Honors College Thesis

 

Gene Structure and Expression of the Rice S-Domain Kinase (SD-RLK) Gene Subfamily Public Deposited

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https://ir.library.oregonstate.edu/concern/honors_college_theses/h702qd435

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  • The S-domain subfamily of receptor-like kinases (SD-RLKs) in plants is poorly characterized and the majority of genes have unknown functions. The goal of this study was to study the expansion of rice (Oryza sativa) SD-RLK subfamily, and characterize gene and protein structure and expression of its members using publicly available genomic resources and datasets. Sequence similarity, domain structure information, and gene locations were used to determine likely similarities between proteins, as well as likely pseudogenes and tandem duplication events. Gene expression information was obtained from public databases regarding tissue specific baseline gene expression and differential expression in response to both abiotic and biotic stresses. We found that members of the SD-RLK family are expressed and regulated in response to a broad variety of stress and developmental signals. Overall, we found that in rice, 127/144 genes of this family are expressed under normal growth conditions, 7 genes are expressed only under stress conditions, and 10 genes show no expression. 92 genes show differential expression under biotic stress and 97 genes show differential expression under abiotic stress condition. Our analysis led to association of these genes with important developmental processes (e.g. tissue/organ specific expression) and response to various pathogens and abiotic stress factors. This study will help to improve functional annotations of these genes and provides data-driven hypothesis about the role of SD-RLK family genes in biotic and abiotic pathways in rice, which can be tested experimentally in future. Key Words: Oryza sativa, rice, SD-RLK, kinase, bioinformatics, tandem duplication, stress response
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  • Pending Publication
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  • 2020-06-05 to 2021-01-06

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