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Yao Y, Sun K, Yang Q, Zhou Z, Shao C, Qian X, Tang Q, Xie J. Assessing Autosomal InDel Loci With Multiple Insertions or Deletions of Random DNA Sequences in Human Genome. Front Genet 2022; 12:809815. [PMID: 35178073 PMCID: PMC8844376 DOI: 10.3389/fgene.2021.809815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple mutational events of insertion/deletion occurring at or around InDel sites could form multi-allelic InDels and multi-InDels (abbreviated as MM-InDels), while InDels with random DNA sequences could imply a unique mutation event at these loci. In this study, preliminary investigation of MM-InDels with random sequences was conducted using high-throughput phased data from the 1000 Genomes Project. A total of 3,599 multi-allelic InDels and 6,375 multi-InDels were filtered with multiple alleles. A vast majority of the obtained MM-InDels (85.59%) presented 3 alleles, which implies that only one secondary insertion or deletion mutation event occurred at these loci. The more frequent presence of two adjacent InDel loci was observed within 20 bp. MM-InDels with random sequences presented an uneven distribution across the genome and showed a correlation with InDels, SNPs, recombination rate, and GC content. The average allelic frequencies and prevalence of multi-allelic InDels and multi-InDels presented similar distribution patterns in different populations. Altogether, MM-InDels with random sequences can provide useful information for population resolution.
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Affiliation(s)
- Yining Yao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kuan Sun
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qinrui Yang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Zhihan Zhou
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chengchen Shao
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaoqin Qian
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiqun Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianhui Xie
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
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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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Fu R, Ren T, Li W, Liang J, Mo G, Luo W, He D, Liang S, Zhang X. A Novel 65-bp Indel in the GOLGB1 Gene Is Associated with Chicken Growth and Carcass Traits. Animals (Basel) 2020; 10:ani10030475. [PMID: 32178328 PMCID: PMC7142648 DOI: 10.3390/ani10030475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 01/18/2023] Open
Abstract
Simple Summary Many Chinese-local chickens show slow-growing and low-producing performance, which is not conductive to the development of the poultry industry. The identification of thousands of indels in the last twenty years has helped us to make progress in animal genetics and breeding. Golgin subfamily B member 1 (GOLGB1) is located on chromosome 1 in chickens. Previous study showed that a large number of QTLs on the chicken chromosome 1 were related to the important economic traits. However, the biological function of GOLGB1 gene in chickens is still unclear. In this study, we detected a novel 65-bp indel in the fifth intron of the chicken GOLGB1 gene. Correlation analysis between the 65-bp indel and chicken growth and carcass traits was performed through a yellow chicken population, which is commercial. Results revealed that this 65-bp indel was significantly associated with chicken body weight, highly significantly associated with neck weight, abdominal fat weight, abdominal fat percentage, and the yellow index b of breast. These findings hinted that the 65-bp indel in GOLGB1 could be assigned to a molecular marker in chicken breeding and enhance production in the chicken industry. Abstract Golgin subfamily B member 1 (GOLGB1) gene encodes the coat protein 1 vesicle inhibiting factor, giantin. Previous study showed that mutations of the GOLGB1 gene are associated with dozens of human developmental disorders and diseases. However, the biological function of GOLGB1 gene in chicken is still unclear. In this study, we detected a novel 65-bp insertion/deletion (indel) polymorphism in the chicken GOLGB1 intron 5. Association of this indel with chicken growth and carcass traits was analyzed in a yellow chicken population. Results showed that this 65-bp indel was significantly associated with chicken body weight (p < 0.05), highly significantly associated with neck weight, abdominal fat weight, abdominal fat percentage and the yellow index b of breast (p < 0.01). Analysis of genetic parameters indicated that “I” was the predominant allele. Except for the yellow index b of breast, II genotype individuals had the best growth characteristics, by comparison with the ID genotype and DD genotype individuals. Moreover, the mRNA expression of GOLGB1 was detected in the liver tissue of chicken with different GOLGB1 genotypes, where the DD genotype displayed high expression levels. These findings hinted that the 65-bp indel in GOLGB1 could be assigned to a molecular marker in chicken breeding and enhance production in the chicken industry.
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Affiliation(s)
- Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Jiaying Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Guodong Mo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Danlin He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Shaodong Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (R.F.); (T.R.); (W.L.); (J.L.); (G.M.); (W.L.); (D.H.); (S.L.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- Correspondence:
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Barton HJ, Zeng K. The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome. Genome Biol Evol 2019; 11:1514-1524. [PMID: 30924871 PMCID: PMC6543879 DOI: 10.1093/gbe/evz068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2019] [Indexed: 12/11/2022] Open
Abstract
Insertions and deletions (INDELs) remain understudied, despite being the most common form of genetic variation after single nucleotide polymorphisms. This stems partly from the challenge of correctly identifying the ancestral state of an INDEL and thus identifying it as an insertion or a deletion. Erroneously assigned ancestral states can skew the site frequency spectrum, leading to artificial signals of selection. Consequently, the selective pressures acting on INDELs are, at present, poorly resolved. To tackle this issue, we have recently published a maximum likelihood approach to estimate the mutation rate and the distribution of fitness effects for INDELs. Our approach estimates and controls for the rate of ancestral state misidentification, overcoming issues plaguing previous INDEL studies. Here, we apply the method to INDEL polymorphism data from ten high coverage (∼44×) European great tit (Parus major) genomes. We demonstrate that coding INDELs are under strong purifying selection with a small proportion making it into the population (∼4%). However, among fixed coding INDELs, 71% of insertions and 86% of deletions are fixed by positive selection. In noncoding regions, we estimate ∼80% of insertions and ∼52% of deletions are effectively neutral, the remainder show signatures of purifying selection. Additionally, we see evidence of linked selection reducing INDEL diversity below background levels, both in proximity to exons and in areas of low recombination.
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Affiliation(s)
- Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
| | - Kai Zeng
- Department of Animal and Plant Sciences, University of Sheffield, United Kingdom
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Evolutionary Genomics of Colias Phosphoglucose Isomerase (PGI) Introns. J Mol Evol 2012; 74:96-111. [DOI: 10.1007/s00239-012-9492-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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