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Zhang Z, Liu C, Hao W, Yin W, Ai S, Zhao Y, Duan Z. Novel Single Nucleotide Polymorphisms and Haplotype of MYF5 Gene Are Associated with Body Measurements and Ultrasound Traits in Grassland Short-Tailed Sheep. Genes (Basel) 2022; 13:genes13030483. [PMID: 35328037 PMCID: PMC8949509 DOI: 10.3390/genes13030483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Myogenic factor 5 plays active roles in the regulation of myogenesis. The aim of this study is to expose the genetic variants of the MYF5 and its association with growth performance and ultrasound traits in grassland short-tailed sheep (GSTS) in China. The combination technique of sequencing and SNaPshot revealed seven SNPs in ovine MYF5 from 533 adult individuals (male 103 and female 430), four of which are novel ones located at g.6838G > A, g.6989 G > T, g.7117 C > A in the promoter region and g.9471 T > G in the second intron, respectively. Genetic diversity indexes showed the seven SNPs in low or intermediate level, but each of them conformed HWE (p > 0.05) in genotypic frequencies. Association analysis indicated that g.6838G > A, g.7117 C > A, g.8371 T > C, g.9471 T > G, and g.10044 C > T had significant effects on growth performance and ultrasound traits. The diplotypes of H1H3 and H2H3 had higher body weight and greater body size, and haplotype H3 had better performance on meat production than the others. In addition, the dual-luciferase reporter assay showed that there are two active regions in the MYF5 promoter located at −1799~−1197 bp and −514~−241 bp, respectively, but g.6838G > A and g.7117 C > A were out of the region, suggesting these two SNPs influence the phenotype by other pathway. The results suggest that the MYF5 gene might be applied as a promising candidate of functional genetic marker in GSTS breeding.
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Affiliation(s)
- Zhichao Zhang
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Liu
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Wenjing Hao
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Weiwen Yin
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Sitong Ai
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
| | - Yanfang Zhao
- Animal Disease Prevention and Control Center, Ewenki Autonomous Banner, Hulunbuir 021000, China;
| | - Ziyuan Duan
- Genetic Resources Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (Z.Z.); (C.L.); (W.H.); (W.Y.); (S.A.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
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Yu H, Zou W, Xin S, Wang X, Mi C, Dai G, Zhang T, Zhang G, Xie K, Wang J, Qiu C. Association Analysis of Single Nucleotide Polymorphisms in the 5' Regulatory Region of the IL-6 Gene with Eimeria tenella Resistance in Jinghai Yellow Chickens. Genes (Basel) 2019; 10:genes10110890. [PMID: 31694169 PMCID: PMC6896108 DOI: 10.3390/genes10110890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 01/06/2023] Open
Abstract
Interleukin 6 (IL-6) is an immunoregulatory cytokine involved in various inflammatory and immune responses. To investigate the effects of single nucleotide polymorphisms (SNPs) and haplotypes of IL-6 on resistance to Eimeria tenella (E. tenella), SNPs in the 5' regulatory region of IL-6 were detected with direct sequencing, and the effects of SNPs and haplotypes on resistance to E. tenella were analyzed by the least square model in Jinghai yellow chickens. Nineteen SNPs were identified in the 5' regulation region of IL-6, among which three SNPs were newly discovered. The SNP association analysis results showed that nine of the SNPs were significantly associated with E. tenella resistance indexes; the A-483G locus was significantly associated with the GSH-Px, IL-2, and IL-17 indexes (p < 0.05); the C-447G locus was significantly associated with the SOD, GSH-Px, IL-17, and IL-2 indexes (p < 0.05); and the G-357A locus had significant effects on the CAT and IL-16 indexes (p < 0.05). Haplotype analysis showed that H2H3 and H2H5 were favorable haplotype combinations with good coccidium resistance. Furthermore, we used qRT-PCR and observed that the expression of IL-6 in the infection group was higher than that in the control group in the liver, proventriculus, small intestine, thymus, kidney, and bursa of Fabricius and extremely significantly different than that in the cecum especially (p < 0.01). In summary, SNPs and haplotypes in the 5' regulatory region of IL-6 have important effects on E. tenella resistance, and the results will provide a reference for molecular marker selection of E. tenella resistance in Jinghai yellow chickens.
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Affiliation(s)
- Hailiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Wenbin Zou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Shijie Xin
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Xiaohui Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Changhao Mi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
- Correspondence: ; Tel.: +86-139-5275-0903
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (H.Y.); (W.Z.); (S.X.); (X.W.); (C.M.); (T.Z.); (G.Z.); (K.X.); (J.W.)
| | - Cong Qiu
- Jiangsu Jinghai Poultry Group Co., Ltd., Haimen 226100, China;
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Xue Q, Zhang G, Li T, Ling J, Zhang X, Wang J. Transcriptomic profile of leg muscle during early growth in chicken. PLoS One 2017; 12:e0173824. [PMID: 28291821 PMCID: PMC5349469 DOI: 10.1371/journal.pone.0173824] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/26/2017] [Indexed: 11/27/2022] Open
Abstract
The early growth pattern, especially the age of peak growth, of broilers affects the time to market and slaughter weight, which in turn affect the profitability of the poultry industry. However, the underlying mechanisms regulating chicken growth and development have rarely been studied. This study aimed to identify candidate genes involved in chicken growth and investigated the potential regulatory mechanisms of early growth in chicken. RNA sequencing was applied to compare the transcriptomes of chicken muscle tissues at three developmental stages during early growth. In total, 978 differentially expressed genes (DEGs) (fold change ≥ 2; false discovery rate < 0.05) were detected by pairwise comparison. Functional analysis showed that the DEGs are mainly involved in the processes of cell growth, muscle development, and cellular activities (such as junction, migration, assembly, differentiation, and proliferation). Many of the DEGs are well known to be related to chicken growth, such as MYOD1, GH, IGF2BP2, IGFBP3, SMYD1, CEBPB, FGF2, and IGFBP5. KEGG pathway analysis identified that the DEGs were significantly enriched in five pathways (P < 0.1) related to growth and development: extracellular matrix–receptor interaction, focal adhesion, tight junction, insulin signaling pathway, and regulation of the actin cytoskeleton. A total of 42 DEGs assigned to these pathways are potential candidate genes inducing the difference in growth among the three developmental stages, such as MYH10, FGF2, FGF16, FN1, CFL2, MAPK9, IRS1, PHKA1, PHKB, and PHKG1. Thus, our study identified a series of genes and several pathways that may participate in the regulation of early growth in chicken. These results should serve as an important resource revealing the molecular basis of chicken growth and development.
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Affiliation(s)
- Qian Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
- * E-mail: (JW); (GZ)
| | - Tingting Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Jiaojiao Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Xiangqian Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
- * E-mail: (JW); (GZ)
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Yin ZZ, Dong XY, Dong DJ, Ma YZ. Association of MYF5 and KLF15 gene polymorphisms with carcass traits in domestic pigeons (Columba livia). Br Poult Sci 2016; 57:612-618. [PMID: 27180898 DOI: 10.1080/00071668.2016.1190000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) in the exons of the myogenic factor 5 (MYF5) and Kruppel-like factor 15 (KLF15) genes were identified and analysed by using DNA sequencing methods in 60 female domestic pigeons (Columba livia). Five SNPs (T5067A, C5084T, C5101T, T5127A and C5154G) were detected in exon 3 of MYF5 and 6 SNPs (C1398T, C1464T, G1542A, C1929T, G1965A and A2355G) were found in exon 2 of KLF15, respectively. The analysis revealed three genotypes, in which the AA genotype was dominant and the A allele showed a dominant advantage. For the MYF5 gene, the C5084T and T5127A SNP genotypes were significantly associated with carcass traits of pigeons. Within those two SNPs, the BB genotype showed relatively higher trait association values than those of AA or AB genotypes. No significant association was observed between the KLF15 SNP genotypes and carcass traits. These results indicated that the MYF5 gene is a potential major gene affecting carcass traits in domestic pigeons. The BB genotype of the C5084T and T5127A SNPs could be a potential candidate genetic marker for marker-assisted selection in pigeon.
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Affiliation(s)
- Z Z Yin
- a Animal Science College , Zhejiang University , Hangzhou , China
| | - X Y Dong
- a Animal Science College , Zhejiang University , Hangzhou , China
| | - D J Dong
- a Animal Science College , Zhejiang University , Hangzhou , China
| | - Y Z Ma
- a Animal Science College , Zhejiang University , Hangzhou , China
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Genome-wide association study of antibody level response to NDV and IBV in Jinghai yellow chicken based on SLAF-seq technology. J Appl Genet 2015; 56:365-73. [PMID: 25588649 DOI: 10.1007/s13353-014-0269-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/10/2014] [Accepted: 12/29/2014] [Indexed: 12/21/2022]
Abstract
Newcastle disease (ND) and avian infectious bronchitis (IB) are contagious diseases of chickens. To identify genes associated with antibody levels against ND and IB, a genome-wide association study was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in Jinghai yellow chickens. This determined six single-nucleotide polymorphisms (SNPs) that were associated with antibody levels against Newcastle disease virus (NDV): rsZ2494661, rsZ2494710, rs1211307701, rs1211307711, rs1218289310 and rs420701988. Of these, rsZ2494661 and rsZ2494710 reached the 5 % Bonferroni genome-wide significance level (5.5E-07) and they were both 134.7 kb downstream of the SETBP1 gene. The remaining four SNPs had 'suggestive' genome-wide significance levels (1.1E-05) and they were within or near the Plexin B1, LRRN1 and PDGFC genes. IB had two SNPs associated with antibody levels: rs149988433 and rs16170823; both reached chromosome-wide significance levels and they were near the USP7 and TRIM27 genes, respectively. Bioinformatics, GO annotation and pathway analysis indicated that five of these genes (Plexin B1, TRIM27, PDGFC, SETBP1 and USP7) may be important for the generation of protective antibodies against NDV and infectious bronchitis virus (IBV). This paves the way for further research on host immune responses against NDV.
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Bhattacharya TK, Chatterjee RN, Dushyanth K, Shukla R. Cloning, characterization and expression of myostatin (growth differentiating factor-8) gene in broiler and layer chicken (Gallus gallus). Mol Biol Rep 2014; 42:319-27. [PMID: 25479731 DOI: 10.1007/s11033-014-3753-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/16/2014] [Indexed: 10/24/2022]
Abstract
A study was conducted to characterize myostatin gene in broiler and layer chicken and to explore mRNA expression profile in these two varieties of chicken. The myostatin cDNAs of broiler and layer varieties were cloned and sequenced. The total length of the cDNA was 1128 bp. The differences of nucleotides between PB-1 broiler and IWI layer were C > 65 > T, C > 306 > T and C > 1094 > T while those between CB broiler and IWI layer were C > 65 > T, C > 195 > G, G > 234 > A, C > 306 > T, T > 939 > C, C > 961 > T, G > 966T and C > 1094 > T. The amino acid differences of myostatin protein between PB-1 and IWI strains were alanine > 22 > valine and proline > 365 > leucine while those between CB and IWI strains were alanine > 22 > valine, histidine > 321 > tyrosine and proline > 365 > leucine. The phylogenetic study revealed closeness of PB-1 and control broiler forming a cluster, which was also closely related to IWI layer chicken formed a separate cluster. The gene was cloned and expressed in E. coli. The gene expression profile in muscle was different between broiler and layer strains. Between two broiler strains, the pattern of expression was similar. Between IWI layer and either PB-1 or CB broilers, differences in expression was found at different time points, particularly at second, fourth and seventh weeks of age. The myostatin expression was significantly associated with body weights in chicken. It is concluded that myostatin gene sequences varied at nucleotide as well as amino acid level between broiler and layer chicken varieties and the gene also expressed differentially in these two varieties.
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Affiliation(s)
- T K Bhattacharya
- Directorate of Poultry Research, Rajendranagar, Hyderabad, 500 030, India,
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