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Registro Completo |
Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
Data corrente: |
16/08/2021 |
Data da última atualização: |
17/08/2021 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
BRUSCADIN, J. J.; SOUZA, M. M. de; OLIVEIRA, K. S. de; ROCHA, M. I. P.; AFONSO, J.; CARDOSO, T. F.; ZERLOTINI NETO, A.; COUTINHO, L. L.; NICIURA, S. C. M.; REGITANO, L. C. de A. |
Afiliação: |
JENNIFER JESSICA BRUSCADIN, UFSCAR; MARCELA MARIA DE SOUZA, IOWA STATE UNIVERSITY; KARINA SANTOS DE OLIVEIRA, UFSCAR; MARINA IBELLI PEREIRA ROCHA, UFSCAR; JULIANA AFONSO, ESALQ/USP; TAINÃ FIGUEIREDO CARDOSO; ADHEMAR ZERLOTINI NETO, CNPTIA; LUIZ LEHMANN COUTINHO, ESALQ/USP; SIMONE CRISTINA MEO NICIURA, CPPSE; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
Título: |
Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. |
Ano de publicação: |
2021 |
Fonte/Imprenta: |
Scientific Reports, v. 11, p. 1-14, 2021. |
DOI: |
https://doi.org/10.1038/s41598-021-86782-2 |
Idioma: |
Inglês |
Notas: |
Article number: 7321. |
Conteúdo: |
Abstract. Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. MenosAbstract. Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that var... Mostrar Tudo |
Palavras-Chave: |
Allele-specific expression; Allelic expression; Expressão alélica; Imprint genômico; Loci de característica quantitativa; Polimorfismo de nucleotídeo único. |
Thesagro: |
Bos Indicus; Gado Nelore. |
Thesaurus Nal: |
Genomic imprinting; Quantitative trait loci; Single nucleotide polymorphism. |
Categoria do assunto: |
-- G Melhoramento Genético |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/225232/1/MuscleAlleleSpecific.pdf
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Marc: |
LEADER 03076naa a2200385 a 4500 001 2133623 005 2021-08-17 008 2021 bl uuuu u00u1 u #d 024 7 $ahttps://doi.org/10.1038/s41598-021-86782-2$2DOI 100 1 $aBRUSCADIN, J. J. 245 $aMuscle allele-specific expression QTLs may affect meat quality traits in Bos indicus.$h[electronic resource] 260 $c2021 500 $aArticle number: 7321. 520 $aAbstract. Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes. 650 $aGenomic imprinting 650 $aQuantitative trait loci 650 $aSingle nucleotide polymorphism 650 $aBos Indicus 650 $aGado Nelore 653 $aAllele-specific expression 653 $aAllelic expression 653 $aExpressão alélica 653 $aImprint genômico 653 $aLoci de característica quantitativa 653 $aPolimorfismo de nucleotídeo único 700 1 $aSOUZA, M. M. de 700 1 $aOLIVEIRA, K. S. de 700 1 $aROCHA, M. I. P. 700 1 $aAFONSO, J. 700 1 $aCARDOSO, T. F. 700 1 $aZERLOTINI NETO, A. 700 1 $aCOUTINHO, L. L. 700 1 $aNICIURA, S. C. M. 700 1 $aREGITANO, L. C. de A. 773 $tScientific Reports$gv. 11, p. 1-14, 2021.
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Embrapa Pecuária Sudeste (CPPSE) |
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Registro Completo
Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia; Embrapa Semiárido. |
Data corrente: |
13/09/2021 |
Data da última atualização: |
15/09/2021 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Circulação/Nível: |
A - 1 |
Autoria: |
RIBEIRO, T. P.; LOURENCO, I. T.; MELO, B. P. de; MORGANTE, C. V.; SALLES FILHO, A.; LINS, C. B. J.; FERREIRA, G. F.; MELLO, G. N.; MACEDO, L. L. P. de; LUCENA, W. A.; SILVA, M. C. M. da; OLIVEIRA‑NETO, O. B.; SA, M. F. G. de. |
Afiliação: |
THUANNE PIRES RIBEIRO, UNB; ISABELA TRISTAN LOURENCO TESSUTTI, Cenargen; BRUNO PAES DE MELO, UFV; CAROLINA VIANNA MORGANTE, CPATSA; ALVARO SALLES FILHO, UCB; CAMILA BARROZO JESUS LINS; GILANNA FALCÃO FERREIRA; GLÊNIA NUNES MELLO; LEONARDO LIMA PEPINO DE MACEDO, Cenargen; WAGNER ALEXANDRE LUCENA, Cenargen; MARIA CRISTINA MATTAR DA SILVA, Cenargen; OSMUNDO BRILHANTE OLIVEIRA‑NETO, Faculdade Planalto Central; MARIA FATIMA GROSSI DE SA, Cenargen. |
Título: |
Improved cotton transformation protocol mediated by Agrobacterium and biolistic combined-methods. |
Ano de publicação: |
2021 |
Fonte/Imprenta: |
Planta, v. 254, 20, 2021. |
ISSN: |
1432-2048; 0032-0935 |
DOI: |
https://doi-org.ez103.periodicos.capes.gov.br/10.1007/s00425-021-03666-5 |
Idioma: |
Inglês |
Conteúdo: |
Cotton (Gossypium spp.) is the most important crop for natural textile fiber production worldwide. Nonetheless, one of the main challenges in cotton production are the losses resulting from insect pests, pathogens, and abiotic stresses. One effective way to solve these issues is to use genetically modified (GM) varieties. Herein, we describe an improved protocol for straightforward and cost-effective genetic transformation of cotton embryo axes, merging biolistics and Agrobacterium. The experimental steps include (1) Agrobacterium preparation, (2) seed sterilization, (3) cotton embryo excision, (4) lesion of shoot-cells by tungsten bombardment, (5) Agrobacterium-mediated transformation, (6) embryo co-culture, (7) regeneration and selection of transgenic plants in vitro, and (8) molecular characterization of plants. Due to the high regenerative power of the embryonic axis and the exceptional ability of the meristem cells for plant regeneration through organogenesis in vitro, this protocol can be performed in approximately 4?10 weeks, with an average plant regeneration of about 5.5% (±?0.53) and final average transformation efficiency of 60% (±?0.55). The transgene was stably inherited, and most transgenic plants hold a single copy of the transgene, as desirable and expected in Agrobacterium-mediated transformation. Additionally, the transgene was stably expressed over generations, and transgenic proteins could be detected at high levels in the T2 generation of GM cotton plants. The T2 progeny showed no phenotypic or productivity disparity compared to wild-type plants. Collectively, the use of cotton embryo axes and the enhanced DNA-delivery system by combining particle bombardment and Agrobacterium infection enabled efficient transgenic plant recovery, overcoming usual limitations associated with the recalcitrance of several cotton genotypes subjected to somatic embryogenesis. The improved approach states this method?s success for cotton genetic modification, allowing us to obtain GM cotton plants carrying traits, which are of fundamental relevance for the advancement of global agribusiness. MenosCotton (Gossypium spp.) is the most important crop for natural textile fiber production worldwide. Nonetheless, one of the main challenges in cotton production are the losses resulting from insect pests, pathogens, and abiotic stresses. One effective way to solve these issues is to use genetically modified (GM) varieties. Herein, we describe an improved protocol for straightforward and cost-effective genetic transformation of cotton embryo axes, merging biolistics and Agrobacterium. The experimental steps include (1) Agrobacterium preparation, (2) seed sterilization, (3) cotton embryo excision, (4) lesion of shoot-cells by tungsten bombardment, (5) Agrobacterium-mediated transformation, (6) embryo co-culture, (7) regeneration and selection of transgenic plants in vitro, and (8) molecular characterization of plants. Due to the high regenerative power of the embryonic axis and the exceptional ability of the meristem cells for plant regeneration through organogenesis in vitro, this protocol can be performed in approximately 4?10 weeks, with an average plant regeneration of about 5.5% (±?0.53) and final average transformation efficiency of 60% (±?0.55). The transgene was stably inherited, and most transgenic plants hold a single copy of the transgene, as desirable and expected in Agrobacterium-mediated transformation. Additionally, the transgene was stably expressed over generations, and transgenic proteins could be detected at high levels in the T2 generation of GM cotton plant... Mostrar Tudo |
Palavras-Chave: |
Embryonic axis; Genotype-independent transformation; Modificação genética do algodão. |
Thesagro: |
Agrobacterium Tumefaciens; Algodão; DNA; Gossypium Hirsutum; Método de Melhoramento; Planta Transgênica. |
Thesaurus NAL: |
Abiotic stress; Biolistics; Cotton; Genetic transformation; Genetically modified plants. |
Categoria do assunto: |
-- G Melhoramento Genético |
Marc: |
LEADER 03519naa a2200457 a 4500 001 2134441 005 2021-09-15 008 2021 bl uuuu u00u1 u #d 022 $a1432-2048; 0032-0935 024 7 $ahttps://doi-org.ez103.periodicos.capes.gov.br/10.1007/s00425-021-03666-5$2DOI 100 1 $aRIBEIRO, T. P. 245 $aImproved cotton transformation protocol mediated by Agrobacterium and biolistic combined-methods.$h[electronic resource] 260 $c2021 520 $aCotton (Gossypium spp.) is the most important crop for natural textile fiber production worldwide. Nonetheless, one of the main challenges in cotton production are the losses resulting from insect pests, pathogens, and abiotic stresses. One effective way to solve these issues is to use genetically modified (GM) varieties. Herein, we describe an improved protocol for straightforward and cost-effective genetic transformation of cotton embryo axes, merging biolistics and Agrobacterium. The experimental steps include (1) Agrobacterium preparation, (2) seed sterilization, (3) cotton embryo excision, (4) lesion of shoot-cells by tungsten bombardment, (5) Agrobacterium-mediated transformation, (6) embryo co-culture, (7) regeneration and selection of transgenic plants in vitro, and (8) molecular characterization of plants. Due to the high regenerative power of the embryonic axis and the exceptional ability of the meristem cells for plant regeneration through organogenesis in vitro, this protocol can be performed in approximately 4?10 weeks, with an average plant regeneration of about 5.5% (±?0.53) and final average transformation efficiency of 60% (±?0.55). The transgene was stably inherited, and most transgenic plants hold a single copy of the transgene, as desirable and expected in Agrobacterium-mediated transformation. Additionally, the transgene was stably expressed over generations, and transgenic proteins could be detected at high levels in the T2 generation of GM cotton plants. The T2 progeny showed no phenotypic or productivity disparity compared to wild-type plants. Collectively, the use of cotton embryo axes and the enhanced DNA-delivery system by combining particle bombardment and Agrobacterium infection enabled efficient transgenic plant recovery, overcoming usual limitations associated with the recalcitrance of several cotton genotypes subjected to somatic embryogenesis. The improved approach states this method?s success for cotton genetic modification, allowing us to obtain GM cotton plants carrying traits, which are of fundamental relevance for the advancement of global agribusiness. 650 $aAbiotic stress 650 $aBiolistics 650 $aCotton 650 $aGenetic transformation 650 $aGenetically modified plants 650 $aAgrobacterium Tumefaciens 650 $aAlgodão 650 $aDNA 650 $aGossypium Hirsutum 650 $aMétodo de Melhoramento 650 $aPlanta Transgênica 653 $aEmbryonic axis 653 $aGenotype-independent transformation 653 $aModificação genética do algodão 700 1 $aLOURENCO, I. T. 700 1 $aMELO, B. P. de 700 1 $aMORGANTE, C. V. 700 1 $aSALLES FILHO, A. 700 1 $aLINS, C. B. J. 700 1 $aFERREIRA, G. F. 700 1 $aMELLO, G. N. 700 1 $aMACEDO, L. L. P. de 700 1 $aLUCENA, W. A. 700 1 $aSILVA, M. C. M. da 700 1 $aOLIVEIRA‑NETO, O. B. 700 1 $aSA, M. F. G. de 773 $tPlanta$gv. 254, 20, 2021.
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