Abstract
BackgroundRhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. Oryza longistaminata, a perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. In this study, an effort was taken to get insights into the genes and molecular mechanisms underlying the rhizomatous trait in O. longistaminata by comparative analysis of the genome-wide tissue-specific gene expression patterns of five different tissues of O. longistaminata using the Affymetrix GeneChip Rice Genome Array.ResultsA total of 2,566 tissue-specific genes were identified in five different tissues of O. longistaminata, including 58 and 61 unique genes that were specifically expressed in the rhizome tips (RT) and internodes (RI), respectively. In addition, 162 genes were up-regulated and 261 genes were down-regulated in RT compared to the shoot tips. Six distinct cis-regulatory elements (CGACG, GCCGCC, GAGAC, AACGG, CATGCA, and TAAAG) were found to be significantly more abundant in the promoter regions of genes differentially expressed in RT than in the promoter regions of genes uniformly expressed in all other tissues. Many of the RT and/or RI specifically or differentially expressed genes were located in the QTL regions associated with rhizome expression, rhizome abundance and rhizome growth-related traits in O. longistaminata and thus are good candidate genes for these QTLs.ConclusionThe initiation and development of the rhizomatous trait in O. longistaminata are controlled by very complex gene networks involving several plant hormones and regulatory genes, different members of gene families showing tissue specificity and their regulated pathways. Auxin/IAA appears to act as a negative regulator in rhizome development, while GA acts as the activator in rhizome development. Co-localization of the genes specifically expressed in rhizome tips and rhizome internodes with the QTLs for rhizome traits identified a large set of candidate genes for rhizome initiation and development in rice for further confirmation.
Highlights
Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia
Using an F2 and two backcross populations derived from crosses between an O. longistaminata accession and an O. sativa line, RD23, Hu et al (2003) reported that the rhizome expression in O. longistaminata is controlled by two dominant-complementary genes, Rhz2 and Rhz3 on rice chromosome 3 and 4 [11]
The microarray experiments identified a total of 21,372 genes that were expressed in at least one of the five sampled tissues of O. longistaminata, including 16,981 genes expressed in rhizome tips (RT), 15,662 genes expressed in rhizome internodes (RI), 16026 genes expressed in shoot tips (ST), 15,732 genes expressed in shoot internodes (SI), and 15,294 genes expressed in young leaves (YL)
Summary
Rhizomatousness is a key component of perenniality of many grasses that contribute to competitiveness and invasiveness of many noxious grass weeds, but can potentially be used to develop perennial cereal crops for sustainable farmers in hilly areas of tropical Asia. A perennial wild rice with strong rhizomes, has been used as the model species for genetic and molecular dissection of rhizome development and in breeding efforts to transfer rhizome-related traits into annual rice species. O. longistaminata provides a model system for genetic and molecular dissection of the rhizomatous trait in grasses. Many additional QTLs affecting abundance of rhizomes in O. longistaminata were identified, and found to correspond to the locations of the rhizome-controlling QTLs in S. propinquum [11]. All these results provided the basis for cloning genes related to the rhizomatous traits in rice
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