| 1. |
- Hassan, Sameer, et al.
(författare)
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In silico based screening of WRKY genes for identifying functional genes regulated by WRKY under salt stress
- 2019
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Ingår i: Computational Biology and Chemistry. - : Elsevier BV. - 1476-9271. ; 83
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Tidskriftsartikel (refereegranskat)abstract
- Soil salinization is an increasing global threat to economically important agricultural crops such as bread wheat (Triticum aestivum L.). A main regulator of plants’ responses to salt stress is WRKY transcription factors, a protein family that binds to DNA and alters the rate of transcription for specific genes. In this study, we identified 297 WRKY genes in the Chinese Spring wheat genome (Ensembl Plants International Wheat Genome Sequencing Consortium (IWGSC)), of which 126 were identified as putative. We classified 297 WRKY genes into three Groups: I, II (a–e) and III based on phylogenetic analysis. Principal component analysis (PCA) of WRKY proteins using physicochemical properties resulted in a very similar clustering as that observed through phylogenetic analysis. The 5‘ upstream regions (−2 000 bp) of 107 891 sequences from the wheat genome were used to predict WRKY transcription factor binding sites, and from this we identified 31 296 genes with putative WRKY binding motifs using the Find Individual Motif Occurrences (FIMO) tool. Among these predicted genes, 47 genes were expressed during salt stress according to a literature survey. Thus, we provide insight into the structure and diversity of WRKY domains in wheat and a foundation for future studies of DNA-binding specificity and for analysis of the transcriptional regulation of plants’ response to different stressors, such as salt stress, as addressed in this study. © 2019 Elsevier Ltd
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| 2. |
- Lethin, Johanna, et al.
(författare)
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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines
- 2020
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Ingår i: Bmc Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance. Results After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0-30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested. Conclusion The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.
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| 3. |
- Lethin, Johanna, et al.
(författare)
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Improved Salinity Tolerance-Associated Variables Observed in EMS Mutagenized Wheat Lines
- 2022
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Ingår i: International Journal of Molecular Sciences. - : MDPI AG. - 1422-0067 .- 1661-6596. ; 23:19
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Tidskriftsartikel (refereegranskat)abstract
- Salinity tolerance-associated phenotypes of 35 EMS mutagenized wheat lines originating from BARI Gom-25 were compared. Vegetative growth was measured using non-destructive image-based phenotyping. Five different NaCl concentrations (0 to 160 mM) were applied to plants 19 days after planting (DAP 19), and plants were imaged daily until DAP 38. Plant growth, water use, leaf Na+, K+ and Cl- content, and thousand kernel weight (TKW) were measured, and six lines were selected for further analysis. In saline conditions, leaf Na+, K-+,K- and Cl- content variation on a dry weight basis within these six lines were similar to 9.3, 1.4, and 2.4-fold, respectively. Relative to BARI Gom-25, two (OA6, OA62) lines had greater K+ accumulation, three (OA6, OA10, OA62) had 50-75% lower Na+:K+ ratios, and OA62 had similar to 30% greater water-use index (WUI). OA23 had similar to 2.2-fold greater leaf Na+ and maintained TKW relative to BARI Gom-25. Two lines (OA25, OA52) had greater TKW than BARI Gom-25 when grown in 120 mM NaCl but similar Na+:K+, WUI, and biomass accumulation. OA6 had relatively high TKW, high leaf K-+,K- and WUI, and low leaf Na+ and Cl-. Phenotypic variation revealed differing associations between the parameters measured in the lines. Future identification of the genetic basis of these differences, and crossing of lines with phenotypes of interest, is expected to enable the assessment of which combinations of parameters deliver the greatest improvement in salinity tolerance.
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| 4. |
- Lethin, Johanna
(författare)
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Mutagenesis in wheat: An approach to make saline green!
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The raising salinity in the soils around the world have been widely studied during the last decades due to the massive loss in agricultural land. Today, nearly 8% of the world’s arable land can no longer be used for crop cultivation due to salt contaminations, and more than half of the countries in the world are affected. Wheat is the second most grown cereal after corn and covers more growth area on the earth than any other crop. Wheat production therefore needs to be increased to meet the demand of a growing world population. Thus, the possibility to grow wheat on salt-effected soil is crucial to feed the population and avoid economic loss for the countries involved. In this thesis, the Bangladeshi wheat variety of BARI Gom-25 that is moderately salt tolerant was used as a source to create a mutagenized population with point mutations, and thereafter it acted as a control to the mutated lines. The benefit of point mutations is that a population with high genetic variation can be created. From such a population novel salt tolerant varieties can be developed, as well as many other valuable traits. From a germination screening of approximately 2000 lines on saline filter paper (200 mM NaCl), 70 lines were identified that exhibited a higher germination rate than the BARI Gom-25 control. These lines were further tested in the field in Bangladesh (Paper I). Thirty-five of those lines were also analyzed in the Australian Plant Phenomics Facility at Adelaide. In these experiments yield, growth, ion content, and water use were determined (Paper II). In Paper III and IV bioinformatic tools were used as an approach to look for transcription factor genes in the wheat genome involved in salt tolerance. The focus was on two different transcription factor families; WRKY (Paper III) and MYB (Paper IV). These studies illustrated the importance of the biological regulation of salt tolerance, and enhanced the understanding behind the mechanisms involved. Moreover, it highlighted putative target genes regulated by WRKY and MYB transcription factors that could be key ones to understand findings from Paper I and II. This thesis points out the importance of salt tolerant crops in general, and wheat in particular, and shows how mutational breeding can be a great asset in the development of salt tolerant varieties. Specific mutagenized wheat lines with strong salt tolerance are identified based on their performance against various parameters, and the importance of WRKY and MYB transcription factor families in the biological regulation of salt tolerance is shown. Finally, downstream candidate genes encoding the observed phenotypes observed.
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| 5. |
- Mousavi, Hesam, et al.
(författare)
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Effects of Increasing Salinity by Drip Irrigation on Total Grain Weight Show High Yield Potential of Putative Salt-Tolerant Mutagenized Wheat Lines
- 2022
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Ingår i: Sustainability. - : MDPI AG. - 2071-1050. ; 14:9
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Tidskriftsartikel (refereegranskat)abstract
- Twenty-three lines from a mutagenized Bangladeshi BARI Gom-25 wheat population that included previously identified salt-tolerant lines, and the BARI Gom-25 control variety, were cultivated in a drip-irrigated salinity test field at Salt Farm Texel, Netherlands, to assess their performance during salt stress in European climatic conditions. Lines were tested at irrigation salinity levels of 1, 4, 8, 12, 16, and 20 dS m(-1) in four repetitions of plots with 24 plants per plot. Average plant height, tiller number, spike length, frequency of live plants, and total grain weight (TGW) were recorded as functions of seasonal mean pore water salinity in the soil. Increases in salinity triggered reductions in all evaluated variables of the assessed lines and the control variety. However, nine mutagenized lines had at least twofold higher mean TGW than the control variety, 18.73 +/- 4.19 g/plot at 1-16 dS m(-1) salinity levels. Common models of salt tolerance confirmed this pattern, but there were no clear differences in salinity tolerance parameter estimates between the mutagenized lines and the control variety. Thus, despite the apparent similarity in responses of all lines to salinity increase, we clearly identified lines that tended to have higher TGW at given salinities than the control variety. This higher TGW at the full range of salinity treatments indicates not only a possible higher salinity tolerance but a higher yield potential as well. The mechanisms involved clearly warrant further attention.
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| 6. |
- Sukumaran, Selvakumar, et al.
(författare)
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Genome-Wide Analysis of MYB Transcription Factors in the Wheat Genome and Their Roles in Salt Stress Response
- 2023
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Ingår i: Cells. ; 12:10
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Tidskriftsartikel (refereegranskat)abstract
- Large and rapidly increasing areas of salt-affected soils are posing major challenges for the agricultural sector. Most fields used for the important food crop Triticum aestivum (wheat) are expected to be salt-affected within 50 years. To counter the associated problems, it is essential to understand the molecular mechanisms involved in salt stress responses and tolerance, thereby enabling their exploitation in the development of salt-tolerant varieties. The myeloblastosis (MYB) family of transcription factors are key regulators of responses to both biotic and abiotic stress, including salt stress. Thus, we used the Chinese spring wheat genome assembled by the International Wheat Genome Sequencing Consortium to identify putative MYB proteins (719 in total). Protein families (PFAM) analysis of the MYB sequences identified 28 combinations of 16 domains in the encoded proteins. The most common consisted of MYB_DNA-binding and MYB-DNA-bind_6 domains, and five highly conserved tryptophans were located in the aligned MYB protein sequence. Interestingly, we found and characterized a novel 5R-MYB group in the wheat genome. In silico studies showed that MYB transcription factors MYB3, MYB4, MYB13 and MYB59 are involved in salt stress responses. qPCR analysis confirmed upregulation of the expression of all these MYBs in both roots and shoots of the wheat variety BARI Gom-25 (except MYB4, which was downregulated in roots) under salt stress. Moreover, we identified nine target genes involved in salt stress that are regulated by the four MYB proteins, most of which have cellular locations and are involved in catalytic and binding activities associated with various cellular and metabolic processes.
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