- -

Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes

Mostrar el registro completo del ítem

Huang, B.; Hu, G.; Wang, K.; Frasse, P.; Maza, E.; Djari, A.; Deng, W.... (2021). Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes. Nature Communications. 12(1):1-14. https://doi.org/10.1038/s41467-021-27117-7

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/189409

Ficheros en el ítem

Thumbnail
Nombre: HuangHuWang - ...
Tamaño: 1.658Mb
Formato: PDF
Descripción: Versión editorial
Abrir/Preview

Metadatos del ítem

Título: Interaction of two MADS-box genes leads to growth phenotype divergence of all-flesh type of tomatoes
Autor: Huang, Baowen Hu, Guojian Wang, Keke Frasse, Pierre Maza, Elie Djari, Anis Deng, Wei Pirrello, Julien Burlat, Vincent Pons Puig, Clara GRANELL RICHART, ANTONIO Li, Zhengguo van der Rest, Benoit Bouzayen, Mondher
Fecha difusión:
Resumen:
[EN] All-flesh tomato cultivars are devoid of locular gel and exhibit enhanced firmness and improved postharvest storage. Here, we show that SlMBP3 is a master regulator of locular tissue in tomato fruit and that a deletion ...[+]
Derechos de uso: Reconocimiento (by)
Fuente:
Nature Communications. (issn: 2041-1723 )
DOI: 10.1038/s41467-021-27117-7
Editorial:
Nature Publishing Group
Versión del editor: https://doi.org/10.1038/s41467-021-27117-7
Código del Proyecto:
info:eu-repo/grantAgreement/EC/H2020/101000716/EU
info:eu-repo/grantAgreement/EC/H2020/679796/EU
Agradecimientos:
The authors are grateful to L. Lemonnier and D. Saint-Martin for transformation and cultivation of tomato plants and GeT-PlaGe core facility (INRAe Toulouse) for ChIP deep sequencing. The authors also want to thank Dr. ...[+]
Tipo: Artículo

References

Klee, H. J. & Giovannoni, J. J. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45, 41–59 (2011).

Osorio, S. et al. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. Plant Biotechnol. J. 18, 106–118 (2020).

Shi, Y. et al. A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening. Proc. Natl Acad. Sci. 118, e2102486118 (2021). [+]
Klee, H. J. & Giovannoni, J. J. Genetics and control of tomato fruit ripening and quality attributes. Annu. Rev. Genet. 45, 41–59 (2011).

Osorio, S. et al. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. Plant Biotechnol. J. 18, 106–118 (2020).

Shi, Y. et al. A tomato LATERAL ORGAN BOUNDARIES transcription factor, SlLOB1, predominantly regulates cell wall and softening components of ripening. Proc. Natl Acad. Sci. 118, e2102486118 (2021).

Wang, D., Yeats, T. H., Uluisik, S., Rose, J. K. C. & Seymour, G. B. Fruit softening: revisiting the role of pectin. Trends Plant Sci. 23, 302–310 (2018).

Uluisik, S. et al. Genetic improvement of tomato by targeted control of fruit softening. Nat. Biotechnol. 34, 950–952 (2016).

Musseau, C. et al. Identification of two new mechanisms that regulate fruit growth by cell expansion in tomato. Front. Plant Sci. 8, 1–15 (2017).

Pattison, R. J. et al. Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiol. 168, 1684–1701 (2015).

Mounet, F. et al. Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiol. 149, 1505–1528 (2009).

Lemaire-Chamley, M. et al. Changes in transcriptional profiles are associated with early fruit tissue specialization in tomato. Plant Physiol. 139, 750–769 (2005).

Cheng, G. W. & Huber, D. J. Alterations in structural polysaccharides during liquefaction of tomato locule tissue. Plant Physiol. 111, 447–457 (1996).

Vrebalov, J. et al. Fleshy fruit expansion and ripening are regulated by the tomato SHATTERPROOF gene TAGL1. Plant Cell 21, 3041–3062 (2009).

Giménez, E. et al. Transcriptional activity of the MADS box ARLEQUIN/TOMATO AGAMOUS-LIKE1 gene is required for cuticle development of tomato fruit. Plant Physiol. 168, 1036–1048 (2015).

Schilling, S., Pan, S., Kennedy, A. & Melzer, R. MADS-box genes and crop domestication: the jack of all traits. J. Exp. Bot. 69, 1447–1469 (2018).

Ezquer, I. et al. The developmental regulator SEEDSTICK controls structural and mechanical properties of the Arabidopsis seed coat. Plant Cell 28, 2478–2492 (2016).

Singh, R. et al. The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature 500, 340–344 (2013).

Zhang, J. et al. An AGAMOUS MADS-box protein, SlMBP3, regulates the speed of placenta liquefaction and controls seed formation in tomato. J. Exp. Bot. 70, 909–924 (2019).

Pinyopich, A. et al. Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature 424, 85–88 (2003).

Favaro, R. et al. MADS-box protein complexes control carpel and ovule development in Arabidopsis. Plant Cell 15, 2603–2611 (2003).

Huang, B. et al. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits. J. Exp. Bot. 68, 4869–4884 (2017).

Lemaire-Chamley, M. et al. NMR-Based tissular and developmental metabolomics of tomato fruit. Metabolites 9, 93 (2019).

Fujisawa, M. et al. Transcriptional regulation of fruit ripening by tomato FRUITFULL homologs and associated MADS box proteins. Plant Cell 26, 89–101 (2014).

Fernandez-Pozo, N. et al. The tomato expression atlas. Bioinformatics 33, 2397–2398 (2017).

Mathieu-Rivet, E. et al. Functional analysis of the anaphase promoting complex activator CCS52A highlights the crucial role of endo-reduplication for fruit growth in tomato. Plant J. 62, 727–741 (2010).

Chevalier, C. et al. Endoreduplication and fruit growth in tomato: evidence in favour of the karyoplasmic ratio theory. J. Exp. Bot. 65, 2731–2746 (2014).

Perrot-Rechenmann, C. Cellular responses to auxin: division versus expansion. Cold Spring Harb. Perspect. Biol. 2, a001446–a001446 (2010).

Seo, D. H., Jeong, H., Choi, Y. Do & Jang, G. Auxin controls the division of root endodermal cells. Plant Physiol. 0, 1–10 (2021).

Liu, L. et al. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. J. Exp. Bot. https://doi.org/10.1093/jxb/erab401 (2021).

Heijmans, K. et al. Redefining C and D in the petunia ABC. Plant Cell 24, 2305–2317 (2012).

Brooks, C., Nekrasov, V., Lippman, Z. B. & Van Eck, J. Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol. 166, 1292–1297 (2014).

Sarrion-Perdigones, A. et al. Goldenbraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology. Plant Physiol. 162, 1618–1631 (2013).

Chen, Y. et al. Roles of SlETR7, a newly discovered ethylene receptor, in tomato plant and fruit development. Hortic. Res. 7, 17 (2020).

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

Auwera, G. A. et al. From FastQ data to high‐confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinforma. 43, 11.10.1–11.10.33 (2013).

Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).

Duruflé, H. et al. Cell wall modifications of two Arabidopsis thaliana ecotypes, Col and Sha, in response to sub-optimal growth conditions: an integrative study. Plant Sci. 263, 183–193 (2017).

Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).

Hao, Y. et al. Auxin response factor SlARF2 Is an essential component of the regulatory mechanism controlling fruit ripening in tomato. PLOS Genet 11, e1005649 (2015).

Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915 (2019).

Anders, S., Pyl, P. T. & Huber, W. HTSeq-A python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

Thimm, O. et al. MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37, 914–939 (2004).

Song, L., Koga, Y. & Ecker, J. R. Profiling of transcription factor binding events by chromatin immunoprecipitation sequencing (ChIP-seq). Curr. Protoc. Plant Biol. 1, 293–306 (2016).

Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).

Ma, W., Noble, W. S. & Bailey, T. L. Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat. Protoc. 9, 1428–1450 (2014).

Zouine, M. et al. TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks. Plant J. 92, 727–735 (2017).

Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem