This Is AuburnElectronic Theses and Dissertations

Small RNAs in Gossypium and Their Roles in the Response to Heat Stress




Hongtao, Hu

Type of Degree



Biological Sciences


Small regulatory RNAs, which usually are 20 to 24 nt in length, play crucial roles in plant growth, development, and stress response. Based on their origin, biogenesis and function, plant small RNAs can be classified into two major classes, hairpin RNAs (hpRNAs) and short interfering siRNAs (siRNAs). hpRNAs and siRNAs can be subdivided into two and three subfamilies, respectively. hpRNAs, including microRNAs (miRNAs) and other hairpin RNAs (ohpRNAs), are produced from hairpin-shaped precursors. siRNAs are produced from double-stranded precursors and requires RNA dependent Polymerase. siRNAs can be categorized into three subfamilies, repeat-associated siRNAs (ra-siRNAs), pha-siRNAs, and cis natural antisense RNAs (cis-nat siRNAs). In general, miRNAs regulate gene expression at transcription level, while siRNAs can do either postranscriptionally or transcriptionally. In addition, ra-siRNAs are considered to regulate gene expression by DNA methylation. Gossypium plants, such as G. hirsutum and G. barbadense, are economically important plants, and provide natural fiber for textile industry. In addition, they also are important sources for proteins and seed oils. Heat stress caused by elevated high temperature is an important factor that affects diverse physiological processes of plants, resulting serious loss in yield. The mechanism of heat response has been extensively studied in anatomical, biochemical, and gene levels. But till one decade year ago, gene expression regulated by small RNAs is shown to be important for animal and plant stress response. Growing studies have shown that small RNAs, primarily miRNAs and siRNAs, are involved in heat stress response in plants. In Arabidopsis, Oryza, or Medicago, the small RNA loci have been thoroughly annotated, which identified a large number of small RNAs that regulates stress response. However, little is known about Gossypium small RNAs and their regulatory roles in heat stress response. To annotate Gossypium small RNAs and study their roles, we constructed and sequenced forty four small RNAs libraries from eight different tissues from two different Gossypium species, G. raimondii and G. hirsutum. The samples were collected from heat-stressed or non-heat-stressed seedlings grown in growth chamber, or plants grown in fields under high temperature summer. Two deep sequencing methods, ABI Solid and Illumina, were employed to sequence the small RNA libraries. This generated approximately 790 million sequencing reads, which enabled us to annotate a large number of miRNAs, ohpRNAs, ra-siRNAs, pha-siRNAs and cis-nat siRNAs. Expression analysis revealed that a large number of small RNAs were significantly regulated between heat-stressed and non-heat-stressed tissues, or between heat-susceptible and heat-tolerant genotypes. Some small RNAs were differentially expressed among different tissues. This suggested that small RNAs might be involved in the stress response of Gossypium plants to heat stress and might play crucial roles in Gossypium heat stress tolerance. This work in this study developed a systematical method in analyzing the small RNA transcriptomes and in annotating the small RNA loci in the genome. This would facilitate the study in the small RNAs and their regulatory mechanism in plant heat tolerance.