12267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2014] [Indexed: 01/04/2023]
Abstract
Phenotypic diversity is a direct consequence resulting mainly from the impact of underlying genetic variation, and recent studies have shown that copy number variation (CNV) is emerging as an important contributor to both phenotypic variability and disease susceptibility. Herein, we performed a genome-wide CNV scan in 96 chickens from 12 diversified breeds, benefiting from the high-density Affymetrix 600 K SNP arrays. We identified a total of 231 autosomal CNV regions (CNVRs) encompassing 5.41 Mb of the chicken genome and corresponding to 0.59% of the autosomal sequence. The length of these CNVRs ranged from 2.6 to 586.2 kb with an average of 23.4 kb, including 130 gain, 93 loss and eight both gain and loss events. These CNVRs, especially deletions, had lower GC content and were located particularly in gene deserts. In particular, 102 CNVRs harbored 128 chicken genes, most of which were enriched in immune responses. We obtained 221 autosomal CNVRs after converting probe coordinates to Galgal3, and comparative analysis with previous studies illustrated that 153 of these CNVRs were regarded as novel events. Furthermore, qPCR assays were designed for 11 novel CNVRs, and eight (72.73%) were validated successfully. In this study, we demonstrated that the high-density 600 K SNP array can capture CNVs with higher efficiency and accuracy and highlighted the necessity of integrating multiple technologies and algorithms. Our findings provide a pioneering exploration of chicken CNVs based on a high-density SNP array, which contributes to a more comprehensive understanding of genetic variation in the chicken genome and is beneficial to unearthing potential CNVs underlying important traits of chickens.
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Affiliation(s)
- G Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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31
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Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation. G3-GENES GENOMES GENETICS 2015; 5:517-29. [PMID: 25653314 PMCID: PMC4390568 DOI: 10.1534/g3.115.016865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.
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Ma J, Yang J, Zhou L, Ren J, Liu X, Zhang H, Yang B, Zhang Z, Ma H, Xie X, Xing Y, Guo Y, Huang L. A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. PLoS Genet 2014; 10:e1004710. [PMID: 25340394 PMCID: PMC4207639 DOI: 10.1371/journal.pgen.1004710] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/26/2014] [Indexed: 11/19/2022] Open
Abstract
Glycolytic potential (GP) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield. We have previously mapped a major quantitative trait loci (QTL) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross. We herein performed a systems genetic analysis to identify the causal variant underlying the phenotype QTL (pQTL). We first conducted genome-wide association analyses in the F2 intercross and an F19 Sutai pig population. The QTL was then refined to an 180-kb interval based on the 2-LOD drop method. We then performed expression QTL (eQTL) mapping using muscle transcriptome data from 497 F2 animals. Within the QTL interval, only one gene (PHKG1) has a cis-eQTL that was colocolizated with pQTL peaked at the same SNP. The PHKG1 gene encodes a catalytic subunit of the phosphorylase kinase (PhK), which functions in the cascade activation of glycogen breakdown. Deep sequencing of PHKG1 revealed a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon. The aberrant transcript induces nonsense-mediated decay, leading to lower protein level and weaker enzymatic activity in affected animals. The mutation causes an increase of 43% in GP and a decrease of>20% in water-holding capacity of pork. These effects were consistent across the F2 and Sutai populations, as well as Duroc × (Landrace × Yorkshire) hybrid pigs. The unfavorable allele exists predominantly in Duroc-derived pigs. The findings provide new insights into understanding risk factors affecting glucose metabolism, and would greatly contribute to the genetic improvement of meat quality in Duroc related pigs. Glycogen storage diseases (GSD) are a group of inherited disorders characterized by storage of excess glycogen, which are mainly caused by the abnormality of a particular enzyme essential for releasing glucose from glycogen. GSD-like conditions have been described in a wide variety of species. Pigs are a valuable model for the study of human GSD. Moreover, pigs affected by GSD usually produce inferior pork with a lower ultimate pH (so-called “acid meat”) and less processing yield due to post-mortem degradation of the excess glycogen. So far, only one causal variant, PRKAG3 R225Q, has been identified for GSD in pigs. Here we reported a loss-of-function mutation in the PHKG1 gene that causes the deficiency of the glycogen breakdown, consequently leading to GSD and acid meat in Duroc-sired pigs. Eliminating the undesirable mutation from the breeding stock by a diagnostic DNA test will greatly reduce the incidence of GSD and significantly improve pork quality and productivity in the pig.
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Affiliation(s)
- Junwu Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
- * E-mail: (JM); (LH)
| | - Jie Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lisheng Zhou
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Xianxian Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Hui Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Huanban Ma
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Xianhua Xie
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Yuyun Xing
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Yuanmei Guo
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, P.R. China
- * E-mail: (JM); (LH)
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Roux PF, Boutin M, Désert C, Djari A, Esquerré D, Klopp C, Lagarrigue S, Demeure O. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken. PLoS One 2014; 9:e111299. [PMID: 25333370 PMCID: PMC4205046 DOI: 10.1371/journal.pone.0111299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/22/2014] [Indexed: 12/30/2022] Open
Abstract
In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.
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Affiliation(s)
- Pierre-François Roux
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Morgane Boutin
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Colette Désert
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | | | - Diane Esquerré
- INRA, UMR1388 GenPhySE, GeT-PlaGe, Castanet-Tolosan, France
| | | | - Sandrine Lagarrigue
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Olivier Demeure
- INRA, UMR1348 PEGASE, Saint-Gilles, France
- Agrocampus Ouest, UMR1348 PEGASE, Rennes, France
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Stern DL. Identification of loci that cause phenotypic variation in diverse species with the reciprocal hemizygosity test. Trends Genet 2014; 30:547-54. [PMID: 25278102 DOI: 10.1016/j.tig.2014.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 12/18/2022]
Abstract
The reciprocal hemizygosity test is a straightforward genetic test that can positively identify genes that have evolved to contribute to a phenotypic difference between strains or between species. The test involves a comparison between hybrids that are genetically identical throughout the genome except at the test locus, which is rendered hemizygous for alternative alleles from the two parental strains. If the two reciprocal hemizygotes display different phenotypes, then the two parental alleles must have evolved. New methods for targeted mutagenesis will allow application of the reciprocal hemizygosity test in many organisms. This review discusses the principles, advantages, and limitations of the test.
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Affiliation(s)
- David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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Wang Z, Zhang H, Yang H, Wang S, Rong E, Pei W, Li H, Wang N. Genome-wide association study for wool production traits in a Chinese Merino sheep population. PLoS One 2014; 9:e107101. [PMID: 25268383 PMCID: PMC4182092 DOI: 10.1371/journal.pone.0107101] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 08/14/2014] [Indexed: 01/01/2023] Open
Abstract
Genome-wide association studies (GWAS) provide a powerful approach for identifying quantitative trait loci without prior knowledge of location or function. To identify loci associated with wool production traits, we performed a genome-wide association study on a total of 765 Chinese Merino sheep (JunKen type) genotyped with 50 K single nucleotide polymorphisms (SNPs). In the present study, five wool production traits were examined: fiber diameter, fiber diameter coefficient of variation, fineness dispersion, staple length and crimp. We detected 28 genome-wide significant SNPs for fiber diameter, fiber diameter coefficient of variation, fineness dispersion, and crimp trait in the Chinese Merino sheep. About 43% of the significant SNP markers were located within known or predicted genes, including YWHAZ, KRTCAP3, TSPEAR, PIK3R4, KIF16B, PTPN3, GPRC5A, DDX47, TCF9, TPTE2, EPHA5 and NBEA genes. Our results not only confirm the results of previous reports, but also provide a suite of novel SNP markers and candidate genes associated with wool traits. Our findings will be useful for exploring the genetic control of wool traits in sheep.
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Affiliation(s)
- Zhipeng Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hui Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, P.R. China
| | - Shouzhi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Enguang Rong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Wenyu Pei
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
| | - Hui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
- * E-mail: (NW); (HL)
| | - Ning Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang province, Harbin, P. R. China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, P. R. China
- * E-mail: (NW); (HL)
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The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/904281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.
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Turkheimer FE, Bodini B, Politis M, Pariante CM, Ciccarelli O, Yeo RA. The X-Linked Hypothesis of Brain Disorders. Neuroscientist 2014; 21:589-98. [DOI: 10.1177/1073858414545999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this article, we propose an X-linked hypothesis of brain disorders that postulates a neuronal origin of those neurodegenerative and psychiatric disorders with a greater male prevalence. The hypothesis is based on the accumulated genetics and genomic evidence linking X chromosome genes and transcripts to neuronal cells. The behavioral genetics literature has long pointed to the link between postsynaptic protein complexes coded on chromosome X and mental retardation. More recently, novel genomic evidence has emerged of X-linked mRNA overexpression of neuronal source in the human brain. We review the evidence for this hypothesis and its consistency with the distribution across genders of brain disorders of known aetiology. We then provide examples of the utilization of this hypothesis in the investigation of the pathophysiology of complex brain disorders in both the stratification of disease cohorts and the development of realistic preclinical models. We conclude by providing a general framework for testing its validity, which will be exploited in future studies, and provide future directions for research.
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Affiliation(s)
| | - Benedetta Bodini
- Institute of Psychiatry, King’s College London, UK
- Institut du Cerveau et de la Moelle épinière, Hôpital Pitié-Salpêtrière, UPMC, Paris, France
| | - Marios Politis
- Department of Clinical Neuroscience, King’s College London, UK
| | | | | | - Ronald A. Yeo
- Department of Psychology, University of New Mexico, Albuquerque, NM, USA
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Effect of polymorphisms in the CSN3 (κ-casein) gene on milk production traits in Chinese Holstein Cattle. Mol Biol Rep 2014; 41:7585-93. [DOI: 10.1007/s11033-014-3648-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/27/2014] [Indexed: 02/07/2023]
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40
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Kadarmideen HN. Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Yamada T. Genetic dissection of marbling trait through integration of mapping and expression profiling. Anim Sci J 2014; 85:349-55. [DOI: 10.1111/asj.12179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/19/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture; Niigata University; Niigata Japan
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Masopust M, Weisz F, Bartenschlager H, Knoll A, Vykoukalová Z, Geldermann H, Cepica S. Porcine ubiquitin-like 5 (UBL5) gene: genomic organization, polymorphisms, mRNA cloning, splicing variants and association study. Mol Biol Rep 2014; 41:2353-62. [PMID: 24458823 DOI: 10.1007/s11033-014-3089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
Ubiquitin-like 5 (UBL5), which is supposed to be involved in regulation of feed intake, energy metabolism, obesity and type 2 diabetes, is located at position 62.1 cM on the pig chromosome 2 region harbouring quantitative trait loci for carcass and meat quality. The 4,354 bp genomic sequence (FR798948) of the porcine gene encompassing the promoter and entire gene was cloned by polymerase chain reaction. Comparative sequencing revealed 13 polymorphisms in noncoding regions. Synthesis of full-length cDNA sequences using rapid amplification of 5' and 3' ends showed three splice variants. Variants 1 and 2 differ in transcription length for the untranslated part of exon 1 with deduced protein of 73 amino acid (aa) residues and 100 % identities between human, mouse and other species. Variant 3, with 4 bp deletion at the 3' end of exon 2, encodes a truncated protein with 28 aa residues. In a Wild boar×Meishan F2 population (n = 334) with 47 recorded traits, loci FR798948:g.2788G>A and FR798948:g.2141T>C were associated at nominal P < 0.05 with fat deposition, growth and fattening and muscling but after adjustment for multiple testing (Benjamini and Hochberg, J R Stat Soc B 57:289-300, 1995) only eight fat deposition traits showed suggestive association with FR798948:g.2788G>A at adjusted P < 0.10. In a Meishan×Large White (MLW) cross (n = 562) with six trait records available, FR798948:g.2141T>C showed suggestive association with growth (adjusted P = 0.0690). As association mapping conducted in the outbred MLW population is more precise than in the three generation F2 population the UBL5 gene tends to be associated with growth rather than with fat accretion.
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Affiliation(s)
- Martin Masopust
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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Fan WL, Ng CS, Chen CF, Lu MYJ, Chen YH, Liu CJ, Wu SM, Chen CK, Chen JJ, Mao CT, Lai YT, Lo WS, Chang WH, Li WH. Genome-wide patterns of genetic variation in two domestic chickens. Genome Biol Evol 2013; 5:1376-92. [PMID: 23814129 PMCID: PMC3730349 DOI: 10.1093/gbe/evt097] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ∼23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ∼7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
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Affiliation(s)
- Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Ferreira AM, Bislev SL, Bendixen E, Almeida AM. The mammary gland in domestic ruminants: a systems biology perspective. J Proteomics 2013; 94:110-23. [PMID: 24076120 DOI: 10.1016/j.jprot.2013.09.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/04/2013] [Accepted: 09/17/2013] [Indexed: 11/16/2022]
Abstract
UNLABELLED Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. BIOLOGICAL SIGNIFICANCE Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance.
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Affiliation(s)
- Ana M Ferreira
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal; BCV Laboratory, Instituto de Tecnologia Química e Biológica/Universidade Nova de Lisboa (ITQB/UNL), Oeiras, Portugal
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Duan Y, Brenig B, Wu X, Ren J, Huang L. The G32E functional variant reduces activity of PPARD by nuclear export and post-translational modification in pigs. PLoS One 2013; 8:e75925. [PMID: 24058710 PMCID: PMC3776753 DOI: 10.1371/journal.pone.0075925] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/22/2013] [Indexed: 01/25/2023] Open
Abstract
Peroxisome proliferator-activated receptor beta/delta (PPARD) is a crucial and multifaceted determinant of diverse biological functions including lipid metabolism, embryonic development, inflammatory response, wound healing and cancer. Recently, we proposed a novel function of porcine PPARD (sPPARD) in external ear development. A missense mutation (G32E) in an evolutionary conservative domain of sPPARD remarkably increases external ear size in pigs. Here, we investigated the underlying molecular mechanism of the causal mutation at the cellular level. Using a luciferase reporter system, we showed that the G32E substitution reduced transcription activity of sPPARD in a ligand-dependent manner. By comparison of the subcellular localization of wild-type and mutated sPPARD in both PK-15 cells and pinna cartilage-derived primary chondrocytes, we found that the G32E substitution promoted CRM-1 mediated nuclear exportation of sPPARD. With the surface plasmon resonance technology, we further revealed that the G32E substitution had negligible effect on its ligand binding affinity. Finally, we used co-immunoprecipitation and luciferase reporter assays to show that the G32E substitution greatly reduced ubiquitination level by blocking ubiquitination of the crucial A/B domain and consequently decreased transcription activity of sPPARD. Taken together, our findings strongly support that G32E is a functional variant that plays a key role in biological activity of sPPARD, which advances our understanding of the underlying mechanism of sPPARD G32E for ear size in pigs.
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Affiliation(s)
- Yanyu Duan
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China
- Institute of Veterinary Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Xiaohui Wu
- Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China
- * E-mail: (JR); (LH)
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China
- * E-mail: (JR); (LH)
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Garcia-Gámez E, Gutiérrez-Gil B, Suarez-Vega A, de la Fuente LF, Arranz JJ. Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches. J Dairy Sci 2013; 96:6059-69. [PMID: 23810588 DOI: 10.3168/jds.2013-6824] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/22/2013] [Indexed: 12/20/2022]
Abstract
In this study, 2 procedures were used to analyze a data set from a whole-genome scan, one based on linkage analysis information and the other combing linkage disequilibrium and linkage analysis (LDLA), to determine the quantitative trait loci (QTL) influencing milk production traits in sheep. A total of 1,696 animals from 16 half-sib families were genotyped using the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) and analysis was performed using a daughter design. Moreover, the same data set has been previously investigated through a genome-wide association (GWA) analysis and a comparison of results from the 3 methods has been possible. The linkage analysis and LDLA methodologies yielded different results, although some significantly associated regions were common to both procedures. The linkage analysis detected 3 overlapping genome-wise significant QTL on sheep chromosome (OAR) 2 influencing milk yield, protein yield, and fat yield, whereas 34 genome-wise significant QTL regions were detected using the LDLA approach. The most significant QTL for protein and fat percentages was detected on OAR3, which was reported in a previous GWA analysis. Both the linkage analysis and LDLA identified many other chromosome-wise significant associations across different sheep autosomes. Additional analyses were performed on OAR2 and OAR3 to determine the possible causality of the most significant polymorphisms identified for these genetic effects by the previously reported GWA analysis. For OAR3, the analyses demonstrated additional genetic proof of the causality previously suggested by our group for a single nucleotide polymorphism located in the α-lactalbumin gene (LALBA). In summary, although the results shown here suggest that in commercial dairy populations, the LDLA method exhibits a higher efficiency to map QTL than the simple linkage analysis or linkage disequilibrium methods, we believe that comparing the 3 analysis methods is the best approach to obtain a global picture of all identifiable QTL segregating in the population at both family-based and population-based levels.
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Affiliation(s)
- E Garcia-Gámez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, 24071 León, Spain
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Cepica S, Zambonelli P, Weisz F, Bigi M, Knoll A, Vykoukalová Z, Masopust M, Gallo M, Buttazzoni L, Davoli R. Association mapping of quantitative trait loci for carcass and meat quality traits at the central part of chromosome 2 in Italian Large White pigs. Meat Sci 2013; 95:368-75. [PMID: 23747631 DOI: 10.1016/j.meatsci.2013.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/24/2013] [Accepted: 05/01/2013] [Indexed: 01/13/2023]
Abstract
Association mapping of the central part of porcine chromosome 2 harboring QTLs for carcass and meat quality traits was performed with 17 gene-tagged SNPs located between 44.0 and 77.5 Mb on a physical map (Sscrofa10.2) in Italian Large White pigs. For the analyzed animals records of estimated breeding values for average daily gain, back fat thickness, lean cuts, ham weight, feed conversion ratio, pH1, pHu, CIE L*, CIE a*, CIE b* and drip loss were available. A significant QTL for fat deposition (adjusted P=0.0081) and pH1 (adjusted P=0.0972) to MYOD1 at position 44.4 Mb and a QTL for growth and meatiness (adjusted P=0.0238-0.0601) to UBL5 at position 68.9 Mb were mapped. These results from association mapping are much more accurate than those from linkage mapping and facilitate further search for position candidate genes and causative mutations needed for application of markers through marker assisted selection.
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Affiliation(s)
- S Cepica
- Institute of Animal Physiology and Genetics, The Academy of Sciences of the Czech Republic, Liběchov, Czech Republic.
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48
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Abstract
The analysis of complex genetic traits, including mapping and identification of causative genes, has long been an enigma of genetic biology, whether in the animal sciences or in medical sciences. Traits of agricultural interest and traits of medical interest are often under the influence of both environmental factors and multiple genes, each with modest contributions to the total variance in the trait. Although the number of known mutations underlying complex traits is still relatively small, advances in genomics have greatly enhanced traditional pathways to their analysis and gene mining. The candidate gene approach, linkage analysis, and association studies are all significantly more powerful with recent advances in genome mapping, sequencing, and analysis of individual variation. Avenues to gene discovery are discussed with emphasis on genome wide association studies (GWAS) and the use of single nucleotide polymorphisms (SNPs) as revealed by increasingly powerful commercially available microarrays.
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Affiliation(s)
- James E Womack
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
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Effect of a Single-Nucleotide Polymorphism in the Cholecystokinin Type A Receptor Gene on Growth Traits in the Hinai-dori Chicken Breed. J Poult Sci 2013. [DOI: 10.2141/jpsa.0120130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Peters SO, Kizilkaya K, Garrick DJ, Fernando RL, Reecy JM, Weaber RL, Silver GA, Thomas MG. Bayesian genome-wide association analysis of growth and yearling ultrasound measures of carcass traits in Brangus heifers1. J Anim Sci 2012. [DOI: 10.2527/jas.2011-4507] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- S. O. Peters
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces 88003
- Department of Animal Sciences, University of Missouri, Columbia 65211
| | - K. Kizilkaya
- Department of Animal Science, Iowa State University, Ames 50011
- Department of Animal Science, Adnan Menderes University, Aydin 09100, Turkey
| | - D. J. Garrick
- Department of Animal Science, Iowa State University, Ames 50011
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - R. L. Fernando
- Department of Animal Science, Iowa State University, Ames 50011
| | - J. M. Reecy
- Department of Animal Science, Iowa State University, Ames 50011
| | - R. L. Weaber
- Department of Animal Sciences, University of Missouri, Columbia 65211
| | - G. A. Silver
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces 88003
| | - M. G. Thomas
- Department of Animal and Range Sciences, New Mexico State University, Las Cruces 88003
- Department of Animal Sciences, Colorado State University, Fort Collins 80523
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