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Title:Comparative transcriptomics and co-expression networks reveal tissue- and genotype-specific responses of QDTYS to reproductive-stage drought stress in rice (Oryza sativa l.)
Author(s):Tarun, Jeshurun Asher M.
Director of Research:Kretzschmar, Tobias
Doctoral Committee Chair(s):Juvik, John A
Doctoral Committee Member(s):Brown, Patrick J; Sacks, Erik J; Schroeder, Nathan E
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):co-expression networks
drought-tolerant yield
reproductive-stage drought
qDTYs
rice
transcriptomics
Abstract:Rice (Oryza sativa L.) is more sensitive to drought stress than other cereals. Particularly during reproductive stages, drought causes yield reductions of 50-80%. With at least 25 million hectares of drought-prone rainfed rice, drought remains a major environmental constraint to rice production. While a few gene-expression profiling studies in rice in response to drought at the reproductive stage have been conducted, our knowledge of biological mechanisms in this respect is limited. Analysis tends to be restricted relative to the drought susceptible Nipponbare-reference genome, potentially missing genes unique to tolerant donor genomes. The objectives of this Ph.D. research were i) understand the genome-wide transcriptional changes at the reproductive-stage using above-ground tissues, ii) identify drought-responsive modules and pathways and assess their potential role and contribution for reproductive-stage drought tolerance, and iii) evaluate the similarities and dissimilarities of drought quantitative trait loci, across three representative genomes and discuss the potential involvement of the identified candidate genes for drought tolerance. The research objectives were addressed through RNA-Sequencing the flag-leaf and panicle tissues using a Drought-Tolerant Yield introgression line, DTY-IL, and the recurrent parent Swarna, under moderate reproductive-stage drought stress. Also, RNA-Sequencing analysis was done using the Nipponbare-reference approach and analyzed using the representative genome from indica and aus subpopulation. We employed RNA-Seq to independently analyzed transcriptomes of flag-leaf and panicle tissues of DTY-IL and Swarna under the well-watered condition and after two weeks of moderate reproductive-stage drought stress. Differential expression analysis showed a distinct gene expression profile between the two genotypes and tissues. In flag-leaf, Differentially Expressed Genes (DEGs) downregulated in Swarna under drought were related to post-translational modifications and photosynthesis. At the same time, upregulated DEGs in DTY-IL were enriched for antioxidant enzymes. In panicle, DEGs downregulated in Swarna under drought were involved in DNA damage repair pathways and photosynthesis. Simultaneously, DEGs upregulated in DTY-IL under drought were enriched for post-translational modification, especially ‘phosphorylation.’ A co-expression network approach across flag-leaf and panicle tissues in drought-stressed and control plants identified drought-responsive modules of putatively co-regulated genes within each network. In flag leaf, M14 showed distinct upregulation of cell-wall biogenesis and cytoskeleton-related genes in DTY-IL under drought. This lack of cell wall remodeling in Swarna was suggested to contribute to the leaf-rolling phenotype observed under drought. M16, on the other hand, was associated with the downregulation of photosynthesis-related genes in Swarna under drought. In the panicle, modules M10 and M15 showed upregulation of several secondary metabolic pathway genes in DTY-IL. M10 further showed significant upregulation of several receptor kinases in DTY-IL. Hub genes of importance in differential drought responses included an expansion in the flag leaf and two peroxidases in the panicle. Overlaying differential expression data with allelic variation in DTY-IL quantitative trait loci allowed for the prioritization of candidate genes. They included a differentially regulated auxin-responsive protein, with DTY-IL-specific amino acid changes in conserved domains, as well as a protein kinase with a DTY-IL-specific frameshift in the C-terminal region. An additional candidate gene was identified in MH63 in the indica genome to be a potential negative regulator of drought. The approach highlights how the integration of differential expression and allelic variation can help discover mechanisms and putative causal contributions underlying quantitative trait loci for drought-tolerant yield.
Issue Date:2021-04-15
Type:Thesis
URI:http://hdl.handle.net/2142/110635
Rights Information:Copyright 2021 Jeshurun Asher Tarun
Date Available in IDEALS:2021-09-17
Date Deposited:2021-05


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