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

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 poor source of iron and zinc content. We have characterized root transcriptome of diverse indica rice cultivars for expression of ten known metal homeostasis related genes in plants grown under controlled condition [with fe(III)-HEDTA iron source]. Fe/Zn contents of root and shoot tissues were also determined. Expression analysis showed expression of OsFRO2, OsZIP9, OsYSL3, OsIRT-1 and OsZip5 in most of the cultivars. The cDNA amplicons of OsFRO2 and OsZIP9 from different cultivars were analysed for sequence homology and several variation in their nucleotide sequences among rice genotypes. More than 94% sequence homology was observed for both the genes. We analysed the genomic region underlying these genes to obtain information about possible spatial localization based on overlapping ESTs and MPSS tags. Also, 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.