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Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus

BACKGROUND: Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of seve...

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Autores principales: Ribeiro, Cintia L., Silva, Cynthia M., Drost, Derek R., Novaes, Evandro, Novaes, Carolina R. D. B., Dervinis, Christopher, Kirst, Matias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793515/
https://www.ncbi.nlm.nih.gov/pubmed/26983547
http://dx.doi.org/10.1186/s12870-016-0753-0
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author Ribeiro, Cintia L.
Silva, Cynthia M.
Drost, Derek R.
Novaes, Evandro
Novaes, Carolina R. D. B.
Dervinis, Christopher
Kirst, Matias
author_facet Ribeiro, Cintia L.
Silva, Cynthia M.
Drost, Derek R.
Novaes, Evandro
Novaes, Carolina R. D. B.
Dervinis, Christopher
Kirst, Matias
author_sort Ribeiro, Cintia L.
collection PubMed
description BACKGROUND: Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development. RESULTS: Parental individuals and progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7–10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway. CONCLUSIONS: This study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of the Trp pathway flux appears to be directed to the synthesis of indole glucosinolates (IG), as suggested by the over-expression of SUR2. Individuals that are efficient in AR formation may utilize alternative (non-Trp) pathways to synthesize IAA, based on the observation that they down-regulate the expression of TSA1, one of the critical steps in the synthesis of tryptophan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0753-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-47935152016-03-16 Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus Ribeiro, Cintia L. Silva, Cynthia M. Drost, Derek R. Novaes, Evandro Novaes, Carolina R. D. B. Dervinis, Christopher Kirst, Matias BMC Plant Biol Research Article BACKGROUND: Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development. RESULTS: Parental individuals and progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7–10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway. CONCLUSIONS: This study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of the Trp pathway flux appears to be directed to the synthesis of indole glucosinolates (IG), as suggested by the over-expression of SUR2. Individuals that are efficient in AR formation may utilize alternative (non-Trp) pathways to synthesize IAA, based on the observation that they down-regulate the expression of TSA1, one of the critical steps in the synthesis of tryptophan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0753-0) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-16 /pmc/articles/PMC4793515/ /pubmed/26983547 http://dx.doi.org/10.1186/s12870-016-0753-0 Text en © Ribeiro et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Ribeiro, Cintia L.
Silva, Cynthia M.
Drost, Derek R.
Novaes, Evandro
Novaes, Carolina R. D. B.
Dervinis, Christopher
Kirst, Matias
Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title_full Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title_fullStr Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title_full_unstemmed Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title_short Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
title_sort integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in populus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793515/
https://www.ncbi.nlm.nih.gov/pubmed/26983547
http://dx.doi.org/10.1186/s12870-016-0753-0
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