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Lin W, Ren T, Li W, Liu M, He D, Liang S, Luo W, Zhang X. Novel 61-bp Indel of RIN2 Is Associated With Fat and Hatching Weight Traits in Chickens. Front Genet 2021; 12:672888. [PMID: 34276778 PMCID: PMC8280519 DOI: 10.3389/fgene.2021.672888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022] Open
Abstract
The Ras and Rab interactor 2 (RIN2) gene, which encodes RAS and Rab interacting protein 2, can interact with GTP-bound Rab5 and participate in early endocytosis. This study found a 61-bp insertion/deletion (indel) in the RIN2 intron region, and 3 genotypes II, ID, and DD were observed. Genotype analysis of mutation sites was performed on 665 individuals from F2 population and 8 chicken breeds. It was found that the indel existed in each breed and that yellow feathered chickens were mainly of the DD genotype. Correlation analysis of growth and carcass traits in the F2 population of Xinghua and White Recessive Rock chickens showed that the 61-bp indel was significantly correlated with abdominal fat weight, abdominal fat rate, fat width, and hatching weight (P < 0.05). RIN2 mRNA was expressed in all the tested tissues, and its expression in abdominal fat was higher than that in other tissues. In addition, the expression of the RIN2 mRNA in the abdominal fat of the DD genotype was significantly higher than that of the II genotype (P < 0.05). The transcriptional activity results showed that the luciferase activity of the pGL3-DD vector was significantly higher than that of the pGL3-II vector (P < 0.01). Moreover, the results indicate that the polymorphisms in transcription factor binding sites (TFBSs) of 61-bp indel may affect the transcriptional activity of RIN2, and thus alter fat traits in chicken. The results of this study showed that the 61-bp indel was closely related to abdominal fat-related and hatching weight traits of chickens, which may have reference value for molecular marker-assisted selection of chickens.
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Affiliation(s)
- Wujian Lin
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Manqing Liu
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Danlin He
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Shaodong Liang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Wen Luo
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding, and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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Li W, Liu D, Tang S, Li D, Han R, Tian Y, Li H, Li G, Li W, Liu X, Kang X, Li Z. A multiallelic indel in the promoter region of the Cyclin-dependent kinase inhibitor 3 gene is significantly associated with body weight and carcass traits in chickens. Poult Sci 2019; 98:556-565. [PMID: 30169814 DOI: 10.3382/ps/pey404] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 08/22/2018] [Indexed: 11/20/2022] Open
Abstract
Many studies have reported that cyclin-dependent kinase inhibitor 3 (CDKN3) is involved in the cell cycle. However, the function of CDKN3 has not been well elucidated in organisms. In this study, a multiallelic indel caused by a 19-bp fragment and a 2 × 19 bp fragment was shown for the first time to be inserted into the promoter of the CDKN3 gene in 1994 chickens from 9 different breeds. In addition, 6 genotypes (C5C5, C4C4, C3C3, C4C5, C3C4, and C3C5) were observed (C3C3, C4C4, C5C5 have 3 × 19 bp, 4 × 19 bp, and 5 × 19 bp, respectively). Among these genotypes, the C4C4 genotype was the most dominant genotype in 9 breeds. The results of χ2 analysis of CDKN3 gene in different breeds showed that there were significant differences in the distribution of genotypes among different cultivars (P < 0.01). In addition, association study with F2 chicken resource population which produced by Anka and Gushi chickens showed that the C3C4 genotypes had the greatest semi-evisceration weight (SEW, 1163.94 ± 46.84), evisceration weight (EW, 964.15 ± 41.16), head weight (HW, 45.55 ± 1.43), claw weight (CW, 63.42±2.86), wing weight (WW, 129.15±5.48), liver weight (LW, 29.96±1.27), carcass weight (cW, 1286.96±49.53), weight at 10 (1190.68±45.68) and 12 (1430.65±54.45) wk, followed by C3C3, C4C4, C5C5, C4C5, whereas C3C5 genotypes having the lowest SEW (989.21±47.71), EW (841.38±40.55), HW (41.03±1.46), CW (54.36±2.81), WW (116.31±5.39), LW (27.31±1.25), cW (1093.29±49.99), weight at 10 (1036.10±44.99) and 12 (1246.28±53.59) wk. Expression levels of CDKN3 in breast muscle of chickens with C4C4 (0.72±0.02), C3C3 (0.95±0.41), and C4C5 (0.74±0.13) genotypes were significantly lower than those with C5C5 (1.80±0.01) and C3C5 (2.14±0.17) genotypes (P < 0.05). In conclusion, we investigated the effect of a multiallelic indel in the CDKN3 gene on the economic traits of chickens, and this indel was significantly associated with growth and carcass traits in chickens. Collectively, our findings provide useful information about the repeat sequence indel in the promoter region of the CDKN3 gene as a potential molecular marker for chicken breeding.
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Affiliation(s)
- Wenya Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Danli Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Shuqi Tang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China
| | - Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Hong Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450002, Henan, China
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Xin S, Wang X, Dai G, Zhang J, An T, Zou W, Zhang G, Xie K, Wang J. Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens. Genes (Basel) 2018; 9:genes9090446. [PMID: 30200658 PMCID: PMC6162446 DOI: 10.3390/genes9090446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 11/16/2022] Open
Abstract
The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region -2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [-357 (G > A), -447 (C > G), and -663 (A > G)] in the 5' regulatory region and one in the 3' non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5' regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.
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Affiliation(s)
- Shijie Xin
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
| | - Xiaohui Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
| | - Guojun Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
| | - Jingjing Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
| | - Tingting An
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
| | - Wenbin Zou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Key Lab for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou 225009, China.
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
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Abstract
Some mutations (or 'major genes') have a desirable effect in heterozygous carriers but an undesirable effect in homozygous carriers. When these mutations affect a trait of significant economic importance, their eradication, depending on their effect and frequency, may be counterproductive. This is especially the case of major genes affecting the ovulation rate and thus the prolificacy in meat sheep populations. To manage such situations, a mating design based on the major genotypes of reproducers has to be optimized. Both the effect of the major gene and the cost of genotyping candidates at this locus influence the expected genetic progress and profitability of the breeding plan. The aim of this study was to determine the optimal combination of matings that maximizes profitability at the level of the whole population (nucleus + commercial flocks). A deterministic model was developed and, using sequential quadratic programming methodology, the optimal strategy (optimal combination of matings) that maximized the economic gain achieved by the population across a range of genotype effects and genotyping costs was determined. The optimal strategy was compared with simpler and more practical strategies based on a limited number of parental genotype mating types. Depending on the genotype effect and genotyping costs, the optimal strategy varied, such that either the heterozygous frequency and/or polygenic gain was maximized with a large number of animals genotyped, or when genotyping costs were higher, the optimization led to lower heterozygous frequency and/or polygenic gain with fewer animals genotyped. Comparisons showed that some simpler strategies were close to the optimal strategy. An overlapping model was then derived as an application of the real case of the French Lacaune meat sheep OVI-TEST breeding program. Results showed that a practical strategy based on mating non-carriers to heterozygous carriers was only slightly less effective than the optimal strategy, with a reduction in efficiency from 3% to 8%, depending on the genotyping costs. Based on only two different parental genotype mating types, this strategy would be easy to implement.
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