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Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions

Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples co...

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Autores principales: Yin, Jie, Gosney, Michael J., Dilkes, Brian P., Mickelbart, Michael V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508522/
https://www.ncbi.nlm.nih.gov/pubmed/31245703
http://dx.doi.org/10.1002/pld3.32
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author Yin, Jie
Gosney, Michael J.
Dilkes, Brian P.
Mickelbart, Michael V.
author_facet Yin, Jie
Gosney, Michael J.
Dilkes, Brian P.
Mickelbart, Michael V.
author_sort Yin, Jie
collection PubMed
description Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long‐chain fatty acid derivatives as compared to SH, whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F(1) hybrids than the mid‐parent averages and the accumulation of 17% of the metabolites in F(1) plants transgressed the level in both parents. Concentrations of several metabolites in F(1) hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly identified high‐quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment.
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spelling pubmed-65085222019-06-26 Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions Yin, Jie Gosney, Michael J. Dilkes, Brian P. Mickelbart, Michael V. Plant Direct Original Research Eutrema salsugineum is a model species for the study of plant adaptation to abiotic stresses. Two accessions of E. salsugineum, Shandong (SH) and Yukon (YK), exhibit contrasting morphology and biotic and abiotic stress tolerance. Transcriptome profiling and metabolic profiling from tissue samples collected during the dark period were used to investigate the molecular and metabolic bases of these contrasting phenotypes. RNA sequencing identified 17,888 expressed genes, of which 157 were not in the published reference genome, and 65 of which were detected for the first time. Differential expression was detected for only 31 genes. The RNA sequencing data contained 14,808 single nucleotide polymorphisms (SNPs) in transcripts, 3,925 of which are newly identified. Among the differentially expressed genes, there were no obvious candidates for the physiological or morphological differences between SH and YK. Metabolic profiling indicated that YK accumulates free fatty acids and long‐chain fatty acid derivatives as compared to SH, whereas sugars are more abundant in SH. Metabolite levels suggest that carbohydrate and respiratory metabolism, including starch degradation, is more active during the first half of the dark period in SH. These metabolic differences may explain the greater biomass accumulation in YK over SH. The accumulation of 56% of the identified metabolites was lower in F(1) hybrids than the mid‐parent averages and the accumulation of 17% of the metabolites in F(1) plants transgressed the level in both parents. Concentrations of several metabolites in F(1) hybrids agree with previous studies and suggest a role for primary metabolism in heterosis. The improved annotation of the E. salsugineum genome and newly identified high‐quality SNPs will permit accelerated studies using the standing variation in this species to elucidate the mechanisms of its diverse adaptations to the environment. John Wiley and Sons Inc. 2018-02-22 /pmc/articles/PMC6508522/ /pubmed/31245703 http://dx.doi.org/10.1002/pld3.32 Text en © 2018 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Research
Yin, Jie
Gosney, Michael J.
Dilkes, Brian P.
Mickelbart, Michael V.
Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title_full Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title_fullStr Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title_full_unstemmed Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title_short Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions
title_sort dark period transcriptomic and metabolic profiling of two diverse eutrema salsugineum accessions
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508522/
https://www.ncbi.nlm.nih.gov/pubmed/31245703
http://dx.doi.org/10.1002/pld3.32
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