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Sun Y, Li Y, Jiang X, Wu Q, Lin R, Chen H, Zhang M, Zeng T, Tian Y, Xu E, Zhang Y, Lu L. Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck. Poult Sci 2024; 103:104032. [PMID: 39003796 DOI: 10.1016/j.psj.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yan Li
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, P.R. China
| | - Qiong Wu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Min Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Tao Zeng
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Yong Tian
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Enrong Xu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yeqiong Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China..
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Ma H, Lin B, Yan Z, Tong Y, Liu H, He X, Zhang H. Phenotypic Identification, Genetic Characterization, and Selective Signal Detection of Huitang Duck. Animals (Basel) 2024; 14:1747. [PMID: 38929366 PMCID: PMC11201145 DOI: 10.3390/ani14121747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/17/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
The Huitang duck (HT), a long-domesticated elite local breed from Hunan Province, China, with excellent meat quality, has not had its population genetic structure and genomic selective sweeps extensively studied to date. This study measured the phenotypic characteristics of HT and conducted comparative analysis between HT and 16 different duck breeds, including wild, indigenous, and meat breeds, to characterize its population structure and genetic potential. The results revealed that HT is a dual-purpose indigenous breed with a genetic background closely related to the Youxian sheldrake and Linwu ducks. In the selective sweep analysis between HT and Linwu ducks, genes such as PLCG2, FN1, and IGF2BP2, which are associated with muscle growth and development, were identified near the 27 selection signals. The comparison between HT and Jinding ducks revealed 68 selective signals that contained important genes associated with ovarian development (GRIK4, MAP3K8, and TGIF1) and egg-laying behaviors (ERBB4). Selective sweep analysis between HT and Youxian sheldrake ducks found 93 selective regions covering genes related to both meat (IGF1R and IGFBP5) and egg-production (FOXO3 and ITPR1) traits. Our study may provide novel knowledge for exploring the population structure and genetic potential of HT, offering a theoretical basis for its breeding strategies in the future.
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Affiliation(s)
- Haojie Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
| | - Bingjin Lin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
| | - Zhiyao Yan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
| | - Yueyue Tong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
| | - Huichao Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
| | - Xi He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
- Hunan Engineering Research Center of Poultry Production Safety, Changsha 410128, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha 410128, China
| | - Haihan Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China; (H.M.); (B.L.); (Z.Y.); (Y.T.); (H.L.); (X.H.)
- Hunan Engineering Research Center of Poultry Production Safety, Changsha 410128, China
- Ministry of Education Engineering Research Center of Feed Safety and Efficient Use, Changsha 410128, China
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Rohmah L, Darwati S, Ulupi N, Khaerunnisa I, Sumantri C. Polymorphism of prolactin (PRL) gene exon 5 and its association with egg production in IPB-D1 chickens. Arch Anim Breed 2022; 65:449-455. [PMID: 36643022 PMCID: PMC9832302 DOI: 10.5194/aab-65-449-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The prolactin (PRL) gene regulates the egg production and incubation in laying chickens. Local chickens' reproductive systems will disrupt as a result of the incubation period activity, and they will lay fewer eggs. This study aimed to determine the prolactin gene polymorphism in IPB-D1 hens and its relationship to egg production. The polymorphism of the exon 5 prolactin gene was examined on 112 samples of the IPB-D1 chicken DNA collection from the Division of Animal Genetics and Breeding, Faculty of Animal Sciences, IPB University. By performing the phenol-chloroform method, the genomic DNA was obtained. A polymerase chain reaction (PCR) product with a size of 557 bp was produced as a result of the DNA amplification. Three single-nucleotide sequences were discovered. Three single-nucleotide polymorphisms (SNPs), g.7835A > G, g.7886A > T, and g.8052T > C, were found in exon 5 of the PRL gene. Each mutation was polymorphic and in Hardy-Weinberg equilibrium. The point mutation g.8052T > C significantly impacted the egg production of IPB-D1 chickens, according to the SNP association analysis on egg production, and may serve as a marker to enhance the selection for the features of egg production in IPB-D1 chickens.
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Affiliation(s)
- Lailatul Rohmah
- Department of Animal Production and Technology, Faculty of Animal
Sciences, IPB University, Bogor 16680, Indonesia
| | - Sri Darwati
- Department of Animal Production and Technology, Faculty of Animal
Sciences, IPB University, Bogor 16680, Indonesia
| | - Niken Ulupi
- Department of Animal Production and Technology, Faculty of Animal
Sciences, IPB University, Bogor 16680, Indonesia
| | - Isyana Khaerunnisa
- Research Center for Applied Zoology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Cece Sumantri
- Department of Animal Production and Technology, Faculty of Animal
Sciences, IPB University, Bogor 16680, Indonesia
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4
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Garza-Rodríguez ML, Rodríguez-Sanchez IP, González-Álvarez R, Luna M, Burciaga-Flores CH, Alcorta-Nuñez F, Solis-Coronado O, Bautista de Lucio VM, Ramírez-Correa GA, Vidal-Gutiérrez O, Pérez-Ibave DC. Prolactin Expression in the Baboon ( Papio hamadryas) Eye. Animals (Basel) 2022; 12:2288. [PMID: 36078009 PMCID: PMC9455022 DOI: 10.3390/ani12172288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 01/14/2023] Open
Abstract
Prolactin (PRL) is a hormone expressed in lactotrophs cells of the pituitary gland in primates. Extra pituitary expression of PRL has been reported, including the eye; however, expression in the developing eye of primates is limited. The aim of the study was determining the expression of PRL and PRL receptor (PRLR) (mRNAs and proteins) in adult and fetal baboon (Papio hamadryas) ocular tissues. METHODS We analyzed PRL and PRLR in baboon eyes tissues by immunofluorescence. The mRNAs of PRL and PRLR were detected by RT-PCR, cDNA was cloned, and sequenced. Furthermore, we performed a phylogenetic analysis to identify the evolutionary forces that underlie the divergence of PRL and PRLR primate genes. RESULTS We observed the expression of PRL and PRLR (mRNAs and proteins) in all retinal cell lineages of fetal and adult baboon. PRL and PRLR fit the hypothesis of evolutionary purifying gene selection. CONCLUSIONS mRNA and protein of PRL and PRLR are expressed in fetal and adult baboon retinal tissue. PRL may trigger autocrine and paracrine-specific actions in retinal cell lines.
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Affiliation(s)
- María Lourdes Garza-Rodríguez
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
| | - Iram Pablo Rodríguez-Sanchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico
| | | | - Maricela Luna
- Departamento de Neurobiología Celular y Molecular, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla 76230, Mexico
| | - Carlos Horacio Burciaga-Flores
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
| | - Fernando Alcorta-Nuñez
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
| | - Orlando Solis-Coronado
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
- División de Anatomía Patológica, Hospital General “Dr. Manuel Gea González”, Secretaría de Salud, Ciudad de México 14080, Mexico
| | - Víctor Manuel Bautista de Lucio
- Departamento de Microbiología y Proteómica Ocular, Instituto de Oftalmología “Fundación de Asistencia Privada Conde de Valenciana”, Ciudad de México 06800, Mexico
| | - Genaro A. Ramírez-Correa
- Department of Molecular Science, University of Texas Health Rio Grande Valley, McAllen, TX 78550, USA
| | - Oscar Vidal-Gutiérrez
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
| | - Diana Cristina Pérez-Ibave
- Servicio de Oncología, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey 64440, Mexico
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5
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Bello SF, Adeola AC, Nie Q. The study of candidate genes in the improvement of egg production in ducks – a review. Poult Sci 2022; 101:101850. [PMID: 35544958 PMCID: PMC9108513 DOI: 10.1016/j.psj.2022.101850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/01/2022] Open
Abstract
Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.
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Gao J, Xu W, Zeng T, Tian Y, Wu C, Liu S, Zhao Y, Zhou S, Lin X, Cao H, Lu L. Genome-Wide Association Study of Egg-Laying Traits and Egg Quality in LingKun Chickens. Front Vet Sci 2022; 9:877739. [PMID: 35795788 PMCID: PMC9251537 DOI: 10.3389/fvets.2022.877739] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/23/2022] [Indexed: 11/23/2022] Open
Abstract
Egg production is the most important trait of laying hens. To identify molecular markers and candidate genes associated with egg production and quality, such as body weight at first oviposition (BWF), the number of eggs produced in 500 days (EN500), egg weight (EW), egg shell thickness (EST), egg shell strength (ESS), and Haugh unit (HU), a genome-wide analysis was performed in 266 LingKun Chickens. The results showed that thirty-seven single nucleotide polymorphisms (SNPs) were associated with all traits (p < 9.47 × 10−8, Bonferroni correction). These SNPs were located in close proximity to or within the sequence of the thirteen candidate genes, such as Galanin And GMAP Prepropeptide (GAL), Centromere Protein (CENPF), Glypican 2 (GPC2), Phosphatidylethanolamine N-Methyltransferase (PEMT), Transcription Factor AP-2 Delta (TFAP2D), and Carboxypeptidase Q (CPQ) gene related to egg-laying and Solute Carrier Family 5 Member 7 (SLC5A7), Neurocalcin Delta (NCALD), Proteasome 20S Subunit Beta 2 (PSMB2), Slit Guidance Ligand 3 (SLIT3), and Tubulin Tyrosine Ligase Like 7 (TTLL7) genes related to egg quality. Interestingly, one of the genes involved in bone formation (SLIT3) was identified as a candidate gene for ESS. Our candidate genes and SNPs associated with egg-laying traits were significant for molecular breeding of egg-laying traits and egg quality in LingKun chickens.
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Affiliation(s)
- Jinfeng Gao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Chunqin Wu
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Suzhen Liu
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Yan Zhao
- Wenzhou Vocational College of Science and Technology, Wenzhou, China
| | - Shuhe Zhou
- Wenzhou Golden Land Agricultural Development Co., Ltd., Wenzhou, China
| | - Xinqin Lin
- Wenzhou Golden Land Agricultural Development Co., Ltd., Wenzhou, China
| | - Hongguo Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Hongguo Cao
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- *Correspondence: Lizhi Lu
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Han X, Song Z, Wang W, Tang H. Polymorphism in the 5' regulatory region of CTNNB1 gene and association with age at first lay and egg production. Br Poult Sci 2022; 63:510-518. [PMID: 35164622 DOI: 10.1080/00071668.2022.2042484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. The Wnt signalling pathway is centred on the fact that catenin beta-1(CTNNB1) participates in the regulation of ovarian follicle development. The aim of the following study was to identify the polymorphism in the 5' regulatory region of the chicken CTNNB1 gene and evaluate the association between SNPs and egg production traits.2. The study demonstrated that the 5' regulatory region of the CTNNB1 gene has ten SNPs in the chicken flock. After Bonferroni correction for multiple testing, five SNPs (rs315692306, 2:g43385123, rs735854102, 2:g43385457 and rs737907370) were significantly correlated with egg laying traits.3. An association study of the haplotypes with egg laying traits revealed that both haplotypes in block 1 (consisting of rs735052881, rs740662190, rs315692306, and 2:43385123) and block 2 (consisting of rs735854102 and 2:g43385457) were associated with point of lay age and the number of eggs laid at 18-23 weeks. Prediction of transcription factor binding sites showed that transcription factors changed after mutation in block 2. The luciferase assay revealed that the priming activity of the CA haplotype in block2 was the highest.4. Taken together, the rs315692306, 2:g43385123, rs735854102, 2:g43385457 and rs737907370 in the 5' regulatory region of the CTNNB1 gene have significant impacts on egg production.
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Affiliation(s)
- Xu Han
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Zhifang Song
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
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Liao CM, Tan GH, You MF, Li JZ, Wu L, Qin YY, Zhang YY. Genetic variants in SCNN1B and AHCYL1 are associated with eggshell quality in Chinese domestic laying ducks ( Anas platyrhynchos). Br Poult Sci 2021; 63:454-465. [PMID: 34923880 DOI: 10.1080/00071668.2021.2019678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. The objective of this study was to investigate the evolution of SCNN1B and AHCYL1 proteins among 10 domestic and mammalian animals, to uncover the expression patterns of SCNN1B and AHCYL1 genes in ducks, identify the genetic variants of the SCNN1B and AHCYL1 genes and analyse their effects on eggshell quality.2. Expression profiles of the SCNN1B and AHCYL1 genes in Sansui female ducks were determined using real-time fluorescence quantitative PCR to identify SNPs. The duck SCNN1B and AHCYL1 genes were amplified to identify SNPs. A total of 502 Sansui female ducks were genotyped by sequencing, and the associations between the mRNA expression/SNP genotypes and six eggshell quality indices were analysed using PASW Statistics 18.0.3. The results showed that the SCNN1B and AHCYL1 proteins are highly conserved in different mammalian or domestic animals, especially the AHCYL1 protein. The SCNN1B and AHCYL1 genes were widely expressed in different tissues of male and female ducks, and expression level in the uterus was greater than in other tissues. The expression of SCNN1B and AHCYL1 during oviposition cycle indicated that expression levels were related to the eggshell mineralisation stage.4. The mRNA expression levels of uterine SCNN1B and AHCYL1 genes were positively correlated with eggshell strength (ESS), percentage (ESP) and weight (ESW) (P<0.05), respectively. Ten novel SNPs in SCNN1B and AHCYL1 genes from Chinese domestic laying ducks were identified through PCR amplicon sequencing.5. Genetic association analysis indicated g.797509 C > T, g.797573 C > T and g.797834 C > T in SCNN1B gene and g.169244 T > A, g.169265 T > C and g.175311T > C in AHCYL1 gene had a significant effect on eggshell quality. Correlation analysis between the SNP genotype and SCNN1B and AHCYL1 genes expression in the uterus showed that the genotypes of g.797509 C>T, g.797573 C>T, g.797834 C>T, g.169244 T>A and g.175311T>C sites affected the expression of SCNN1B and AHCYL1 genes in utero (P<0.05).6. The study indicated SCNN1B and AHCYL1 as candidate genes to improve eggshell traits in ducks.
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Affiliation(s)
- Chao-Mei Liao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Guang-Hui Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Ming-Fang You
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Jie-Zhang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
| | - Lei Wu
- China Guizhou Anshun Lihua Animal Husbandry Co., Ltd
| | - Yuan-Yu Qin
- Agriculture and Rural Bureau of zhijin county, Guizhou Province, China
| | - Yi-Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, People's Republic of China
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9
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Asiamah CA, Liu Y, Ye R, Pan Y, Lu LL, Zou K, Zhao Z, Jiang P, Su Y. Polymorphism analysis and expression profile of the estrogen receptor 2 gene in Leizhou black duck. Poult Sci 2021; 101:101630. [PMID: 35033905 PMCID: PMC8762077 DOI: 10.1016/j.psj.2021.101630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/13/2021] [Accepted: 11/25/2021] [Indexed: 12/30/2022] Open
Abstract
Our previous study on the ovarian transcriptomic analysis in Leizhou black duck revealed that the ESR2 gene was involved in hormone regulation in reproduction and the estrogen signaling pathway related to reproductive performance was enriched. This suggested that ESR2 may have a functional role in the reproductive performance of the Leizhou black duck. Thus, this study aimed at evaluating the polymorphism of the ESR2 gene and its association with egg-laying traits and the distribution pattern of ESR2 mRNA in laying and non-laying Leizhou black ducks. In this study, genomic DNA was extracted from blood samples of 101 Leizhou black ducks to identify single nucleotide polymorphisms (SNPs) of the ESR2 gene to elucidate molecular markers highly associated with egg-laying traits. Four each of laying and non-laying Leizhou black ducks were selected to collect different tissues to analyze the ESR2 gene expression. A total of 23 SNPs were identified and association analysis of the single SNP sites showed that SNPs g.56805646 T>C and exon 3-20G>A were significantly (P < 0.05) associated with egg weight. Ducks with CT and AG genotypes had significantly higher (P < 0.05) egg weights than their respective other genotypes. Haplotype association analysis of g.56805646 T>C and exon 3-20G>A showed that the haplotypes were significantly associated with egg weight. Higher egg weight was seen in individuals with H3H4 haplotypes. In the hypothalamus-pituitary-gonadal (HPG) axis, the results of qRT/PCR showed that ESR2 mRNA was significantly (P < 0.05) expressed in the ovaries of both duck groups than in the hypothalamus and pituitary. In the oviduct, ESR2 was significantly (P < 0.05) higher in the infundibulum and magnum of laying and non-laying ducks respectively. This study provides a molecular marker for selecting Leizhou black ducks for egg production. In addition, it offers theoretical knowledge for studying the related biological functions of the ESR2 gene at the cellular level.
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Affiliation(s)
- Collins Amponsah Asiamah
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Yuanbo Liu
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Rungen Ye
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Yiting Pan
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Li-Li Lu
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Kun Zou
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Zhihui Zhao
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Ping Jiang
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China
| | - Ying Su
- College of Coastal Agriculture, Guangdong Ocean University, Zhanjiang, 524025, Guangdong, PR China.
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Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method. Mol Biol Rep 2021; 48:3629-3635. [PMID: 33893925 PMCID: PMC8065318 DOI: 10.1007/s11033-021-06349-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/08/2021] [Indexed: 12/14/2022]
Abstract
PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.
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11
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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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12
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Tan GH, Li JZ, Zhang YY, You MF, Liao CM, Zhang YG. Association of PRKCA expression and polymorphisms with layer duck eggshell quality. Br Poult Sci 2020; 62:8-16. [PMID: 32893664 DOI: 10.1080/00071668.2020.1817329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
1. Eggshell quality is important for the poultry industry. Calcium is deposited during eggshell formation, and protein kinase C alpha (PRKCA) is involved in transmembrane transport of calcium ions in cells. However, the biological function of PRKCA in poultry is still not understood. Therefore, the aim of this study was to explore the association of mRNA expression and single nucleotide polymorphisms (SNPs) of the PRKCA gene with eggshell quality in laying ducks. 2. The mRNA expression and SNPs of the PRKCA gene were detected by real-time fluorescence quantitative PCR (qRT-PCR) and sequencing of PCR products in 45-week-old female Sansui ducks, which is a high production layer duck breed in China. The association of mRNA expression and SNPs in the PRKCA gene with layer duck eggshell traits was analysed using SPSS (v18.0) software. 3. The results demonstrated that PRKCA mRNA was widely expressed in all examined tissues, and expression was highest in kidney and lowest in the gizzard. Furthermore, the PRKCA mRNA level in uterus was significantly positively correlated with eggshell strength and eggshell weight (P < 0.05). Three novel SNPs, the synonymous mutations of g.9571770 T > C in exon 5, g.9583222 C > T and g.9583227 G > A in exon 7, were found in the PRKCA gene, giving four haplotypes and 10 diplotypes, which affected the mRNA secondary structure and free energy. The g.9583222 C > T and g.9583227 G > A mutations were significantly associated with eggshell strength (P < 0.05). Diplotype H1H1 was advantageous for increasing the strength and thickness of an eggshell. 4. In conclusion, the study showed that the mRNA transcription and genetic variation in the PRKCA gene could significantly affect the strength of duck eggshell and that the PRKCA gene is an important candidate gene for improving eggshell quality in poultry.
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Affiliation(s)
- G H Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University , Guiyang, Guizhou, People's Republic of China
| | - J Z Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University , Guiyang, Guizhou, People's Republic of China
| | - Y Y Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University , Guiyang, Guizhou, People's Republic of China
| | - M F You
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University , Guiyang, Guizhou, People's Republic of China
| | - C M Liao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University , Guiyang, Guizhou, People's Republic of China
| | - Y G Zhang
- Tiantang Town Agricultural Technology Management Station , Tongren City, People's Republic of China
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13
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Sun Y, Wu Q, Pan J, Li T, Liu L, Chen D, Zhang X, Chen H, Li Y, Lin R. Identification of differentially expressed genes and signalling pathways in the ovary of higher and lower laying ducks. Br Poult Sci 2020; 61:609-614. [PMID: 33012177 DOI: 10.1080/00071668.2020.1792834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1. Ovarian transcriptomic profiling between birds showing high egg number (HEN) and birds of low egg number (LEN) in Longyan Shan-ma ducks at 71 weeks of age was carried out using Illumina Hiseq 2500 technology. 2. A total of 343 differentially expressed genes (DEGs, 269 upregulated and 74 downregulated) were identified between HEN and LEN ovaries. These DEGs were enriched in 30 Gene Ontology terms. Pathway functional analysis found that the DEGs were enriched in 10 metabolic pathways (P < 0.05), one of which was regulation of the actin cytoskeleton pathway (Q < 0.05). 3. Three integrin family genes, ITGB2, ITGB5 and ITGA8 were differentially expressed in the RNA-seq and qPCR experiments. 4. The DEGs and signalling pathways identified in ovarian tissue in this study provide new insights into high egg production in Longyan Shan-ma duck.
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Affiliation(s)
- Y Sun
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology , Longyan, Fujian, P.R. China.,Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University , Longyan, Fujian, P.R. China
| | - Q Wu
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology , Longyan, Fujian, P.R. China.,Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University , Longyan, Fujian, P.R. China
| | - J Pan
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China
| | - T Li
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China
| | - L Liu
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China
| | - D Chen
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China
| | - X Zhang
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China
| | - H Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District , Longyan, P.R. China
| | - Y Li
- College of Life Science, Longyan University , Longyan, Fujian, P.R. China.,Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology , Longyan, Fujian, P.R. China.,Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Fujian Province University , Longyan, Fujian, P.R. China
| | - R Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District , Longyan, P.R. China
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Zou K, Asiamah CA, Lu LL, Liu Y, Pan Y, Chen T, Zhao Z, Su Y. Ovarian transcriptomic analysis and follicular development of Leizhou black duck. Poult Sci 2020; 99:6173-6187. [PMID: 33142535 PMCID: PMC7647846 DOI: 10.1016/j.psj.2020.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/10/2020] [Accepted: 08/15/2020] [Indexed: 12/19/2022] Open
Abstract
This study investigated the factors that caused the differences in egg production during the development of ovarian follicles in Leizhou black ducks. Leizhou black ducks population was divided into 2 groups as high-yield group (HG) and low-yield group (LG). The number of eggs (NE), age at first egg (AFE), weight at first egg, and egg weight (EW) of both groups were recorded, and differences were analyzed using the t test. The logistic model was used to simulate the egg production curves to analyze the production rules. The ovarian follicles of both duck groups were collected to count the number of different grades sized follicles, weigh the ovaries, and observe follicular sections to analyze the developmental differences. Ovarian transcriptomic sequencing was performed to investigate differentially expressed genes and signal pathways in both duck groups. The results revealed a significant difference (P < 0.01) in the NE laid, AFE, and EW between both groups. Comparatively, HG had significantly more (P < 0.01) large yellow follicles (LYF) than LG. The density of medullary layer cells of the follicle section was greater in HG than LG ducks. Transcriptome sequencing revealed a total of 1,027 differentially expressed genes between the HG and LG ducks of which 495 genes were upregulated, and 532 genes were downregulated. Fifty genes were related to reproduction and reproductive processes. Kyoto Encyclopedia of Genes and Genomes–enriched signaling pathways revealed 274 signal pathways enriched in these differentially expressed genes of which the steroid biosynthesis pathway was significantly enriched. Analysis (Q < 0.05) showed that HSD3β → gonadotropin-releasing hormone (GnRH) and estrogen receptor (ESR) → LHβ/ERK1/2 were enriched in the steroid biosynthesis signal pathway. Follicle-stimulating hormone signal pathway mediated by HSD3β → GnRH and ESR → LHβ/ERK1/2 may be involved in ovarian follicle development to regulate LYF reserve process and affect its ovulation cycle, which in turn influence the egg production of Leizhou black ducks.
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Affiliation(s)
- Kun Zou
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | | | - Li-Li Lu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Yuanbo Liu
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Yiting Pan
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Tongxin Chen
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China
| | - Zhihui Zhao
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China.
| | - Ying Su
- College of Agriculture, Guangdong Ocean University, Zhanjiang 524025, PR China.
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