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agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species. BIOLOGY 2021; 10:biology10080790. [PMID: 34440019 PMCID: PMC8389679 DOI: 10.3390/biology10080790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface.
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Li H, Yu H, Li Q. Striated myosin heavy chain gene is a crucial regulator of larval myogenesis in the pacific oyster Crassostrea gigas. Int J Biol Macromol 2021; 179:388-397. [PMID: 33689771 DOI: 10.1016/j.ijbiomac.2021.03.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/25/2023]
Abstract
Pacific oyster (Crassostrea gigas), the most productive economical bivalve mollusc, is identified as an attractive model for developmental studies due to its classical mosaic developmental pattern. Myosin heavy chain is a structural and functional component of myosin, the key muscle protein of thick filament. Here, full length cDNA of striated myosin heavy chains in C. gigas (CgSmhc) was obtained, and the expression profiles were examined in different development stage. CgSmhc had a high expression level in trochophore and D-shaped stage during embryo-larval stage. In adult, CgSmhc was a muscle-specific gene and primarily expressed in muscle tissues. Then, activity of 5' flanking region of CgSmhc were examined through an reconstructed EGFP vector. The results indicated that 3098 bp 5'-flanking region of CgSmhc owned various conserved binding sites of myogenesis-related regulatory elements, and the 2000 bp 5'-flanking sequence was sufficient to induce the CgSmhc expression. Subsequently, the CRISPR/Cas9-mediated target disruption of CgSmhc was generated by co-injection of Cas9mRNA and CgSmhc-sgRNAs into one-cell stage embryos of C. gigas. Loss of CgSmhc had a visible effect on the sarcomeric organization of thin filaments in larval musculature, indicating that CgSmhc was required during larval myogenesis to regulate the correct assembly of sarcomere.
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Affiliation(s)
- Huijuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China.
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Vinh NT, Giang NTP, Linh NV, Dang PK, Cahn NX, Giang NTC, Doan BH, Anh NT, Thinh NH. Single Nucleotide Polymorphisms of Candidate Genes Related to Egg Production Traits in Vietnamese Indigenous Chickens. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2021. [DOI: 10.1590/1806-9061-2020-1298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- NT Vinh
- Viet nam National University of Agriculture, Vietnam
| | - NTP Giang
- Viet nam National University of Agriculture, Vietnam
| | - NV Linh
- Vietnam Academy of Science and Technology, Vietnam
| | - PK Dang
- Viet nam National University of Agriculture, Vietnam
| | - NX Cahn
- Viet nam National University of Agriculture, Vietnam
| | - NTC Giang
- Viet nam National University of Agriculture, Vietnam
| | - BH Doan
- Viet nam National University of Agriculture, Vietnam
| | - NT Anh
- Viet nam National University of Agriculture, Vietnam
| | - NH Thinh
- Viet nam National University of Agriculture, Vietnam
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Purwantini D, Santosa RSS, Santosa SA, Susanto A, Candrasari DP, Ismoyowati I. Prolactin gene polymorphisms and associations with reproductive traits in Indonesian local ducks. Vet World 2020; 13:2301-2311. [PMID: 33363319 PMCID: PMC7750233 DOI: 10.14202/vetworld.2020.2301-2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/28/2020] [Indexed: 12/05/2022] Open
Abstract
Background and Aim: Reproductive traits play an important role in population increases and the egg production (EP) abilities of Indonesian local ducks (ILD). The prolactin (PRL) gene is a single chain polypeptide hormone belonging to a family of growth hormone genes that are mainly synthesized in the anterior pituitary gland in all vertebrates. It has a significant effect on reproductive traits and EP. Single nucleotide polymorphisms (SNPs) present in PRL are a useful molecular marker for EP. This study aimed to identify the PRL polymorphisms based on these SNPs and to uncover the associations with reproductive traits in ILD. Materials and Methods: A total of 280 ILDs consisting of Tegal and Magelang (F0) ducks and their reciprocal crosses, namely, Gallang (F1) and Maggal (F1), were maintained and specific variables were recorded, that is, age at first egg, body weight at first egg, first egg weight, and EP, for 90 days. Allele and genotype frequencies were used to determine the Hardy-Weinberg (H-W) equilibrium. The association between the SNP genotypes of PRL and reproductive traits was analyzed using one-way analysis of variance, following the GLM procedure of SAS. The genotypic effects on the reproductive traits were determined using regression analysis. Results: This study successfully amplified a polymerase chain reaction product of 190 bp, which was used to identify the SNP. Results indicated that PRL in ILDs is polymorphic. A SNP was found at position 164 nt (c.164G >A), consisting of three different genotypes, namely, GG, GA, and AA. The genotypes of Tegal and Magelang (F0), and Gallang (F1) populations were not in H-W equilibrium. The Maggal population (F1) was in H-W equilibrium. Significant associations were detected between the genotypes and EP in all ILDs (p<0.01), following a regression line of y=2.337x+64.605, with a determination coefficient of 0.0188 (r=0.14). Conclusion: PRL can be recommended as a candidate gene for reproductive traits in ILD, especially EP.
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Affiliation(s)
| | | | | | - Agus Susanto
- Faculty of Animal Science, University of Jenderal Soedirman, Indonesia
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Akhatayeva Z, Mao C, Jiang F, Pan C, Lin C, Hao K, Lan T, Chen H, Zhang Q, Lan X. Indel variants within the PRL and GHR genes associated with sheep litter size. Reprod Domest Anim 2020; 55:1470-1478. [PMID: 32762057 DOI: 10.1111/rda.13796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/01/2020] [Indexed: 12/27/2022]
Abstract
Growth hormone and prolactin belong to the class of peptide hormones that have a wide range of regulatory functions. In this study, polymorphisms of growth hormone receptor (GHR) and prolactin (PRL) genes were analysed as candidate genes, which are responsible for the litter size in Australian White (AUW) sheep. According to the statistical analyses results, the polymorphism information content (PIC) values of the PRL-P1-ins-23 bp, GHR-P2-del-23 bp and GHR-P8-del-23 bp were 0.371, 0.366 and 0.375, respectively, which indicates the high genetic polymorphism in AUW sheep. Moreover, all indel loci are not conformed to the HWE (p < .05). Further, our findings revealed that the PRL-P1-ins-23 bp polymorphism in the ovine PRL gene was significantly related to the first parity litter size (p = .001) and the DD genotype displaying the highest genotypic mean. Meanwhile, the GHR-P2-del-23 bp and GHR-P8-23 bp indels in the ovine GHR gene were significantly correlated with first parity litter size (p < .05), and the individuals with the genotype II showed significantly higher litter size than others. Collectively, these results demonstrated that our findings could be useful for future sheep breeding strategies based on the molecular-assisted selection (MAS).
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Affiliation(s)
- Zhanerke Akhatayeva
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cui Mao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Fugui Jiang
- Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China.,Shandong Key Lab of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chunjian Lin
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Kunjie Hao
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Tianxin Lan
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd., Tianjin, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Dong J, Chen Z, Sun C, Tian Y, Hu J, Lu M, Ye X. Cloning, SNP detection, and growth correlation analysis of the 5' flanking regions of two myosin heavy chain-7 genes in Mandarin fish (Siniperca chuatsi). Comp Biochem Physiol B Biochem Mol Biol 2018; 228:10-16. [PMID: 30419288 DOI: 10.1016/j.cbpb.2018.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022]
Abstract
Myosin heavy chains (MYHs) play important roles in muscle growth and contraction. In fish, MYHs contribute to hyperplasia and hypertrophy of muscle fibers, which can continue into adult life and thus result in indeterminate growth in some species. We previously identified two MYH genes, MYH-7a and MYH-7b, that are differentially expressed in Mandarin fish (Siniperca chuatsi) and appear to function in early growth. However, the regulatory role of their 5' flanking regions is unknown. To examine the effects of single nucleotide polymorphisms (SNPs) in these regions, we used genome walking to amplify their flanking sequences and analyzed the regulatory elements and binding sites. A single SNP locus was found in the flanking sequence of each gene. These SNP loci are located in the conserved glucocorticoid receptor binding region (MYH-7a: G-614A; Allele frequency: G:A = 94.9:5.1; GG (89.76) and AG (10.24) genotypes) and the LIM homeobox domain transcription factor binding sequence (MYH-7b: C-1933A; Allele frequency: C:A = 54.8:45.2; AA (20.82), AC (48.81), and CC (30.37) genotypes). At the G-614A loci, the GG genotype exhibited more superior growth traits (total length, body length, body height, etc.) than the AG genotype, with the exception of caudal peduncle length. Alternatively, at the C-1933A loci, the AC and AA genotypes showed significant differences in all growth traits, except for head length, with AC exhibiting superior traits. The AA and CC genotypes showed significant differences in caudal peduncle length and height, while no differences were observed between the AC and CC genotypes. Thus, these SNPs in the 5' flanking regions of MYH-7a and MYH-7b are correlated with superior growth and can be used for selecting Mandarin fish during breeding.
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Affiliation(s)
- Junjian Dong
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhihang Chen
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Chengfei Sun
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jie Hu
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Maixin Lu
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Xing Ye
- Key Laboratory of Tropical & Subtropical Fisheries Resource Application & Cultivation, Ministry of Agriculture, Pearl River Fisheries Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China.
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Mo C, Huang L, Cui L, Lv C, Lin D, Song L, Zhu G, Li J, Wang Y. Characterization of NMB, GRP and their receptors (BRS3, NMBR and GRPR) in chickens. J Mol Endocrinol 2017; 59:61-79. [PMID: 28500250 DOI: 10.1530/jme-17-0020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 05/03/2017] [Indexed: 12/30/2022]
Abstract
The two structurally and functionally related peptides, gastrin-releasing peptide (GRP) and neuromedin B (NMB) play critical roles in many physiological/pathological processes in mammals. However, the information regarding the expression and functionality of avian NMB, GRP and their receptors is limited. Here, we characterized cNMB, cGRP and their receptors (cNMBR, cGRPR and cBRS3) in chickens. Our results showed that: (1) cNMBR and cGRPR expressed in CHO cells could be potently activated by cNMB and cGRP, respectively, as monitored by cell-based luciferase reporter assays, indicating that cNMBR and cGRPR are cNMB- and cGRP-specific receptors; strikingly, BRS3 of chickens (/spotted gars), which is orthologous to mouse bombesin receptor subtype-3 (BRS3), could be potently activated by GRP and NMB, demonstrating that both peptides are the endogenous ligands for chicken (/spotted gar) BRS3; (2) quantitative real-time PCR (qPCR) revealed that cGRPR is widely expressed in chicken tissues with abundant expression in the ovary, pancreas, proventriculus, spinal cord and brain, whereas cNMB, cNMBR and cBRS3 are mainly expressed in the brain and testes; (3) interestingly, qPCR, Western blot and immunostaining revealed that cGRP is predominantly expressed in the anterior pituitary and mainly localized to LH-cells, suggesting that cGRP is likely a novel pituitary hormone in chickens. In summary, our data help to uncover the roles of GRP, NMB and their receptors in birds, and provide the first persuasive evidence from an evolutionary prospective that in vertebrates, GRP and NMB are the endogenous ligands for BRS3, an orphan receptor that has puzzled endocrinologists for more than two decades.
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Affiliation(s)
- Chunheng Mo
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Long Huang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Lin Cui
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Can Lv
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Dongliang Lin
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Liang Song
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Guoqiang Zhu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Juan Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Yajun Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of EducationCollege of Life Sciences, Sichuan University, Chengdu, People's Republic of China
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Mitrofanova OV, Dementeva NV, Krutikova AA, Yurchenko OP, Vakhrameev AB, Terletskiy VP. Association of polymorphic variants in MSTN, PRL, and DRD2 genes with intensity of young animal growth in Pushkin breed chickens. CYTOL GENET+ 2017. [DOI: 10.3103/s0095452717030082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Transcriptome sequencing reveals genetic mechanisms underlying the transition between the laying and brooding phases and gene expression changes associated with divergent reproductive phenotypes in chickens. Mol Biol Rep 2016; 43:977-89. [PMID: 27389590 DOI: 10.1007/s11033-016-4033-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 06/27/2016] [Indexed: 12/24/2022]
Abstract
Transition from laying to incubation behavior in chicken is an interesting topic in reproductive biology. The decline of incubation behavior in chicken population has led to considerable phenotypic differences in reproductive traits between breeds. However, the exact genetic mechanism of the reproductive phase transition still largely unknown and little is known about the gene expression changes that contribute to the phenotypic differences. We performed mRNA sequencing to investigate the molecular mechanism underlying the transition from laying to brooding and to detect difference in gene regulation underlying the phenotypic diversification using two chicken breeds. The majority of gene expression changes during phase transition were steroidogenesis and hormone-releasing genes. Brooding chickens shared a conservative pattern of greatly inhibited steroidogenic enzyme genes in the pituitary gland, therefore, low levels of steroidogenic enzymes might result in reproductive defects such as ovary regression and brooding onset. The conserved network responsible for brooding behavior was maintained by steroid biosynthesis and hormonal interactions. Interestingly, three transcription factors, SREBF2, NR5A1 and PGR, act as central signal modulators of steroid biosynthesis and hormonal interactions during the transition from laying to brooding modes at the molecular level. Furthermore, Genes correlated with protein synthesis and accumulation showed expression variation between breeds, which might result in different concentrations of and sensitivities to reproduction-related hormones. This study provided a new insight in neuroendocrine system at the molecular level, and helps to understand the genetic and hormonal responses that ultimately translate into behavior in chicken.
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Basheer A, Haley CS, Law A, Windsor D, Morrice D, Talbot R, Wilson PW, Sharp PJ, Dunn IC. Genetic loci inherited from hens lacking maternal behaviour both inhibit and paradoxically promote this behaviour. Genet Sel Evol 2015; 47:100. [PMID: 26718134 PMCID: PMC4697313 DOI: 10.1186/s12711-015-0180-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 12/17/2015] [Indexed: 01/18/2023] Open
Abstract
Background A major step towards the success of chickens as a domesticated species was the separation between maternal care and reproduction. Artificial incubation replaced the natural maternal behaviour of incubation and, thus, in certain breeds, it became possible to breed chickens with persistent egg production and no incubation behaviour; a typical example is the White Leghorn strain. Conversely, some strains, such as the Silkie breed, are prized for their maternal behaviour and their willingness to incubate eggs. This is often colloquially known as broodiness. Results Using an F2 linkage mapping approach and a cross between White Leghorn and Silkie chicken breeds, we have mapped, for the first time, genetic loci that affect maternal behaviour on chromosomes 1, 5, 8, 13, 18 and 19 and linkage group E22C19W28. Paradoxically, heterozygous and White Leghorn homozygous genotypes were associated with an increased incidence of incubation behaviour, which exceeded that of the Silkie homozygotes for most loci. In such cases, it is likely that the loci involved are associated with increased egg production. Increased egg production increases the probability of incubation behaviour occurring because egg laying must precede incubation. For the loci on chromosomes 8 and 1, alleles from the Silkie breed promote incubation behaviour and influence maternal behaviour (these explain 12 and 26 % of the phenotypic difference between the two founder breeds, respectively). Conclusions The over-dominant locus on chromosome 5 coincides with the strongest selective sweep reported in chickens and together with the loci on chromosomes 1 and 8, they include genes of the thyrotrophic axis. This suggests that thyroid hormones may play a critical role in the loss of incubation behaviour and the improved egg laying behaviour of the White Leghorn breed. Our findings support the view that loss of maternal incubation behaviour in the White Leghorn breed is the result of selection for fertility and egg laying persistency and against maternal incubation behaviour.
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Affiliation(s)
- Atia Basheer
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK. .,Animal Breeding and Genetics Section, Department of Livestock Production, University of Veterinary and Animal Sciences, Ravi campus, Lahore, Pakistan.
| | - Chris S Haley
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Andy Law
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Dawn Windsor
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - David Morrice
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK. .,Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3JT, UK.
| | - Richard Talbot
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK. .,Edinburgh Genomics, Ashworth Laboratories, The University of Edinburgh, Edinburgh, EH9 3JT, UK.
| | - Peter W Wilson
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Peter J Sharp
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
| | - Ian C Dunn
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Easter Bush, Midlothian, EH25 9RG, Scotland, UK.
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Kulibaba RA, Podstreshnyi AP. Prolactin and growth hormone gene polymorphisms in chicken lines of Ukrainian selection. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712060060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Chang MT, Cheng YS, Huang MC. Association of prolactin haplotypes with reproductive traits in Tsaiya ducks. Anim Reprod Sci 2012; 135:91-6. [DOI: 10.1016/j.anireprosci.2012.08.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 07/17/2012] [Accepted: 08/18/2012] [Indexed: 11/30/2022]
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Shen X, Zeng H, Xie L, He J, Li J, Xie X, Luo C, Xu H, Zhou M, Nie Q, Zhang X. The GTPase activating Rap/RanGAP domain-like 1 gene is associated with chicken reproductive traits. PLoS One 2012; 7:e33851. [PMID: 22496769 PMCID: PMC3322132 DOI: 10.1371/journal.pone.0033851] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 02/19/2012] [Indexed: 11/28/2022] Open
Abstract
Background Abundant evidence indicates that chicken reproduction is strictly regulated by the hypothalamic-pituitary-gonad (HPG) axis, and the genes included in the HPG axis have been studied extensively. However, the question remains as to whether any other genes outside of the HPG system are involved in regulating chicken reproduction. The present study was aimed to identify, on a genome-wide level, novel genes associated with chicken reproductive traits. Methodology/Principal Finding Suppressive subtractive hybridization (SSH), genome-wide association study (GWAS), and gene-centric GWAS were used to identify novel genes underlying chicken reproduction. Single marker-trait association analysis with a large population and allelic frequency spectrum analysis were used to confirm the effects of candidate genes. Using two full-sib Ningdu Sanhuang (NDH) chickens, GARNL1 was identified as a candidate gene involved in chicken broodiness by SSH analysis. Its expression levels in the hypothalamus and pituitary were significantly higher in brooding chickens than in non-brooding chickens. GWAS analysis with a NDH two tail sample showed that 2802 SNPs were significantly associated with egg number at 300 d of age (EN300). Among the 2802 SNPs, 2 SNPs composed a block overlapping the GARNL1 gene. The gene-centric GWAS analysis with another two tail sample of NDH showed that GARNL1 was strongly associated with EN300 and age at first egg (AFE). Single marker-trait association analysis in 1301 female NDH chickens confirmed that variation in this gene was related to EN300 and AFE. The allelic frequency spectrum of the SNP rs15700989 among 5 different populations supported the above associations. Western blotting, RT-PCR, and qPCR were used to analyze alternative splicing of the GARNL1 gene. RT-PCR detected 5 transcripts and revealed that the transcript, which has a 141 bp insertion, was expressed in a tissue-specific manner. Conclusions/Significance Our findings demonstrate that the GARNL1 gene contributes to chicken reproductive traits.
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Affiliation(s)
- Xu Shen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Hua Zeng
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Liang Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Institute of Animal Science and Veterinary, Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Jun He
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Jian Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiujuan Xie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Chenglong Luo
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Min Zhou
- Biotechnology Institute, Jiang Xi Education College, Nanchang, Jiangxi, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- * E-mail:
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Alipanah M, Shojaian K, Khani Band H. The Polymorphism of Prolactin Gene in Native Chicken Zabol Region. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/javaa.2011.619.621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Alipanah MO, Shojaian K, Bandan HK. The Polymorphism of Prolactin Gene in Native Chicken Zabol Region. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/javaa.2010.3005.3007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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16
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Liu W, Sun D, Yu Y, Li G, Tang S, Zhang Y, Wang Y, Zhang Y. Association of Janus kinase 2 polymorphisms with growth and reproduction traits in chickens. Poult Sci 2010; 89:2573-9. [DOI: 10.3382/ps.2010-00988] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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17
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Zhou M, Du Y, Nie Q, Liang Y, Luo C, Zeng H, Zhang X. Associations between polymorphisms in the chickenVIPgene, egg production and broody traits. Br Poult Sci 2010; 51:195-203. [DOI: 10.1080/00071661003745786] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Xu H, Shen X, Zhou M, Fang M, Zeng H, Nie Q, Zhang X. The genetic effects of the dopamine D1 receptor gene on chicken egg production and broodiness traits. BMC Genet 2010; 11:17. [PMID: 20199684 PMCID: PMC2848132 DOI: 10.1186/1471-2156-11-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 03/03/2010] [Indexed: 11/10/2022] Open
Abstract
Background The elevation of egg production and the inhibition of incubation behavior are the aims of modern poultry production. Prolactin (PRL) gene is confirmed to be critical for the onset and maintenance of these reproductive behaviors in birds. Through PRL, dopamine D1 receptor (DRD1) was also involved in the regulation of chicken reproductive behavior. However, the genetic effects of this gene on chicken egg production and broodiness have not been studied extensively. The objective of this research was to evaluate the genetic effects of the DRD1 gene on chicken egg production and broodiness traits. Results In this study, the chicken DRD1 gene was screened for the polymorphisms by cloning and sequencing and 29 variations were identified in 3,342 bp length of this gene. Seven single nucleotide polymorphism (SNPs) among these variations, including a non-synonymous mutation (A+505G, Ser169Gly), were located in the coding region and were chosen to analyze their association with chicken egg production and broodiness traits in 644 Ningdu Sanhuang individuals. Two SNPs, G+123A and C+1107T, were significantly associated with chicken broody frequency (P < 0.05). Significant association was also found between the G+1065A - C+1107T haplotypes and chicken broody frequency (P < 0.05). In addition, the haplotypes of G+123A and T+198C were significantly associated with weight of first egg (EW) (P = 0.03). On the other hand, the distribution of the DRD1 mRNA was observed and the expression difference was compared between broodiness and non-broodiness chickens. The DRD1 mRNA was predominantly expressed in subcutaneous fat and abdominal fat of non-broodiness chicken, and then in heart, kidney, oviduct, glandular stomach, hypothalamus, and pituitary. In subcutaneous fat and abdominal fat, the level of non-broodiness was 26 to 28 times higher than that of broodiness. In pituitary, it was 5-fold higher. In heart, oviduct, and kidney, a 2-3 times decrease from non-broodiness to broodiness was displayed. In glandular stomach and hypothalamus, the level seen in non-broodiness and broodiness was almost the same. Conclusion The polymorphisms of the DRD1 gene and their haplotypes were associated with chicken broody frequency and some egg production traits. The mRNA distribution was significant different between broodiness and non-broodiness chickens.
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Affiliation(s)
- Haiping Xu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China.
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Xu H, Shen X, Zhou M, Luo C, Kang L, Liang Y, Zeng H, Nie Q, Zhang D, Zhang X. The dopamine D2 receptor gene polymorphisms associated with chicken broodiness. Poult Sci 2010; 89:428-38. [DOI: 10.3382/ps.2009-00428] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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20
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Chu MX, Wang XC, Jin M, Di R, Chen HQ, Zhu GQ, Fang L, Ma YH, Li K. DNA polymorphism of 5' flanking region of prolactin gene and its association with litter size in sheep. J Anim Breed Genet 2009; 126:63-8. [PMID: 19207932 DOI: 10.1111/j.1439-0388.2008.00763.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A single nucleotide polymorphism of 5' flanking region of the prolactin gene was investigated in both high prolificacy breeds (Small Tail Han and Hu sheep) and low prolificacy breeds (Dorset and Suffolk sheep) using polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP). The results indicated that two genotypes (AA and AB) were detected in Small Tail Han sheep (n = 239), only one genotype (AA) was detected in Hu (n = 40), Dorset (n = 50) and Suffolk sheep (n = 39). The mutant homozygous genotype (BB) was not detected in four sheep breeds. In Small Tail Han sheep (n = 239), the frequency of genotypes AA and AB was 0.91 and 0.09, the frequency of the A and B alleles was 0.95 and 0.05, respectively. The fitness tests showed that the Small Tail Han sheep population was in Hardy-Weinberg equilibrium. Sequencing revealed a mutation (G-->T) at the position 63 bp of the 5' flanking region of prolactin gene in AB genotype compared with AA genotype in Small Tail Han sheep. The Small Tail Han ewes with AB genotype had 0.83 (p < 0.05) lambs more than those with AA genotype. These results preliminarily showed that the prolactin locus is either a major gene that influences the high prolificacy in Small Tail Han sheep or is in close linkage with such a gene.
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Affiliation(s)
- M X Chu
- The Key Laboratory of Domestic Animal Genetic Resources and Germplasm Innovation of CAAS, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhou M, Lei M, Rao Y, Nie Q, Zeng H, Xia M, Liang F, Zhang D, Zhang X. Polymorphisms of Vasoactive Intestinal Peptide Receptor-1 Gene and Their Genetic Effects on Broodiness in Chickens. Poult Sci 2008; 87:893-903. [PMID: 18420979 DOI: 10.3382/ps.2007-00495] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- M Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
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Ouyang J, Xie L, Nie Q, Luo C, Liang Y, Zeng H, Zhang X. Single nucleotide polymorphism (SNP) at theGHRgene and its associations with chicken growth and fat deposition traits. Br Poult Sci 2008; 49:87-95. [PMID: 18409081 DOI: 10.1080/00071660801938817] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Fang M, Nie Q, Luo C, Zhang D, Zhang X. An 8bp indel in exon 1 of Ghrelin gene associated with chicken growth. Domest Anim Endocrinol 2007; 32:216-25. [PMID: 16766157 DOI: 10.1016/j.domaniend.2006.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/06/2006] [Accepted: 02/23/2006] [Indexed: 11/28/2022]
Abstract
Ghrelin, acts as the endogenous ligand for growth hormone secretagogues receptor (GHS-R), is a novel growth hormone (GH) releasing peptide with reported effects on food intake in chickens. In this study, an 8 bp indel polymorphism in exon 1 of the chicken Ghrelin (cGHRL) gene was genotyped in a F(2) designed full-sib population to analyze its associations with chicken growth and carcass traits. Later, mRNA level in the proventriculus was determined by real-time PCR to reveal the expression feature of cGHRL gene. Result showed that this 8 bp indel was significantly associated with body weight at the age of 28 days (BW28) and 56 days (BW56), eviscerated weight (EW) and leg muscle weight (LMW) (P<0.05), highly significantly associated with hatch weight (HW), BW14, 21, 35, 42, 49, 90 and body length (BL), dressed weight (DW), eviscerated weight with giblet (EWG), wing weight (WW), breast muscle weight (BMW) and head and neck weight (HNW) (P<0.01). Meanwhile, A allele (with 'CTAACCTG') was positive for chicken growth as individuals with AA genotype had the highest value of all traits. Analysis on cGhrelin mRNA level revealed that it differed significantly among individuals with three genotypes (P<0.05). Individuals with AB genotype had the highest mRNA level, whereas that of AA had the lowest one. It was concluded that this 8 bp indel of cGHRL gene was significantly associated with most body weight and body composition traits, and negative effect of endogenous Ghrelin on chicken growth were indicated by this study.
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Affiliation(s)
- Meixia Fang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China
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