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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Meng W, Chan BW, Ezeonwumelu C, Hébert HL, Campbell A, Soler V, Palmer CN. A genome-wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity. Ophthalmic Genet 2019; 40:252-258. [PMID: 31264924 DOI: 10.1080/13816810.2019.1633549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Background: Diabetic maculopathy is a form of diabetic retinopathy. The visual acuity of one third of patients with diabetic maculopathy will be affected. The purpose of this study was to identify genetic contributors of diabetic maculopathy with decreased visual acuity based on a genome-wide association approach using a well-defined Scottish diabetic cohort. Methods: We used linked e-health records of diabetic patients to define our cases and controls. The cases in this study were defined as type 2 diabetic patients who had ever been recorded in the linked e-health records as having maculopathy (observable or referable) in at least one eye and whose visual acuity of the eye was recorded to have decreased between the first and the last visual acuity record of that eye in the longitudinal e-health records. The controls were defined as a type 2 diabetic individual who had never been diagnosed with maculopathy or retinopathy in the linked e-health records. Anyone who had laser photocoagulation treatment was also excluded from the controls. A standard genome-wide association approach was applied. Results: Overall, we identified 469 cases and 1,374 controls within the Genetics of Diabetes Audit and Research in Tayside Scotland (GoDARTS) dataset. We found that the P value of rs9966620 in the TTC39C gene was 4.13x10-8, which reached genome-wide significance. Conclusions: We suggest that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity. This needs to be confirmed by further replication studies and functional studies.
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Affiliation(s)
- Weihua Meng
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
| | - Brian W Chan
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
| | - Chinenyenwa Ezeonwumelu
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
| | - Harry L Hébert
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
| | - Amy Campbell
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
| | - Vencent Soler
- b Retina unit, Ophthalmology department , Hôpital Pierre Paul Riquet, CHU Toulouse, 31059 Toulouse Cedex 9; Unité "Différenciation Epithéliale et Autoimmunité Rhumatoïde", UMR 1056 Inserm - Université de Toulouse , France
| | - Colin Na Palmer
- a Division of Population Health and Genomics , Medical Research Institute, Ninewells Hospital and School of Medicine, University of Dundee , Dundee , UK
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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