Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Agronomy, Horticulture, and Plant Science

First Advisor

Senthil Subramanian


Soybean, a leguminous plant and rhizobia establishes symbiotic relationships, forming root nodules. Nodule organogenesis starts with cortical cell division forming infection and parenchyma zones which houses N-fixing bacteria and block O2 for nitrogenase enzyme function, respectively. The mechanism by which root cortical cells give rise to two structurally and functionally different nodule tissues is not known. One approach to address this knowledge gap is to evaluate global gene expression patterns in these two tissue types during nodule development. Using INTACT method, we developed two promoters, ENOD2 (nodule parenchyma) and ENOD40 (infection zone) driven nuclear envelope biotin tagging constructs and isolated nuclei from targeted nodule zones with at least 88% purity and more than 50% efficiency. Nuclear transcriptomic validation using pathway analysis showed that cell wall, and lignin metabolic pathway related genes were highly enriched in nodule parenchyma while transport, and amino acid biosynthesis related genes were highly enriched in infection zone/nodule primordium. These were consistent with the currently known functions of these nodule tissue types. Further analysis with transcription factor families showed that members belonging to NIN-like transcription factor family typically associated with symbiosis were highly enriched in nodule primordium/infection zone at 5 and 10dpi (days post inoculation). Hormonal signaling and biosynthesis pathway analysis showed auxin signaling gene (ARF and AUX/IAA family) enriched in infection zone and cytokinin signaling gene related to HK family enriched in nodule parenchyma at 14dpi. This might possibly indicate tissue specific complementary roles of auxin and cytokinin in nodule development. Similarly, an auxin response factor (GLYMA17G37580, potential orthologue of Arabidopsis ARF5) was enriched in ENOD2- and ENOD40- promoter derived tissue at 7 and 10dpi respectively which indicated potential tissue specific roles for auxin during nodule development. Although we found expected expression pattern in two different tissue types, the statistical significance of the difference was < 0.03 due to variation between replicates of the same sample. It is expected that the use of additional replicates should provide more conclusive results. Ultimately, this knowledge is expected in giving a better understanding of specific genes crucial for development and function of two nodule zones.

Library of Congress Subject Headings

Soybean -- Genetics.
Gene expression.


Includes bibliographical references (pages 100-117)



Number of Pages



South Dakota State University


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