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Yang X, Deng F, Wu Z, Chen SY, Shi Y, Jia X, Hu S, Wang J, Cao W, Lai SJ. A Genome-Wide Association Study Identifying Genetic Variants Associated with Growth, Carcass and Meat Quality Traits in Rabbits. Animals (Basel) 2020; 10:ani10061068. [PMID: 32575740 PMCID: PMC7341332 DOI: 10.3390/ani10061068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/13/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Rabbit meat has been widely consumed in China and is considered as an ideal food source due to its high protein, low fat, low cholesterol and low sodium contents. The growth rate, carcass characteristics and meat quality are considered economically important traits in the rabbit industry. Genomic selection (GS) could facilitate genetic selection for important economic traits, however, the lack of molecular markers for these traits limits the application of GS in rabbits. Genome-wide association study (GWAS) has the potential to comprehensively identify trait-associated molecular markers and has been applied in animal and plant research. In this study, GWAS was used to examine growth, carcass and meat quality traits of meat rabbits based on specific-locus amplified fragment sequencing (SLAF-seq) technology to identify significantly associated SNPs and functional genes, to be used as a basis for prompting the application of GS in rabbits. Abstract Growth, carcass characteristics and meat quality are the most important traits used in the rabbit industry. Identification of the candidate markers and genes significantly associated with these traits will be beneficial in rabbit breeding. In this study, we enrolled 465 rabbits, including 16 male Californian rabbits and 17 female Kangda5 line rabbits as the parental generation, along with their offspring (232 male and 200 female), in a genome-wide association study (GWAS) based on SLAF-seq technology. Bodyweight at 35, 42, 49, 56, 63 and 70 d was recorded for growth traits; and slaughter liveweight (84 d) and dressing out percentage were measured as carcass traits; and cooking loss and drip loss were measured as meat quality traits. A total of 5,223,720 SLAF markers were obtained by digesting the rabbit genome using RsaI + EcoRV-HF® restriction enzymes. After quality control, a subset of 317,503 annotated single-nucleotide polymorphisms (SNPs) was retained for subsequent analysis. A total of 28, 81 and 10 SNPs for growth, carcass and meat quality traits, respectively, were identified based on genome-wide significance (p < 3.16 × 10−7). Additionally, 16, 71 and 9 candidate genes were identified within 100 kb upstream or downstream of these SNPs. Further analysis is required to determine the biological roles of these candidate genes in determining rabbit growth, carcass traits and meat quality.
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Affiliation(s)
- Xue Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Feilong Deng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
- Special Key Laboratory of Microbial Resources and Drug Development, Research Center for Medicine and Biology, Zunyi Medical University, Zunyi 563000, China
| | - Zhoulin Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Shi-Yi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Wei Cao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
| | - Song-Jia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; (X.Y.); (F.D.); (Z.W.); (S.-Y.C.); (Y.S.); (X.J.); (S.H.); (J.W.); (W.C.)
- Correspondence:
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Deng MT, Zhu F, Yang YZ, Yang FX, Hao JP, Chen SR, Hou ZC. Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks. BMC Genomics 2019; 20:1. [PMID: 30606130 PMCID: PMC6318962 DOI: 10.1186/s12864-018-5379-1] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/16/2018] [Indexed: 12/26/2022] Open
Abstract
Background Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. Results We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study. Conclusions The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks. Electronic supplementary material The online version of this article (10.1186/s12864-018-5379-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Meng-Ting Deng
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, Beijing, 100107, China
| | - Fang-Xi Yang
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Jin-Ping Hao
- Beijing Golden Star Duck Co., LTD, Beijing, 100076, China
| | - Si-Rui Chen
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and MARA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China.
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Sun F, Tu R, Xia JH, Liu XJ, Yue GH. The FTO Gene Is Associated with Growth and Omega-3/-6 Ratio in Asian Seabass. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:603-610. [PMID: 29766417 DOI: 10.1007/s10126-018-9831-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/29/2018] [Indexed: 06/08/2023]
Abstract
Polymorphisms in the FTO gene are associated with obesity and body mass index in humans and livestock. Little information of whether FTO plays an important role in aquaculture fish species is available. We cloned and characterized the FTO gene in an economically important food fish species: Asian seabass (Lates calcarifer). The full-length cDNA of the gene is 3679 bp, containing an ORF of 1935 bp encoding 644 amino acids, a 216 bp 5' UTR and a 1538 bp 3' UTR. The gene consisted of nine exons and eight introns and was 117,679 bp in length. Phylogenetic analysis revealed that the gene in Asian seabass was closely related to those of Japanese flounder and Nile tilapia. Analysis of its expressions using qRT-PCR showed that it was expressed ubiquitously, but was higher in the liver, stomach and intestine. Comparative analysis of the genomic sequences of part of intron 1 of the gene among 10 unrelated individuals identified two SNPs. Analysis of associations between SNPs and traits (i.e. growth, oil content, omega-3 and -6 contents) in an F2 family demonstrated that the two SNPs were significantly associated with growth, oil content, omega-3 content and omega-3/-6 ratio. Altogether, our data suggest that the gene or/and its linked genes play an important role in growth and fatty acid synthesis, and that the SNPs associated with traits may be used as markers for selecting quicker growth and higher omega-3/-6 ratio at the fingerling stage.
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Affiliation(s)
- Fei Sun
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
| | - Rongjian Tu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jun Hong Xia
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Jun Liu
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
- School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore.
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Ma GW, Chu YK, Zhang WJ, Qin FY, Xu SS, Yang H, Rong EG, Du ZQ, Wang SZ, Li H, Wang N. Polymorphisms of FST gene and their association with wool quality traits in Chinese Merino sheep. PLoS One 2017; 12:e0174868. [PMID: 28384189 PMCID: PMC5383234 DOI: 10.1371/journal.pone.0174868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 03/16/2017] [Indexed: 11/19/2022] Open
Abstract
Follistatin (FST) is involved in hair follicle morphogenesis. However, its effects on hair traits are not clear. This study was designed to investigate the effects of FST gene single nucleotide polymorphisms (SNP) on wool quality traits in Chinese Merino sheep (Junken Type). We performed gene expression analysis, SNP detection, and association analysis of FST gene with sheep wool quality traits. The real-time RT-PCR analysis showed that FST gene was differentially expressed in adult skin between Chinese Merino sheep (Junken Type) and Suffolk sheep. Immunostaining showed that FST was localized in inner root sheath (IRS) and matrix of hair follicle (HF) in both SF and Suffolk sheep. Sequencing analysis identified a total of seven SNPs (termed SNPs 1-7) in the FST gene in Chinese Merino sheep (Junken Type). Association analysis showed that SNP2 (Chr 16. 25,633,662 G>A) was significantly associated with average wool fiber diameter, wool fineness SD, and wool crimp (P < 0.05). SNP4 (Chr 16. 25,633,569 C>T) was significantly associated with wool fineness SD and CV of fiber diameter (P < 0.05). Similarly, the haplotypes derived from these seven identified SNPs were also significantly associated with average wool fiber diameter, wool fineness SD, CV of fiber diameter, and wool crimp (P < 0.05). Our results suggest that FST influences wool quality traits and its SNPs 2 and 4 might be useful markers for marker-assisted selection and sheep breeding.
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Affiliation(s)
- Guang-Wei Ma
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Yan-Kai Chu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Wen-Jian Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Fei-Yue Qin
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Song-Song Xu
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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 Medicine, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, P. R. China
| | - En-Guang Rong
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, P. R. China
| | - Zhi-Qiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Shou-Zhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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 Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, Harbin, P. R. China
- 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:
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