Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions
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The Ohio State University / OhioLINK
2018
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ndltd-OhioLink-oai-etd.ohiolink.edu-osu15143906865659792021-08-03T07:05:08Z Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions Rodrigues da Silva, Danielle Izilda Biochemistry Agronomy Biology Botany Molecular Biology Plant Biology Sugarcane Water Stress Gene Expression Transcriptome Co-Expression Network The exhaustion of oil fields together with the undesirable effects of its use has turned sugarcane into an attractive crop for the biofuel market. The position of Brazil as the world’s major sugarcane producer and the need to expand the planted area to less favorable soils makes the study of drought essential. This work has the aim of providing a comprehensive analysis of sugarcane drought responses in the physiological and molecular levels. In order to do that I followed four strategies. First, I performed the analysis of physiology and transcriptome (microarray) of drought stressed sugarcane plants at 4 days of stress, 6 days of stress and re-watering of a greenhouse experiment. The plant material analyzed was leaves and roots. Second, aiming to complement the data obtained, it was performed RNA-Seq analysis from the most discrepant condition (identified by microarray), from both leaves and roots, third, I performed the analysis of a drought progression experiment through physiology and RT-qPCR of selected genes and forth I built co-expression networks to detect interesting patterns. Physiology analysis showed that plants were under moderate to severe water stress with decreases of up to 97% in photosynthesis. Microarray data identified 575 unique SAS differentially expressed. The analysis of the identified sequences allowed the observation that in leaves after 4 days of stress, the plant is mostly transducing the signal from the environment, while after 6 days and after rehydration there is a functional response of the plant, with re-watering leading the metabolism back to homeostasis. In the case of roots, it was observed a similar response, however roots take longer to go back to the initial condition, with down-regulated genes even after re-watering. There are also pathways presenting a distinct pattern in the analyzed tissues, such as the case of Phenylpropanoid Biosynthesis pathway. Furthermore, while in leaves there is a restriction on photosynthesis, on roots it seems to be a restriction on growth. RNA-Seq de novo assembly showed 28,240 differentially expressed features in leaves and 7,435 in roots, while using the reference genome (unpublished data) it was possible to identify 38,317 differentially expressed genes in leaves and 7,649 in roots, and the analysis of KEGG pathways indicate that ABA has a major role in both leaves and roots responses to drought, but in leaves there is an interplay of phytohormones. Drought progression experiment confirms the results obtained from microarray and shows that when stress is extreme, gene expression starts to decrease, suggesting the plant might be entering in senescence. Co-expression analysis allowed the determination of three modules correlated with physiological parameters altered during water stress, and lead to the identification of some possible hub genes that may be important for sugarcane responses to drought. Furthermore, it was possible to identify genes that through both co-expression and RT-qPCR analysis had similar patterns of expression. Altogether, these results give us a comprehensive view of the alterations in sugarcane responses to water stress and helped us gain insight for defining better suited candidate genes for plant breeding. 2018-05-31 English text The Ohio State University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=osu1514390686565979 http://rave.ohiolink.edu/etdc/view?acc_num=osu1514390686565979 unrestricted This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws. |
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NDLTD |
| language |
English |
| sources |
NDLTD |
| topic |
Biochemistry Agronomy Biology Botany Molecular Biology Plant Biology Sugarcane Water Stress Gene Expression Transcriptome Co-Expression Network |
| spellingShingle |
Biochemistry Agronomy Biology Botany Molecular Biology Plant Biology Sugarcane Water Stress Gene Expression Transcriptome Co-Expression Network Rodrigues da Silva, Danielle Izilda Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| author |
Rodrigues da Silva, Danielle Izilda |
| author_facet |
Rodrigues da Silva, Danielle Izilda |
| author_sort |
Rodrigues da Silva, Danielle Izilda |
| title |
Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| title_short |
Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| title_full |
Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| title_fullStr |
Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| title_full_unstemmed |
Comprehensive analysis of sugarcane (Saccharum spp) gene expression changesin response to drought and re-watering conditions |
| title_sort |
comprehensive analysis of sugarcane (saccharum spp) gene expression changesin response to drought and re-watering conditions |
| publisher |
The Ohio State University / OhioLINK |
| publishDate |
2018 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=osu1514390686565979 |
| work_keys_str_mv |
AT rodriguesdasilvadanielleizilda comprehensiveanalysisofsugarcanesaccharumsppgeneexpressionchangesinresponsetodroughtandrewateringconditions |
| _version_ |
1719453312989790208 |