Selection for improved energy efficiency and drought tolerance in canola results in distinct transcriptome and epigenome changes
Ontology highlight
ABSTRACT:
ORGANISM(S): Brassica napus
PROVIDER: GSE65578 | GEO | 2015/06/28
SECONDARY ACCESSION(S): PRJNA274406
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-06-28 | E-GEOD-65578 | biostudies-arrayexpress
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding. To investigate the epigenetic effect on histone mark distribution of the EUE/PEG selection we performed ChIP-seq analyses. Native ChIP using an anti-H3K4me3 and no antibody (background control) was done on PEG1 and control plants.
2015-06-28 | E-GEOD-65571 | biostudies-arrayexpress
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding. SRA study accession: SRP052946, Bioproject: PRJNA273932. Two canola (Brassica napus L. spp. oleifera (Metzg) Sinsk. f. biennis) epilines with low respiration and high NAD(P)H content were selected. Grinded leaf material from 26 day-old control and both epilines was collected in triplicate and served as input for deep sequencing on Illumina GAIIx.
2015-06-28 | E-GEOD-65572 | biostudies-arrayexpress
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding.
2015-06-28 | GSE65572 | GEO
Project description:Integrated breeding strategies are used to increase both the yield potential and stability of crops. Most of these approaches have a direct genetic basis. The utility of epigenetics in breeding to improve complex traits such as yield and stress tolerance is not clear. A better understanding of the status of the epigenome and its contribution to the agronomic performance would help in developing strategies to incorporate the epigenetic component of complex traits in breeding,Starting from isogenic canola lines, epilines were generated by selecting recursively during three generations for lines with a higher energy use efficiency and drought tolerance. These epilines were more energy use efficient, drought tolerant, high nitrogen use efficient, and higher yielding under suboptimal conditions. Moreover, these characteristics were transgenerational inheritable. Transcriptome comparison with a line selected for energy use efficiency only revealed common differentially expressed genes related to the onset of signaling events regulating stress tolerance. Genes related to salt, osmotic, abscisic acid and drought were specifically differentially expressed in the drought tolerant epilines. The status of the epigenome, scored as differential trimethylation of lysine 4 of histone 3, supports the energy use efficient and drought tolerant phenotype by facilitating transcription of the genes that are found to be differentially expressed.From these results it can be concluded that the epigenome can be shaped by selection to increase yield and stress tolerance. This acquired knowledge will support further development of strategies to incorporate epigenetics in breeding.
2015-06-28 | GSE65571 | GEO
Project description:Modern broiler chickens are a major animal husbandry success story, both in terms of efficient resource utilisation and environmental sustainability. However, continuing artificial selection for both efficiency and rapid growth will be subject to both biological limits and animal welfare concerns. Using a novel analytical energy flow modelling approach, we predict how far such selection can go, given the biological limits of bird energy intake and partitioning of energy. We find that the biological potential for further improvements in efficiency, and hence environmental impact reduction, is minimal relative to past progress already made via artificial selection. An alternative breeding strategy to produce slower-growing birds to meet new welfare standards increases environmental burdens, compared to current birds. This unique analytic approach provides biologically sound guidelines for strategic planning of sustainable broiler production.
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Project description:Poplar is one of the most important tree species in the north temperate zone, but poplar plantations are quite water intensive. We report here that CaMV 35S promoter-driven overexpression of the PdERECTA gene, which is a member of the LRR-RLKs family from Populus nigra × (Populus deltoides × Populus nigra), improves water use efficiency and enhances drought tolerance in triploid white poplar. PdERECTA localizes to the plasma membrane. Overexpression plants showed lower stomatal density and larger stomatal size. The abaxial stomatal density was 24-34% lower and the stomatal size was 12-14% larger in overexpression lines. Reduced stomatal density led to a sharp restriction of transpiration, which was about 18-35% lower than the control line, and instantaneous water use efficiency was around 14-63% higher in overexpression lines under different conditions. These phenotypic changes led to increased drought tolerance. PdERECTA overexpression plants not only survived longer after stopping watering but also performed better when supplied with limited water, as they had better physical and photosynthesis conditions, faster growth rate, and higher biomass accumulation. Taken together, our data suggest that PdERECTA can alter the development pattern of stomata to reduce stomatal density, which then restricts water consumption, conferring enhanced drought tolerance to poplar. This makes PdERECTA trees promising candidates for establishing more water use efficient plantations.
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Project description:Light is one of the most important environmental signals in plant growth, development, and stress response. Green light has been proved to enhance plant defense against biotic and/or abiotic stress. To illustrate the effects of green light partially replaced red light and blue light on the plant under drought condition, cucumber (Cucumis sativus L. cv. Xinchun No. 4) seedlings were treated with short-term drought stress and were concomitantly exposed to four treatments, which were set up by adjusting the relative amount of green light as 0 (RB), 25 (RBG25), 50 (RBG50), and 75 (RBG75) μmol m-2 s-1, respectively, with a total photosynthetic photon flux density of 250 μmol m-2 s-1 and a fixed red-to-blue ratio of 4:1. The results showed that compared with RB, RBG50 significantly increased shoot fresh weight (FW) and dry weight (DW), root DW, plant height, stem diameter, leaf area, and leaf dry mass per unit area (LMA) by 10.61, 7.69, 66.13, 6.22, 10.02, 4.10, and 12.41%, respectively. Also, the addition of green light significantly increased the root volume and root tip number. Moreover, green light partial replacement of red light and blue light increased total water content, especially free water content, improved leaf water status, and alleviated water loss in plants caused by drought stress. Also, the addition of green light increased net photosynthetic rate (Pn), reduced both stomata conductance (gs) and transpiration rate (E), enhanced the intrinsic water-use efficiency (WUE) and instantaneous water-use efficiency (iWUE) of leaves, and increased the content of chlorophylls a and b. Green light substituting a proportion of blue and red light regulated stomatal aperture by significantly increasing abscisic acid (ABA) and γ-aminobutyric acid (GABA) content. In addition, the increase of GABA was resulted from the upregulation of Glutamate Decarboxylase 2 (CsGAD2). However, the relative electrolytic leakage and contents of malondialdehyde (MDA), superoxide anion ( O2- ), and hydrogen peroxide (H2O2) vigorously decreased as the intensity of green light was added to the spectrum under drought. Conclusively, green light partially replaced red light and blue light and improved drought tolerance of cucumber seedlings by upregulating the expression of CsGAD2 gene and promoting the synthesis of GABA. The increase in GABA content further downregulated the expression of aluminum-activated malate transporter 9 (CsALMT9) gene, induced stomata to close, improved water utilization, and alleviated damage caused by drought. This study highlights a role of green light in plant physiological processes. Moreover, analyzing the function of green light on improving drought tolerance of plants could open alternative avenues for improving plant stress resilience.
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Project description:UDP-glucose 4-epimerase (UGE) catalyzes the reversible conversion of UDP-glucose to UDP-galactose. To understand the biological function of UGE from Brassica rapa, the gene BrUGE1 was cloned and introduced into the genome of wild type rice 'Gopum' using the Agrobacterium-mediated transformation method. Four lines which carried a single copy gene were selected and forwarded to T3 generation. Agronomic traits evaluation of the transgenic T3 lines (CB01, CB03, and CB06) under optimal field conditions revealed enriched biomass production particularly in panicle length, number of productive tillers, number of spikelets per panicle, and filled spikelets. These remarkably improved agronomic traits were ascribed to a higher photosynthetic rate complemented with higher CO2 assimilation. Transcripts of BrUGE1 in transgenic lines continuously accumulated at higher levels after the 20% PEG6000 treatment, implying its probable role in drought stress regulation. This was paralleled by rapid accumulation of soluble sugars which act as osmoprotectants, leading to delayed leaf rolling and drying. Our findings suggest the potential of BrUGE1 in improving rice growth performance under optimal and water deficit conditions.
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