Fine Mapping Of Rhizome Gene Rhz2,Rhz3 And Identification Of Rhizome-Specific Genes By Genome-wide Differential Expression Analysis In Oryza Iongistaminata

Cultivation of annual rice on steep hillsides causes soil erosion and reduces farm productivity. A perennial, rhizomatous rice cultivar would produce food and reduce erosion, subsequently, increase food and ecosystem security. A logical donor of the perennial and rhizomatous traits is Oryza longistaminata, a perennial wild rice that produces rhizomes. However, traditional breeding efforts to transfer the trait have not yet been successful. The rhizomatous growth habit in rice is controlled by many genes, and the molecular mechanism related to rhizome initiation and elongation is still unknown. Using the strategies of fine mapping and microarray technology, we fine mapped the rhizome genes that are Rhz2 and Rhz3 which were mapped preliminary via molecular marker on rice chromosome 3 and chromosome 4, respectively. Meanwhile, we also investigated the gene expression patterns in rhizome tips, rhizome internodes, aerial shoot tips, aerial shoot internodes, and young leaves to improve our understanding of rhizome development at the molecular level.There are 4 F3 populations, which derived from the self-crossing generation of F2 individual that selected via MAS, rhizome present, pollen fertility and anther dehiscence from a F2 population within 5261 individuals, were employed to fine map the rhizome genes, Rhz2 and Rhz3. The two dominant-complementary genes controlling rhizomatousness was confirmed. The Rhz2 was fine mapped to the scaffold2675 and scaffold9327 which are coved 178.92kb on the physical map of O. longistaminata on rice chromosome 3 and the Rhz4 was located on the scaffold26912, scaffold30607, scaffold9358 and scaffold6613, which are coved 40.49kb on the physical map of O. longistaminata on rice chromosome 4.Microarray experiments were performed using one Affymetrix GeneChip Rice Genome Array (Santa Clara, CA) for the five samples. The array contains 51,279 probe sets representing 48,564 japonica and 1,260 indica transcripts. Different gene sets were determined exclusively expressed in five tissues.58 genes were identified as prevalent sets in the rhizome tip. Of these, several genes were functionally involved in tiller initiation and elongation. We found 162 genes up-regulated and 261 genes down-regulated in rhizome tips compared to the expression level in shoot tips that we examined. Strikingly, the genes related to phytohormone and the gene families with redundancy function were obviously differentially regulated in these two tissues. Several cis-regulatory elements, including CGACG, GCCCORE, GAGAC and a Myb Core, were highly enriched in the rhizome tip or internode, and two cis-elements, RY repeat and TAAAG, which are implicated in the ABA signaling pathway, were found overrepresented in the rhizome tip in comparison with the shoot tip. A few rhizome-specific expressed genes were co-localized on the rhizome-related QTLs regions, indicating these genes may be good functional candidates for the cloning of rhizome-related genes.The whole genome profiling of O. longistaminata indicated that a very complex gene regulatory network underlies rhizome development and growth, and that there might be an overlapping regulatory mechanism in the establishment of rhizomes and tillers. Phytohormones such as IAA and GA are involved in the signaling pathway in determining rhizomes. Several cis-elements enriched in rhizomes and rhizome-specific genes co-localized on the rhizome-related QTL intervals provide a base for further dissection of the molecular mechanism that controls the rhizomatous growth habit. The fine mapping of the Rhz2 and Rhz3 will facilitate cloning of the genes, which may contribute significantly to our understanding of grass evolution, advance opportunities to develop perennial cereals, and offer insights into environmentally benign wee-control strategies.