Seven miRNAs potentially included in the chilling response of maize plants in early stages of development
Аутори
Božić, ManjaIgnjatović-Micić, Dragana
Delić, Nenad
Mladenović, Marko
Vančetović, Jelena
Banović Đeri, Bojana
Nikolić, Ana
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth,
development and stress responses. They achieve this through mRNA cleavage or translational
inhibition, in a process called RNA interference. Herein, their role in chilling stress response in
young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods.
Bringing light to all aspects of chilling stress response in maize is necessary since earlier
sowing, during colder periods, is one of the most promising strategies of avoiding maize yield
loss due to effects of climate change in these areas.
Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures)
were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings
were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library
preparation were taken after the treatment ended, and single-end 50 bp sequencing was
p...erformed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified
and quantified using adequate bioinformatics tools; and the differential expression analysis
was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs,
after previously executed TPM normalization using the MA-plot-based method with random
sampling model (MARS). The threshold for significantly differential expression was set as the
Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1.
A total of 612 were expressed differentially, but only 55 miRNAs were common for both
genotypes and at the same time differentially expressed between control and treatment
conditions – 40 novel and 15 known. Half of the common miRNAs showed the same
expression patterns in both genotypes, while the other half did not. Among them, seven known
miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p
zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR398a-
3p, and zma-miR528a-3p). These miRNAs were shown to have a role in various abiotic stress
responses, including drought, waterlogging, high salts – but not chilling. While the results point
to their potential role in establishing chilling tolerance in maize seedlings, further research is
necessary to confirm it and connect the miRNAs to their potential targets.
Кључне речи:
maize / abiotic stress / chilling / high-throughput sequencing / miRNAsИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 83-83Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Božić, Manja AU - Ignjatović-Micić, Dragana AU - Delić, Nenad AU - Mladenović, Marko AU - Vančetović, Jelena AU - Banović Đeri, Bojana AU - Nikolić, Ana PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2007 AB - Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth, development and stress responses. They achieve this through mRNA cleavage or translational inhibition, in a process called RNA interference. Herein, their role in chilling stress response in young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods. Bringing light to all aspects of chilling stress response in maize is necessary since earlier sowing, during colder periods, is one of the most promising strategies of avoiding maize yield loss due to effects of climate change in these areas. Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures) were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library preparation were taken after the treatment ended, and single-end 50 bp sequencing was performed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified and quantified using adequate bioinformatics tools; and the differential expression analysis was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs, after previously executed TPM normalization using the MA-plot-based method with random sampling model (MARS). The threshold for significantly differential expression was set as the Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1. A total of 612 were expressed differentially, but only 55 miRNAs were common for both genotypes and at the same time differentially expressed between control and treatment conditions – 40 novel and 15 known. Half of the common miRNAs showed the same expression patterns in both genotypes, while the other half did not. Among them, seven known miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR398a- 3p, and zma-miR528a-3p). These miRNAs were shown to have a role in various abiotic stress responses, including drought, waterlogging, high salts – but not chilling. While the results point to their potential role in establishing chilling tolerance in maize seedlings, further research is necessary to confirm it and connect the miRNAs to their potential targets. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Seven miRNAs potentially included in the chilling response of maize plants in early stages of development EP - 83 SP - 83 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2007 ER -
@conference{ author = "Božić, Manja and Ignjatović-Micić, Dragana and Delić, Nenad and Mladenović, Marko and Vančetović, Jelena and Banović Đeri, Bojana and Nikolić, Ana", year = "2023", abstract = "Micro RNAs (miRNAs) are known regulators of various processes in plants, including growth, development and stress responses. They achieve this through mRNA cleavage or translational inhibition, in a process called RNA interference. Herein, their role in chilling stress response in young maize seedlings (Zea mays L.) is examined, using high-throughput sequencing methods. Bringing light to all aspects of chilling stress response in maize is necessary since earlier sowing, during colder periods, is one of the most promising strategies of avoiding maize yield loss due to effects of climate change in these areas. Sterilized seeds of two maize genotypes (tolerant - T and sensitive - S to low temperatures) were germinated in the dark for five days (optimal conditions), after which the 5-d old seedlings were exposed to chilling conditions for 6h (10° C). Samples for RNA isolation and cDNA library preparation were taken after the treatment ended, and single-end 50 bp sequencing was performed (Illumina® Novaseq 6000). The miRNAs were then filtered, mapped, identified and quantified using adequate bioinformatics tools; and the differential expression analysis was carried out using the DEGseq R package. The analysis was performed on 859 miRNAs, after previously executed TPM normalization using the MA-plot-based method with random sampling model (MARS). The threshold for significantly differential expression was set as the Bayesian adjusted p-value, or q-value < 0.01 and log2 fold change > 1. A total of 612 were expressed differentially, but only 55 miRNAs were common for both genotypes and at the same time differentially expressed between control and treatment conditions – 40 novel and 15 known. Half of the common miRNAs showed the same expression patterns in both genotypes, while the other half did not. Among them, seven known miRNAs showed opposing expression patterns between the genotypes (zma-miR167b-3p zma-miR167e-3p, zma-miR159c-5p, zma-miR164g-3p, zma-miR166a-5p, zma-miR398a- 3p, and zma-miR528a-3p). These miRNAs were shown to have a role in various abiotic stress responses, including drought, waterlogging, high salts – but not chilling. While the results point to their potential role in establishing chilling tolerance in maize seedlings, further research is necessary to confirm it and connect the miRNAs to their potential targets.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Seven miRNAs potentially included in the chilling response of maize plants in early stages of development", pages = "83-83", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2007" }
Božić, M., Ignjatović-Micić, D., Delić, N., Mladenović, M., Vančetović, J., Banović Đeri, B.,& Nikolić, A.. (2023). Seven miRNAs potentially included in the chilling response of maize plants in early stages of development. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 83-83. https://hdl.handle.net/21.15107/rcub_imagine_2007
Božić M, Ignjatović-Micić D, Delić N, Mladenović M, Vančetović J, Banović Đeri B, Nikolić A. Seven miRNAs potentially included in the chilling response of maize plants in early stages of development. in 4th Belgrade Bioinformatics Conference. 2023;4:83-83. https://hdl.handle.net/21.15107/rcub_imagine_2007 .
Božić, Manja, Ignjatović-Micić, Dragana, Delić, Nenad, Mladenović, Marko, Vančetović, Jelena, Banović Đeri, Bojana, Nikolić, Ana, "Seven miRNAs potentially included in the chilling response of maize plants in early stages of development" in 4th Belgrade Bioinformatics Conference, 4 (2023):83-83, https://hdl.handle.net/21.15107/rcub_imagine_2007 .