Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)


Biology and Microbiology

First Advisor

Wanlong Li


gene expression, microRNA, RNA-Seq, root development, Transcriptome, Wheat


Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were successfully assembled into ~91K transcripts coding for functional proteins. Of these ~91K transcripts, 1,728 were differentially expressed in root tip as compared to the rest of the mature tissues. Generation of the root reference transcriptome and the availability of a reasonable reference genome sequence for wheat enabled us to analyze the gene expression in the long root (LR) and VSR. A total of 4,412 genes were differentially expressed in the VSR compared to the LR root tips. A significant portion of the differentially expressed genes functioning in the hormonal responses, regulation of transcription, defense response, reactive oxygen species (ROS), abiotic stress response, lignin biosynthesis, calcium signaling, and autophagy pathways were induced. In addition, several negative regulators of cell proliferation, including homologs of the BIGBROTHER E3 ubiquitin ligase, and negative regulators of root cell elongation, such as genes encoding the FERONIA kinases and a RALF peptide hormone, were also up-regulated in VSR. Consistent with this, a large number of genes for chromatin replication and protein syntheses, including those coding for histones and ribosomal proteins, and cell wall remodeling enzymes, were down-regulated in VSR. The ROS and lignin accumulation in the VSR were further validated by histochemical staining. This research revealed several molecular mechanisms of root development, based on which a working model was proposed to explain the VSR development. Although the related pathways identified in Arabidopsis may play a similar role in wheat, the VSR phenotype is probably governed by a unique mechanism that may be cereal- or wheat-specific.

Library of Congress Subject Headings

Wheat -- Genetics.
Wheat -- Roots.
Gene expression.
Transcription factors.


Includes bibliographical references



Number of Pages



South Dakota State University


In Copyright - Non-Commercial Use Permitted

586919_supp_42787F86-5D6B-11E8-A10E-B7524D662D30.xlsx (299 kB)
Table S1.4: Annotation and the expression profiles of the DETs

586919_supp_6A79051E-5D6B-11E8-B952-27534D662D30.xlsx (439 kB)
Table S3.1. Annotation and the expression profiles of the DEGs

586919_supp_6FB95B1E-5D6B-11E8-9999-2D534D662D30.xlsx (37 kB)
Table S3.2 Annotation and the expression profiles of the differentially expressed miRNA