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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite; Embrapa Suínos e Aves. |
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Data corrente: |
09/03/2023 |
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Data da última atualização: |
09/03/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SILVA, A. N. da; IBELLI, A. M. G.; SAVOLDI, I. R.; CANTAO, M. E.; ZANELLA, E. L.; MARQUES, M. G.; SILVA, M. V. G. B.; PEIXOTO, J. de O.; LEDUR, M. C.; LOPES, J. S.; VARGAS, J. E.; ZANELLA, R. |
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Afiliação: |
ARTHUR NERY DA SILVA, Universidade de Passo Fundo; ADRIANA MERCIA GUARATINI IBELLI, CNPSA; IGOR RICARDO SAVOLDI, Universidade do Contestado/Concórdia; MAURICIO EGIDIO CANTAO, CNPSA; ERALDO LOURENSO ZANELLA, UNIVERSIDADE; MARIANA GROKE MARQUES, CNPSA; MARCOS VINICIUS GUALBERTO B SILVA, CNPGL; JANE DE OLIVEIRA PEIXOTO, CNPSA; MONICA CORREA LEDUR, CNPSA; JADER SILVA LOPES, BRF/Curitiba; JOSÉ EDUARDO VARGAS, Universidade Federal do Paraná; RICARDO ZANELLA, Universidade de Passo Fundo. |
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Título: |
Whole-exome sequencing indicated new candidate genes associated with unilateral cryptorchidism in pigs. |
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Ano de publicação: |
2023 |
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Fonte/Imprenta: |
Sexual Development, 9 Feb 2023. |
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DOI: |
10.1159/000528360 |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract:
Introduction: Cryptorchidism is a hereditary anomaly characterized by the incomplete descent of one or both testicles to the scrotum. One of the challenges of this anomaly is that the retained testicle maintains its endocrine function. As a consequence, cryptorchid animals produce hormone-tainted meat in comparison to castrated animals and are likely to be more aggressive. Cryptorchidism can lead to reduced animal welfare outcomes and cause economic losses. Identifying genetic markers for cryptorchidism is an essential step toward mitigating these negative outcomes and may facilitate genome manipulation to reduce the occurrence of cryptorchidism. Attempts to identify such markers have used genome-wide association studies. Using whole-exome sequencing, we aimed to identify single nucleotide polymorphisms (SNPs) in the coding regions of cryptorchid pigs and to characterize functional pathways concerning these SNPs.
Methods: DNA was extracted and sequenced from 5 healthy and 5 cryptorchid animals from the Landrace breed, using the Illumina HiSeq 2500 platform. Data were pre-processed using the SeqyClean tool and further mapped against the swine reference genome (Sus scrofa 11.1) using BWA software. GATK was used to identify polymorphisms (SNPs and InDels), which were annotated using the VEP tool. Network prediction and gene ontology enrichment analysis were conducted using the Cytoscape platform, and STRING software was used for visualization.
Results: A total of 63 SNPs were identified across the genes PIGB, CCPG1, COMMD9, LDLRAD3, TRIM44, MYLPF, SEPTIN, ZNF48, TIA1, FAIM2, KRT18, FBP1, FBP2, CTSL, DAPK1, DHX8, GPR179, DEPDC1B, ENSSSCG00000049573, ENSSSCG00000016384, ENSSSCG00000022657, ENSSSCG00000038825, and ENSSSCG00000001229. Using pathway enrichment analyses and network prospection, we have identified the following significant adjusted p value threshold of 0.001 involved with the biological function pathways of estrogen signaling, cytoskeleton organization, and the pentose phosphate pathway.
Conclusion: Our data suggest the involvement of new SNPs and genes in developing cryptorchidism in pigs. However, further studies are needed to validate our results in a larger cohort population. Variations in the GPR179 gene, with implications at the protein level, may be associated with the appearance of this anomaly in the swine. Finally, we are showing that the estrogen signaling pathway may be involved in the pathophysiological mechanisms of this congenital anomaly as previously reported in GWAS. MenosAbstract:
Introduction: Cryptorchidism is a hereditary anomaly characterized by the incomplete descent of one or both testicles to the scrotum. One of the challenges of this anomaly is that the retained testicle maintains its endocrine function. As a consequence, cryptorchid animals produce hormone-tainted meat in comparison to castrated animals and are likely to be more aggressive. Cryptorchidism can lead to reduced animal welfare outcomes and cause economic losses. Identifying genetic markers for cryptorchidism is an essential step toward mitigating these negative outcomes and may facilitate genome manipulation to reduce the occurrence of cryptorchidism. Attempts to identify such markers have used genome-wide association studies. Using whole-exome sequencing, we aimed to identify single nucleotide polymorphisms (SNPs) in the coding regions of cryptorchid pigs and to characterize functional pathways concerning these SNPs.
Methods: DNA was extracted and sequenced from 5 healthy and 5 cryptorchid animals from the Landrace breed, using the Illumina HiSeq 2500 platform. Data were pre-processed using the SeqyClean tool and further mapped against the swine reference genome (Sus scrofa 11.1) using BWA software. GATK was used to identify polymorphisms (SNPs and InDels), which were annotated using the VEP tool. Network prediction and gene ontology enrichment analysis were conducted using the Cytoscape platform, and STRING software was used for visualization.
Results: A total of 63 ... Mostrar Tudo |
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Palavras-Chave: |
Criptorquidismo; Sequenciamento completo do exoma; Whole-Exome Sequencing. |
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Thesagro: |
Gene Marcador; Genética Animal; Marcador Genético; Porco; Suíno. |
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Thesaurus Nal: |
Cryptorchidism. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 03604naa a2200373 a 4500
001 2152220
005 2023-03-09
008 2023 bl uuuu u00u1 u #d
024 7 $a10.1159/000528360$2DOI
100 1 $aSILVA, A. N. da
245 $aWhole-exome sequencing indicated new candidate genes associated with unilateral cryptorchidism in pigs.$h[electronic resource]
260 $c2023
520 $aAbstract: Introduction: Cryptorchidism is a hereditary anomaly characterized by the incomplete descent of one or both testicles to the scrotum. One of the challenges of this anomaly is that the retained testicle maintains its endocrine function. As a consequence, cryptorchid animals produce hormone-tainted meat in comparison to castrated animals and are likely to be more aggressive. Cryptorchidism can lead to reduced animal welfare outcomes and cause economic losses. Identifying genetic markers for cryptorchidism is an essential step toward mitigating these negative outcomes and may facilitate genome manipulation to reduce the occurrence of cryptorchidism. Attempts to identify such markers have used genome-wide association studies. Using whole-exome sequencing, we aimed to identify single nucleotide polymorphisms (SNPs) in the coding regions of cryptorchid pigs and to characterize functional pathways concerning these SNPs. Methods: DNA was extracted and sequenced from 5 healthy and 5 cryptorchid animals from the Landrace breed, using the Illumina HiSeq 2500 platform. Data were pre-processed using the SeqyClean tool and further mapped against the swine reference genome (Sus scrofa 11.1) using BWA software. GATK was used to identify polymorphisms (SNPs and InDels), which were annotated using the VEP tool. Network prediction and gene ontology enrichment analysis were conducted using the Cytoscape platform, and STRING software was used for visualization. Results: A total of 63 SNPs were identified across the genes PIGB, CCPG1, COMMD9, LDLRAD3, TRIM44, MYLPF, SEPTIN, ZNF48, TIA1, FAIM2, KRT18, FBP1, FBP2, CTSL, DAPK1, DHX8, GPR179, DEPDC1B, ENSSSCG00000049573, ENSSSCG00000016384, ENSSSCG00000022657, ENSSSCG00000038825, and ENSSSCG00000001229. Using pathway enrichment analyses and network prospection, we have identified the following significant adjusted p value threshold of 0.001 involved with the biological function pathways of estrogen signaling, cytoskeleton organization, and the pentose phosphate pathway. Conclusion: Our data suggest the involvement of new SNPs and genes in developing cryptorchidism in pigs. However, further studies are needed to validate our results in a larger cohort population. Variations in the GPR179 gene, with implications at the protein level, may be associated with the appearance of this anomaly in the swine. Finally, we are showing that the estrogen signaling pathway may be involved in the pathophysiological mechanisms of this congenital anomaly as previously reported in GWAS.
650 $aCryptorchidism
650 $aGene Marcador
650 $aGenética Animal
650 $aMarcador Genético
650 $aPorco
650 $aSuíno
653 $aCriptorquidismo
653 $aSequenciamento completo do exoma
653 $aWhole-Exome Sequencing
700 1 $aIBELLI, A. M. G.
700 1 $aSAVOLDI, I. R.
700 1 $aCANTAO, M. E.
700 1 $aZANELLA, E. L.
700 1 $aMARQUES, M. G.
700 1 $aSILVA, M. V. G. B.
700 1 $aPEIXOTO, J. de O.
700 1 $aLEDUR, M. C.
700 1 $aLOPES, J. S.
700 1 $aVARGAS, J. E.
700 1 $aZANELLA, R.
773 $tSexual Development, 9 Feb 2023.
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Embrapa Suínos e Aves (CNPSA) |
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| Registros recuperados : 14 | |
| 6. |  | RAMIRES, A. C. S.; LAMEIRA, O. A.; SOUZA, I. N. G.; PORTAL, R. K. V. P.; CAMPELO, M. F. Avaliação fenológica do jucá (Libidibia ferrea) Martius ex Tul. (Fabaceae). In: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA DA EMBRAPA AMAZÔNIA ORIENTAL, 23., 2019, Belém, PA. Anais. Belém, PA: Embrapa Amazônia Oriental, 2019. p. 119-123.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 7. | | RAMIRES, A. C. S.; LAMEIRA, O. A.; SOUZA, I. N. G.; PORTAL, R. K. V. P.; CAMPELO, M. F. Análise do período fenológico do açoita-cavalo em relação à precipitação pluviométrica. In: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA DA EMBRAPA AMAZÔNIA ORIENTAL, 23., 2019, Belém, PA. Anais. Belém, PA: Embrapa Amazônia Oriental, 2019. p. 124-127.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 8. | | CAMPELO, M. F.; LAMEIRA, O. A.; MOREIRA, R. K. V. P. P.; PACHECO, N. A.; RAMIRES, A. C. S. Fenologia da espécie Carapa guianensis Aubl. nas condições climatológicas de Belém-PA, Brasil. In: SIMPÓSIO INTERNACIONAL DE CLIMATOLOGIA, 8., 2019, Belém, PA. Anais 2019. [S.l.]: SBMET; [Belém, PA]: UFPA, 2019. p. 141-145.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 9. | | RAMIRES, A. C. S.; LAMEIRA, O. A.; SOUZA, I. N. G.; PORTAL, R. K. V. P.; CAMPELO, M. F. Fenologia reprodutiva da erva cidreira (Verbenaceae). In: SEMINÁRIO DE INICIAÇÃO CIENTÍFICA DA EMBRAPA AMAZÔNIA ORIENTAL, 23., 2019, Belém, PA. Anais. Belém, PA: Embrapa Amazônia Oriental, 2019. p. 128-131.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 10. | | LAMEIRA, O. A.; MOREIRA, R. K. V. P. P.; CAMPELO, M. F.; RODRIGUES, S. de M.; RAMIRES, A. C. S. Relação entre a fenologia da espécie Phyla betulifolia (kunth) Greene e elementos climáticos. Research, Society and Development, v.10, n.5, e50910515159, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 2 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 11. | | LAMEIRA, O. A.; CAMPELO, M. F.; MOREIRA, R. K. V. P. P.; RODRIGUES, S. de M.; RAMIRES, A. C. S. Substratos alternativos para propagação vegetativa de Psychotria ipecacuanha (Brotero) Stokes. Research, Society and Development, v. 10, n. 5, e49210515158, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 2 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 12. | | CAMPELO, M. F.; LAMEIRA, O. A.; RODRIGUES, S. de M.; SILVA, A. C. B. da; SANTOS, M. C. A. dos; MOREIRA, R. K. V. P. P.; MONTEIRO, A. N.; RAMIRES, A. C. S. Efeitos de diferentes concentrações de nitrato de amônio e nitrato de potássio na micropropagação de duas espécies de Hypericum l. Brazilian Journal of Development, v. 6, n. 11 , p. 85050-85056, nov. 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 13. | | LAMEIRA, O. A.; RODRIGUES, S. de M.; SOUZA, I. N. G.; CAMPELO, M. F.; MOREIRA, R. K. V. P. P.; SILVA, A. C. B. da; SANTOS, M. C. A. dos; RAMIRES, A. C. S. Efeitos de diferentes concentrações de nitrato de Amônio e nitrato de potássio na micropropagação de Physalis angulata L. Brazilian Journal of Development, v. 6, n. 11 , p. 85090-85097, nov. 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| 14. | | LAMEIRA, O. A.; RODRIGUES, S. de M.; COSTA, K. J. A.; CAMPELO, M. F.; MOREIRA, R. K. V. P. P.; SILVA, A. C. B. da; RAMIRES, A. C. S.; MONTEIRO, A. N. Efeitos de diferentes concentrações de nitrato de amônio e nitrato de potássio na micropropagação da valeriana officinalis l. (valerianaceae). Brazilian Journal of Development, v. 6, n. 11 , p. 85044-85049, nov. 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Amazônia Oriental. |
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| Registros recuperados : 14 | |
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