Abstract
Oryza meyeriana (O. meyeriana), with a GG genome type (2n = 24), accumulated plentiful excellent characteristics with respect to resistance to many diseases such as rice shade and blast, even immunity to bacterial blight. It is very important to know if the diseases-resistant genes exist and express in this wild rice under native conditions. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq and obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, it was found that there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (japonica-type Nipponbare and indica-type 93–11) genomes revealed that 13% of the O. meyeriana contigs had not been detected in O. sativa. Many diseases-resistant genes, such as bacterial blight resistant, blast resistant, rust resistant, fusarium resistant, cyst nematode resistant and downy mildew gene, were mined from the transcriptomic database. There are two kinds of rice bacterial blight-resistant genes (Xa1 and Xa26) differentially or specifically expressed in O. meyeriana. The 4 Xa1 contigs were all only expressed in root, while three of Xa26 contigs have the highest expression level in leaves, two of Xa26 contigs have the highest expression profile in stems and one of Xa26 contigs was expressed dominantly in roots. The transcriptomic database of O. meyeriana has been constructed and many diseases-resistant genes were found to express under native condition, which provides a foundation for future discovery of a number of novel genes and provides a basis for studying the molecular mechanisms associated with disease resistance in O. meyeriana.
Highlights
The world is facing a new challenge with global population by the middle of last century[1]
To obtain an integrated transcriptome of O. meyeriana, samples collected from roots, stems and leaves were used for RNA-Seq analysis
The genus Oryza includes two cultivated (2n = 24, AA) and 22 wild species (2n = 24, 48) representing the AA, bacterial blight (BB), CC, BBCC, CCDD, EE, FF, GG, KKLL, and HHJJ genome types. Though these wild Oryza species are, grass-like plants which are phenotypically inferior in agronomic traits, such as poor plant type, low grain yield, poor grain type, and are shattering in nature, these wild species are reservoirs of many useful genes, for resistance to major biotic and abiotic stresses[23]
Summary
The world is facing a new challenge with global population by the middle of last century[1]. Part of the solution to increase food production on the same or less cultivated land lies in exploiting the subset of genes lost during the domestication process and subsequent targeted breeding. These valuable genes are found only in the progenitor species gene pool for crop cultivars. Cultivated plants having desirable genes were utilized in intensive breeding projects which focused on increasing yield for particular environments and management systems but this process has narrowed the genetic diversity[2]. Improving our understanding of this tertiary gene pool and exploiting it for crop improvement are paramount to meeting the challenges of feeding the world in this century through the integration of classical genetics and genomics-enabled research paradigms
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