Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)


Plant Science

First Advisor

Senthil Subramanian


Soybean, root nodules, RNAseq, microRNA


Lateral roots and nodules are two important nutrient acquisition organs in soybean. The evolutionary origin of nodules from lateral roots has been highly hypothesized based on morphological similarities and genetic studies, but gene expression profiles during the formation of these organs have not been compared. In addition, the role of post-transcriptional gene regulation during nodule development has not been thoroughly explored. Bridging these knowledge gaps is crucial to develop genetic/biotechnological strategies to optimize nutrient acquisition and sustainable production of crops. To answer some of the outstanding questions about regulation of gene expression during nodule development, (i) global transcriptome analyses of lateral root and nodule were compared to identify organ-specific enrichment patterns of transcription factors and hormone signaling elements; (ii) small RNA and degradome/Parallel Analysis of RNA Ends (PARE) libraries were generated to identify miRNAs and their cleavage products respectively in nodule tissues; (iii) miRNA qPCR quantification methods were optimized; and (iv) the effect of misexpression of selected miRNAs on nodule development were evaluated. Analysis of transcriptome data showed very little overlap in transcription factor expression profiles between emerging nodules and emerging lateral roots. The expression profiles of certain key hormone biosynthesis and signaling genes were distinct between nodules and lateral roots. Interestingly, members of gene families associated with shoot axillary meristem formation were enriched in nodules, but not in lateral roots. Analysis of small RNA and PARE libraries resulted in the identification of 497 previously unknown miRNA precursors and validated 353 miRNA-target pairs. These and additional results suggested that inverse expression of miRNA and target is likely to be one of the mechanisms that direct nodule-specific gene expression. In addition, methods for miRNA quantification by qPCR were optimized, and a potential role for miR169 in regulating hormone homeostasis during nodule development was identified through functional assays. In summary, nodules might have adopted not only the developmental pathways of lateral roots, but also shoot axillary meristems. Furthermore, the inverse expression of miRNAs and their targets between nodules and adjacent root tissues might be a mechanism that spatially limits target gene expression to the nodule and/or root tissues.

Library of Congress Subject Headings

Soybean -- Genetics.
Gene expression.
Genetic transcription -- Regulation.


Includes bibliographical references (page 289-291)



Number of Pages



South Dakota State University


Copyright © 2016 Sajag Adhikari