The following are the supplementary data related to this article. Table S1.   Primers for cloning WRKY genes with complete open reading frames. This program was financially supported in part by the National Science Foundation of China (31171590), the Specialized

Research Fund for the Doctoral Program of Higher Education of China (20090097110010), the Natural Science Foundation of Jiangsu Province, China (BK2010065), and a project funded by the Priority Academic Program Development EPZ015666 molecular weight of Jiangsu Higher Education Institutions. “
“Rice is a staple food for more than half of the world’s population, and rice cultivation is the largest single food-producing use of land, covering 9% of the Earth’s arable land [1]. Growing annual rice on steep hillsides causes soil erosion, reducing farm productivity and damaging resources downhill. Breeding perennial rice varieties with rhizomes is an effective way to solve this problem. Annual soil disturbances associated with tillage would be avoided through the use of a Wnt inhibitor perennial cultivar, and rhizomes would trap soil, preventing erosion. Among the two cultivated and 22 wild rice species studied, Oryza longistaminata is a wild, perennial species from Africa that is characterized by the presence of rhizomatous stems [2] and [3]. Rhizomes enable O. longistaminata to overwinter, producing new plants in the following growing season. O. longistaminata

Methane monooxygenase is the only perennial rice species with the AA genome, allowing it to be used as a donor in breeding programs for perennial upland rice [4] and [5]. However, partial-sterility barriers have impeded the development of perennial rice by conventional breeding [6]. Genetic studies show that the rhizomatous trait in rice is quantitatively controlled by many genes. In our previous study, an F2 and two backcross populations from O. longistaminata and RD23 were used for genetic mapping of the rhizomatous trait. The results revealed two dominant complementary genes that

controlled rhizome expression: Rhz2 and Rhz3, which mapped to rice chromosomes 3 and 4, respectively [7]. A comparative gene expression analysis between aerial shoots (ASs) and rhizomes was performed to identify organ-specific gene expression, and the results indicated that 2566 genes, including transcription factors, were differentially expressed in ASs and rhizomes. A few of these genes were found colocalized in the rhizome-related QTL intervals [8]. Further profiling revealed that primary metabolites and hormones had distinct organ distribution patterns. Metabolites accumulated in stem bases and a higher indole-3-acetic acid-to-zeatin riboside ratio is probably associated with the regulatory metabolism of rhizome formation [9]. These data suggest that rhizome development in O. longistaminata is controlled by a complex molecular genetic network.