Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature
Authors
Božić, ManjaNikolić, Ana
Dudić, Dragana
Ignjatović-Micić, Dragana
Samardžić, Jelena
Delić, Nenad
Banović Đeri, Bojana
Contributors
Matavulj, MilicaConference object (Published version)
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Show full item recordAbstract
Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most
important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction
is climate change, specifically increasing temperatures and drought during the summer, a large number of
strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing
(early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding
high summer temperatures. Thus, development of cold tolerant maize lines became an important goal.
Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly
cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as
Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE)
analysis. Plants were grown under opt...imal, greenhouse conditions and sampled after completing the V4
growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation
by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina
sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a
custom-made bioinformatics pipeline that included high throughput sequence data quality control (using
FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and
mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using
BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2).
DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster
group, 21 of which were statistically supported for differential expression between the two groups and
annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to
cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging
to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4°
C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after
48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and
genetic background. These findings imply differently regulated processes between the analysed Lancaster
and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be
further used for the development of cold tolerant hybrids.
Keywords:
transcriptomics / NGS / DEGs / maize / cold toleranceSource:
Biologia Serbica, 2021, 43, 1 (Special Edition), 106-Publisher:
- Novi Sad : Faculty of Sciences, Department of Biology and Ecology
Note:
- Book of Abstracts: Belgrade BioInformatics Conference 2021
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Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Božić, Manja AU - Nikolić, Ana AU - Dudić, Dragana AU - Ignjatović-Micić, Dragana AU - Samardžić, Jelena AU - Delić, Nenad AU - Banović Đeri, Bojana PY - 2021 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1874 AB - Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction is climate change, specifically increasing temperatures and drought during the summer, a large number of strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing (early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding high summer temperatures. Thus, development of cold tolerant maize lines became an important goal. Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE) analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4 growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a custom-made bioinformatics pipeline that included high throughput sequence data quality control (using FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2). DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster group, 21 of which were statistically supported for differential expression between the two groups and annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4° C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after 48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and genetic background. These findings imply differently regulated processes between the analysed Lancaster and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be further used for the development of cold tolerant hybrids. PB - Novi Sad : Faculty of Sciences, Department of Biology and Ecology C3 - Biologia Serbica T1 - Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature IS - 1 (Special Edition) SP - 106 VL - 43 UR - https://hdl.handle.net/21.15107/rcub_imagine_1874 ER -
@conference{ author = "Božić, Manja and Nikolić, Ana and Dudić, Dragana and Ignjatović-Micić, Dragana and Samardžić, Jelena and Delić, Nenad and Banović Đeri, Bojana", year = "2021", abstract = "Finding new ways of improving crop quality, yield potential and abiotic stress tolerance are some of the most important pursuits in crop production today. As one of the biggest causes of yield and productivity reduction is climate change, specifically increasing temperatures and drought during the summer, a large number of strategies is focussed on lessening their negative effects. Cropping pattern changes include earlier sowing (early spring), when the temperatures are lower, as one of the most promising escape strategies for avoiding high summer temperatures. Thus, development of cold tolerant maize lines became an important goal. Comparative analysis of 46 maize inbred lines belonging to two different genetic backgrounds, one predominantly cold tolerante (marked as Non-Lancaster) and the other predominantly cold sensitive (marked as Lancaster) in the field, was done by whole transriptome sequencing and differential gene expression (DGE) analysis. Plants were grown under optimal, greenhouse conditions and sampled after completing the V4 growth stage. Total RNA isolated from leaves of three plants per inbred line was used for cDNA library preparation by Illumina TruSeq Stranded RNA LT kit. Pair-end sequencing was performed on MiSeq Illumina sequencer using MiSeq Reagent kit, v2 (2 x 150bp). Data manipulation and analysis was performed using a custom-made bioinformatics pipeline that included high throughput sequence data quality control (using FastQC), removal of low quality reads (using Trimmomatic tool, version 0.32), transcriptome assembly and mapping (using Cufflinks, version 2.2.1), expression quantification (using CuffDiff) and DGE analysis (using BLAST2GO and GO analysis Toolkit and Database for Agricultural Community, agriGO v2). DGE analysis revealed 77 differentially expressed genes (DEGs) between the Lancaster and the Non-Lancaster group, 21 of which were statistically supported for differential expression between the two groups and annotated as involved in abiotic stress responses in maize and other plant species. To test DEGs response to cold stress expression of a subset of seven DEGs in eight inbred lines (4 belonging to Lancaster and 4 belonging to Non-Lancaster genetic background) was analyzed under 24h long exposure to low temperatures (6/4° C, 12h photoperiod), with sampling being done 6h and 24h after beginning of the treatment, as well as after 48h of recovery. Six DEGs showed different expression regulation dependent on cold exposure duration and genetic background. These findings imply differently regulated processes between the analysed Lancaster and Non-Lancaster inbred lines, contributing to their different cold response and adaptation, and will be further used for the development of cold tolerant hybrids.", publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology", journal = "Biologia Serbica", title = "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature", number = "1 (Special Edition)", pages = "106", volume = "43", url = "https://hdl.handle.net/21.15107/rcub_imagine_1874" }
Božić, M., Nikolić, A., Dudić, D., Ignjatović-Micić, D., Samardžić, J., Delić, N.,& Banović Đeri, B.. (2021). Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 106. https://hdl.handle.net/21.15107/rcub_imagine_1874
Božić M, Nikolić A, Dudić D, Ignjatović-Micić D, Samardžić J, Delić N, Banović Đeri B. Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature. in Biologia Serbica. 2021;43(1 (Special Edition)):106. https://hdl.handle.net/21.15107/rcub_imagine_1874 .
Božić, Manja, Nikolić, Ana, Dudić, Dragana, Ignjatović-Micić, Dragana, Samardžić, Jelena, Delić, Nenad, Banović Đeri, Bojana, "Differential gene expression analysis of heterotic groups’ maize inbred lines under optimal conditions led to the identification of specific gene regulation under low-temperature" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):106, https://hdl.handle.net/21.15107/rcub_imagine_1874 .