Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus
Abstract
In this study, 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. As a result, 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,more »
- Authors:
- Publication Date:
- Research Org.:
- Univ. of Florida, Gainesville, FL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618603
- Alternate Identifier(s):
- OSTI ID: 1255227
- Grant/Contract Number:
- FG02-05ER64114; SC0003893
- Resource Type:
- Published Article
- Journal Name:
- BMC Plant Biology
- Additional Journal Information:
- Journal Name: BMC Plant Biology Journal Volume: 16 Journal Issue: 1; Journal ID: ISSN 1471-2229
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; adventitious root; QTL; populus, SUR2; vegetative propagation
Citation Formats
Ribeiro, Cintia L., Silva, Cynthia M., Drost, Derek R., Novaes, Evandro, Novaes, Carolina R. D. B., Dervinis, Christopher, and Kirst, Matias. Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus. United Kingdom: N. p., 2016.
Web. doi:10.1186/s12870-016-0753-0.
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. United Kingdom. https://doi.org/10.1186/s12870-016-0753-0
Ribeiro, Cintia L., Silva, Cynthia M., Drost, Derek R., Novaes, Evandro, Novaes, Carolina R. D. B., Dervinis, Christopher, and Kirst, Matias. Wed .
"Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus". United Kingdom. https://doi.org/10.1186/s12870-016-0753-0.
@article{osti_1618603,
title = {Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus},
author = {Ribeiro, Cintia L. and Silva, Cynthia M. and Drost, Derek R. and Novaes, Evandro and Novaes, Carolina R. D. B. and Dervinis, Christopher and Kirst, Matias},
abstractNote = {In this study, 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. As a result, 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. In conclusion, 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.},
doi = {10.1186/s12870-016-0753-0},
journal = {BMC Plant Biology},
number = 1,
volume = 16,
place = {United Kingdom},
year = {Wed Mar 16 00:00:00 EDT 2016},
month = {Wed Mar 16 00:00:00 EDT 2016}
}
https://doi.org/10.1186/s12870-016-0753-0
Web of Science
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