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Sweet potato ( Ipomoea batatas) is one of the major food and vegetable crops around the world. Sweet potato produces two types of roots: storage roots and fibrous roots. The tuberous root is a modified lateral root that functions as a storage organ, and is the portion of the plant consumed by humans. However, the molecular mechanisms controlling transformation of lateral roots to storage roots are still unclear. In this study, we systematically investigated the potential role of 16 conserved microRNAs (miRNAs) in floral root development. miRNAs are an extensive class of small regulatory RNAs controlling almost all biological and metabolic process in plants. Our results show that some miRNAs are expressed in an organ-dependent manner. For example, the expression level of miR156 and miR162 was significantly lower in storage roots than in leaves and fibrous roots. This suggests that miRNAs may play a role during storage root initiation and development. The expression of miR167 is higher in stamens than that in other tissues tested, indicating that miR167 is crucial to stamen development. miR398-a stress-responsive miRNA-may be involved in fibrous root and storage root development. Additionally, three miRNAs, miR160, miR164 and miR166, also appear to be important in fibrous root and storage root development. [ABSTRACT FROM AUTHOR]

Micro RNAs (mi RNAs) have been found to be differentially expressed during cotton fibre development. However, which specific mi RNAs and how they are involved in fibre development is unclear. Here, using deep sequencing, 65 conserved mi RNA families were identified and 32 families were differentially expressed between leaf and ovule. At least 40 mi RNAs were either leaf or ovule specific, whereas 62 mi RNAs were shared in both leaf and ovule. q RT- PCR confirmed these mi RNAs were differentially expressed during fibre early development. A total of 820 genes were potentially targeted by the identified mi RNAs, whose functions are involved in a series of biological processes including fibre development, metabolism and signal transduction. Many predicted mi RNA-target pairs were subsequently validated by degradome sequencing analysis. GO and KEGG analyses showed that the identified mi RNAs and their targets were classified to 1027 GO terms including 568 biological processes, 324 molecular functions and 135 cellular components and were enriched to 78 KEGG pathways. At least seven unique mi RNAs participate in trichome regulatory interaction network. Eleven trans-acting si RNA (tasi RNA) candidate genes were also identified in cotton. One has never been found in other plant species and two of them were derived from MYB and ARF, both of which play important roles in cotton fibre development. Sixteen genes were predicted to be tasi RNA targets, including sucrose synthase and MYB2. Together, this study discovered new mi RNAs in cotton and offered evidences that mi RNAs play important roles in cotton ovule/fibre development. The identification of tasi RNA genes and their targets broadens our understanding of the complicated regulatory mechanism of mi RNAs in cotton. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are an extensive class of small regulatory RNAs. Knowing the specific expression and functions of miRNAs during root-knot nematode (RKN) (Meloidogyne incognita) development could provide fundamental information about RKN development as well as a means to design new strategies to control RKN infection, a major problem of many important crops. Employing high throughput deep sequencing, we identified a total of 45 conserved and novel miRNAs from two developmental stages of RKN, eggs and J2 juveniles, during their infection of cotton (Gossypium hirsutum L.). Twenty-one of the miRNAs were differentially expressed between the two stages. Compared with their expression in eggs, two miRNAs were upregulated (miR252 and miRN19), whereas 19 miRNAs were downregulated in J2 juveniles. Nine miRNAs were expressed at high levels, with >1000 reads per mapped million (RPM) sequenced reads in both eggs and J2 juveniles (miR1, miR124, miR2-3p, miR252, miR279, miR57-5p, miR7904, miR87, and miR92). Three miRNAs were only expressed in eggs (miR4738, miRN3, and miRN5). These differentially expressed miRNAs may control RKN development by regulating specific protein-coding genes in pathways associated with RKN growth and development. [ABSTRACT FROM AUTHOR]

Investigation of cotton response to nematode infection will allow us to better understand the cotton immune defense mechanism and design a better biotechnological approach for efficiently managing pest nematodes in cotton. In this study, we firstly treated cotton by root knot nematode (RKN, Meloidogyne incognita) infections, then we employed the high throughput deep sequencing technology to sequence and genome-widely identify all miRNAs in cotton; finally, we analyzed the functions of these miRNAs in cotton response to RKN infections. A total of 266 miRNAs, including 193 known and 73 novel miRNAs, were identified by deep sequencing technology, which belong to 67 conserved and 66 novel miRNA families, respectively. A majority of identified miRNA families only contain one miRNA; however, miR482 family contains 14 members and some others contain 2–13 members. Certain miRNAs were specifically expressed in RKN-infected cotton roots and others were completely inhibited by RKN infection. A total of 50 miRNAs were differentially expressed after RKN infection, in which 28 miRNAs were up-regulated and 22 were inhibited by RKN treatment. Based on degradome sequencing, 87 gene targets were identified to be targeted by 57 miRNAs. These miRNA-targeted genes are involved in the interaction of cotton plants and nematode infection. Based on GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, 466 genes from all 636 miRNA targets were mapped to 6340 GO terms, 181 genes from 228 targets of differentially expressed miRNAs were mapped to 1588 GO terms. The GO terms were then categorized into the three main GO classes: biological processes, cellular components, and molecular functions. The targets of differentially expressed miRNAs were enriched in 43 GO terms, including 22 biological processes, 10 cellular components, and 11 molecular functions (p < 0.05). Many identified processes were associated with organism responses to the environmental stresses, including regulation of nematode larval development, response to nematode, and response to flooding. Our results will enhance the study and application of developing new cotton cultivars for nematode resistance. • Nematodes altered the expression of miRNAs. • 193 known and 73 novel miRNAs identified in cotton. • 28 miRNAs were induced whereas 22 was inhibited by RKN. • 87 miRNA targets were identified by degradome sequencing. • Cotton miRNAs and their targets may regulate nematode larval development. [ABSTRACT FROM AUTHOR]

The goal of this study was to investigate the impact of potassium deficiency on cotton seedling growth and development at the individual, physiological, biochemical, and molecular levels. Potassium is an important plant nutrient; our results show that potassium deficiency significantly affected cotton seedling growth and development, evidenced by reduced plant height, and total areas of the leaves and roots as well as further reduced both fresh and dry biomass of the entire plants. Potassium deficiency also significantly inhibited root and leaf respiration and leaf photosynthesis. Compared with the controls, potassium deficiency significantly inhibited root elongation and total root surface areas that further inhibited cotton seedlings to uptake nutrients from the medium. Potassium deficiency induced aberrant expression of both microRNAs (miRNAs) and their protein-coding targets. These miRNAs regulate plant root development as well as response to abiotic stresses. Potassium deficiency altered the expression of miRNAs that regulate the expression of protein-coding genes controlling root development and response to potassium deficiency. miRNAs regulate root development and further control plant development in cotton seedlings under potassium deficiency. In summary, potassium deficiency significantly affected the cotton seedling photosynthesis and respiration that resulted in inhibition of cotton seedling growth and development potentially due to the miRNA-mediated mechanism. • Cotton root development and branching were affected by potassium. • Potassium deficiency inhibited cell respiration and leaf photosynthesis. • Potassium treatment altered the expression of microRNAs and their targets. • miRNAs regulate root development and further control plant development in cotton under potassium deficiency. [ABSTRACT FROM AUTHOR]