ARS | Publication request: Characterization of the root transcriptome for iron and zinc homeostasis-related genes in indica rice (Oryza sativa L)

Submitted to: Journal of Plant Biochemistry and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 8, 2010
Publication Date: July 1, 2010
Citation: Chandel, G., Banerjee, S., Vasconcelos, M., Grusak, M.A. 2010. Characterization of the root transcriptome for iron and zinc homeostasis-related genes in indica rice (Oryza sativa L). Journal of Plant Biochemistry and Biotechnology. 19(2):145-152.

Interpretive Summary: Rice is the primary cereal crop and staple food for human populations in several developing countries. Rice is a good source of energy, but a poor dietary source of several minerals. In particular, the micronutrient minerals iron and zinc are found at low concentrations in grains of most rice cultivars. This leads to dietary inadequacies of iron and zinc in many human populations, along with several health-related problems linked to iron and zinc deficiency. To develop strategies that will allow us to provide more dietary iron and zinc in rice grains, we have been interested in identifying the molecular players and processes responsible for moving iron and zinc into the root system of rice plants. The root system is the primary entry point for these minerals into the plant. In this work, we studied several genes that encoded for proteins that help to move iron and zinc across cell membranes. We looked at which of these genes were expressed (that is, turned on) in roots, using various diverse rice cultivars. We showed that some of these genes were turned on in roots of most of the cultivars, thereby demonstrating that these genes played a role in the iron and zinc nutrition of rice plants. We also found several DNA sequence differences amongst cultivars for a few of the genes. This information was used to develop breeding tools that rice breeders could use to select for different copies of these genes. Ultimately, these tools could assist efforts to breed rice cultivars with enhanced levels of iron or zinc in their grains.

Technical Abstract: Micronutrient malnutrition is the most common form of nutrient deficiency among populations having a cereal based-diet. Rice is the staple food for one third of the world’s population, but is a poor source of iron and zinc concentration. We have characterized the root transcriptome of diverse indica rice cultivars for expression of ten known metal homeostasis related genes in plants grown under controlled conditions [with Fe (III)-HEDTA iron source]. Fe/Zn concentrations of root and shoot tissues were also determined. Expression analysis showed expression of OsFRO2, OsZIP9, OsYSL3, OsIRT-1, and OsZip5 expressed in most of the cultivars. The cDNA amplicons of OsFRO2 and OsZIP9 from different cultivars were analyzed for sequence homology and several variations were identified in their nucleotide sequences among the rice genotypes. More than 94% sequence homology was observed for both the genes. We analyzed the genomic region underlying these genes to obtain information about possible spatial localization, based on overlapping ESTs and MPSS tags. In addition, putative SNPs were identified within OsFRO2 and OsZIP9 genes that need to be validated. The sequence based information may be useful in further development of gene specific markers for screening and breeding of high iron and zinc lines.