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Registro Completo |
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Biblioteca(s): |
Embrapa Milho e Sorgo. |
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Data corrente: |
05/10/2023 |
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Data da última atualização: |
09/10/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
CHANDNANI, R.; QIN, T.; YE, H.; HU, H.; PANJVANI, K.; TOKIZAWA, M.; MACIAS, J. M.; MEDINA, A. A.; BERNARDINO, K. C.; PRADIER, P.-L.; BANIK, P.; MOONEY, A.; MAGALHAES, J. V. de; NGUYEN, H. T.; KOCHIAN, L. V. |
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Afiliação: |
RAHUL CHANDNANI, UNIVERSITY OF SASKATCHEWAN; TONGFEI QIN, UNIVERSITY OF SASKATCHEWAN; HENG YE, UNIVERSITY OF MISSOURI; HAIFEI HU, UNIVERSITY OF WESTERN AUSTRALIA; KARIM PANJVANI, UNIVERSITY OF SASKATCHEWAN; MUTSUTOMO TOKIZAWA, UNIVERSITY OF SASKATCHEWAN; JAVIER MORA MACIAS, UNIVERSITY OF SASKATCHEWAN; ALMA ARMENTA MEDINA, UNIVERSITY OF SASKATCHEWAN; KARINE C. BERNARDINO; PIERRE-LUC PRADIER UNIVERSITY OF SASKATCHEWAN, UNIVERSITY OF SASKATCHEWAN; PANKAJ BANIK, UNIVERSITY OF SASKATCHEWAN; ASHLYN MOONEY, UNIVERSITY OF SASKATCHEWAN; JURANDIR VIEIRA DE MAGALHAES, CNPMS; HENRY T. NGUYEN, UNIVERSITY OF MISSOURI; LEON V. KOCHIAN, UNIVERSITY OF SASKATCHEWAN. |
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Título: |
Application of an improved 2-dimensional high-throughput soybean root phenotyping platform to identify novel genetic variants regulating root architecture traits. |
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Ano de publicação: |
2023 |
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Fonte/Imprenta: |
Plant Phenomics, v. 5, article 97, 2023. |
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DOI: |
https://doi.org/10.34133/plantphenomics.0097 |
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Idioma: |
Inglês |
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Conteúdo: |
Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots. MenosNutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (... Mostrar Tudo |
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Thesagro: |
Genética Vegetal; Raiz; Seleção Fenótipa; Soja. |
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Categoria do assunto: |
G Melhoramento Genético |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/doc/1157100/1/Application-of-an-improved-2-dimensional-high-throughput-soybean-root.pdf
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Marc: |
LEADER 02746naa a2200349 a 4500
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005 2023-10-09
008 2023 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.34133/plantphenomics.0097$2DOI
100 1 $aCHANDNANI, R.
245 $aApplication of an improved 2-dimensional high-throughput soybean root phenotyping platform to identify novel genetic variants regulating root architecture traits.$h[electronic resource]
260 $c2023
520 $aNutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.
650 $aGenética Vegetal
650 $aRaiz
650 $aSeleção Fenótipa
650 $aSoja
700 1 $aQIN, T.
700 1 $aYE, H.
700 1 $aHU, H.
700 1 $aPANJVANI, K.
700 1 $aTOKIZAWA, M.
700 1 $aMACIAS, J. M.
700 1 $aMEDINA, A. A.
700 1 $aBERNARDINO, K. C.
700 1 $aPRADIER, P.-L.
700 1 $aBANIK, P.
700 1 $aMOONEY, A.
700 1 $aMAGALHAES, J. V. de
700 1 $aNGUYEN, H. T.
700 1 $aKOCHIAN, L. V.
773 $tPlant Phenomics$gv. 5, article 97, 2023.
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Registro original: |
Embrapa Milho e Sorgo (CNPMS) |
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Registro Completo
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Biblioteca(s): |
Embrapa Soja. |
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Data corrente: |
29/12/2014 |
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Data da última atualização: |
07/04/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
BENCKE-MALATO, M.; CABREIRA, C.; WIEBKE-STROHM, B.; BÜCKER-NETO, L.; MANCINI, E.; OSORIO, M. B.; HOMRICH, M. S.; TURCHETTO-ZOLET, A. C.; CARVALHO, M. C. C. G. de; STOLF, R.; WEBER, R. L. M.; WESTERGAARD, G.; CASTAGNARO, A. P.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C.; MARGIS-PINHEIRO, M.; BODANESE-ZANETTINI, M. H. |
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Afiliação: |
MARTA BENCKE-MALATO, UFRGS; CAROLINE CABREIRA, UFRGS; BEATRIZ WIEBKE-STROHM, UFRGS; LAURO BÜCKER-NETO, UFRGS; ESTEFANIA MANCINI, Instituto de Agrobiotecnologia Rosario SA; MARINA B. OSORIO, UFRGS; MILENA S. HOMRICH, UFRGS; ANDREIA CARINA TURCHETTO-ZOLET, UFRGS; MAYRA C. C. G. DE CARVALHO, CNPSO - estagiária; RENATA STOLF, CNPSO - estagiària; RICARDO L. M. WEBER, UFRGS; GASTÓN WESTERGAARD, Instituto de Agrobiotecnologia Rosario SA; ATÍLIO P. CASTAGNARO, Estación Experimental Agroindustrial Obispo Colombres (EEAOC); RICARDO VILELA ABDELNOOR, CNPSO; FRANCISMAR CORREA MARCELINO-GUIMARÃES, CNPSO; MÁRCIA MARGIS-PINHEIRO, UFRGS; MARIA HELENA BODANESE-ZANETTINI, UFRGS. |
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Título: |
Genome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhizi infection. |
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Ano de publicação: |
2014 |
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Fonte/Imprenta: |
BMC Plant Biology, v. 14, n. 1, article 236, Sept. 2014. |
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Páginas: |
18 p. |
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ISSN: |
1471-2229 |
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DOI: |
10.1186/s12870-014-0236-0 |
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Idioma: |
Inglês |
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Conteúdo: |
Background: Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of WRKY genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to P. pachyrhizi were identified. Results: As a result of a soybean genomic databases search, 182 WRKY-encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to P. pachyrhizi infection were identified using superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight WRKY genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and/or stronger compared with a susceptible genotype in response to P. pachyrhizi infection. Soybean somatic embryos were transformed in order to overexpress or silence WRKY genes. Embryos overexpressing a WRKY gene were obtained, but they were unable to convert into plants. When infected with P. pachyrhizi, the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants. Conclusions: The present study reports a genome-wide annotation of soybean WRKY family. The participation of some members in response to P. pachyrhizi infection was demonstrated. The results contribute to the elucidation of gene function and suggest the manipulation of WRKYs as a strategy to increase fungal resistance in soybean plants. MenosBackground: Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of WRKY genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to P. pachyrhizi were identified. Results: As a result of a soybean genomic databases search, 182 WRKY-encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to P. pachyrhizi infection were identified using superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight WRKY genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and/or stronger compared with a susceptible genotype in response to P. pachyrhizi infection. Soybean somatic embryos were transformed in order to overexpress or silence WRKY genes. Embryos overexpressing a WRKY gene were obtained, but they were unable to convert into plants. When infected with P. pachyrhizi, the leaves of the silenced transgenic line showed a higher number of lesions than ... Mostrar Tudo |
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Thesagro: |
Soja. |
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Thesaurus NAL: |
Soybeans. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/114583/1/Genome-wide-annotation-of-the-soybean-WRKY-family-and-functional-characterization-of-genes-involved-in-response-to-Phakopsora-pachyrhizi-infection.pdf
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Marc: |
LEADER 02998naa a2200373 a 4500
001 2003866
005 2022-04-07
008 2014 bl uuuu u00u1 u #d
022 $a1471-2229
024 7 $a10.1186/s12870-014-0236-0$2DOI
100 1 $aBENCKE-MALATO, M.
245 $aGenome-wide annotation of the soybean WRKY family and functional characterization of genes involved in response to Phakopsora pachyrhizi infection.$h[electronic resource]
260 $c2014
300 $a18 p.
520 $aBackground: Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of the most important soybean diseases. There are evidences that WRKYs are involved in the resistance of some soybean genotypes against that fungus. The number of WRKY genes already annotated in soybean genome was underrepresented. In the present study, a genome-wide annotation of the soybean WRKY family was carried out and members involved in the response to P. pachyrhizi were identified. Results: As a result of a soybean genomic databases search, 182 WRKY-encoding genes were annotated and 33 putative pseudogenes identified. Genes involved in the response to P. pachyrhizi infection were identified using superSAGE, RNA-Seq of microdissected lesions and microarray experiments. Seventy-five genes were differentially expressed during fungal infection. The expression of eight WRKY genes was validated by RT-qPCR. The expression of these genes in a resistant genotype was earlier and/or stronger compared with a susceptible genotype in response to P. pachyrhizi infection. Soybean somatic embryos were transformed in order to overexpress or silence WRKY genes. Embryos overexpressing a WRKY gene were obtained, but they were unable to convert into plants. When infected with P. pachyrhizi, the leaves of the silenced transgenic line showed a higher number of lesions than the wild-type plants. Conclusions: The present study reports a genome-wide annotation of soybean WRKY family. The participation of some members in response to P. pachyrhizi infection was demonstrated. The results contribute to the elucidation of gene function and suggest the manipulation of WRKYs as a strategy to increase fungal resistance in soybean plants.
650 $aSoybeans
650 $aSoja
700 1 $aCABREIRA, C.
700 1 $aWIEBKE-STROHM, B.
700 1 $aBÜCKER-NETO, L.
700 1 $aMANCINI, E.
700 1 $aOSORIO, M. B.
700 1 $aHOMRICH, M. S.
700 1 $aTURCHETTO-ZOLET, A. C.
700 1 $aCARVALHO, M. C. C. G. de
700 1 $aSTOLF, R.
700 1 $aWEBER, R. L. M.
700 1 $aWESTERGAARD, G.
700 1 $aCASTAGNARO, A. P.
700 1 $aABDELNOOR, R. V.
700 1 $aMARCELINO-GUIMARÃES, F. C.
700 1 $aMARGIS-PINHEIRO, M.
700 1 $aBODANESE-ZANETTINI, M. H.
773 $tBMC Plant Biology$gv. 14, n. 1, article 236, Sept. 2014.
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Embrapa Soja (CNPSO) |
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