Abstract
BackgroundThe rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant.ResultsWe used an integrated approach to compare the transcriptome, proteome and metabolome of the rhizome to other tissues of red rice. 116 Gb of transcriptome sequence was obtained from various tissues and used to identify rhizome-specific and preferentially expressed genes, including transcription factors and hormone metabolism and stress response-related genes. Proteomics and metabolomics approaches identified 41 proteins and more than 100 primary metabolites and plant hormones with rhizome preferential accumulation. Of particular interest was the identification of a large number of gene transcripts from Magnaportha oryzae, the fungus that causes rice blast disease in cultivated rice, even though the red rice plants showed no sign of disease.ConclusionsA significant set of genes, proteins and metabolites appear to be specifically or preferentially expressed in the rhizome of O. longistaminata. The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease.
Highlights
The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses
The presence of M. oryzae gene transcripts at a high level in apparently healthy plants suggests that red rice is resistant to this pathogen, and may be able to provide genes to cultivated rice that will enable resistance to rice blast disease
The total transcriptomes from rhizome elongation zone and apical tip tissues, as well as RNA-seq data from other tissues, were obtained using Illumina-based next-generation sequencing technology, yielding more than 465 million 100 bp reads from the rhizome tip and 450 million from the rhizome zone, as well as 135, 129, 151 and 143 million 50 bp reads from whole rhizome, root, leaf and stem tissue samples, respectively
Summary
The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice species with many valuable traits that could be used to improve cultivated rice cultivars, including rhizomatousness, disease resistance and drought tolerance. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth, development and function in this plant. The genome of O. longistaminata is type AA, similar to O. sativa This species is characterized by a number of valuable traits that could be used for improvement of rice cultivars, including long anther [4], large biomass [5], high nitrogen use efficiency [6], resistance to insect pests and disease [7], and the rhizomatous trait. Elucidation of the genetic origin of the rhizomatous trait might facilitate the generation of a perennial form of cultivated rice that would help to reduce soil erosion associated with annual tillage
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