title: Root transcriptome of two contrasting indica rice cultivars uncovers regulators of root development and physiological responses.
abstract: The huge variation in root system architecture (RSA) among different rice (Oryza sativa) cultivars is conferred by their genetic makeup and different growth or climatic conditions. Unlike model plant Arabidopsis, the molecular basis of such variation in RSA is very poorly understood in rice. Cultivars with stable variation are valuable resources for identification of genes involved in RSA and related physiological traits. We have screened for RSA and identified two such indica rice cultivars, IR-64 (OsAS83) and IET-16348 (OsAS84), with stable contrasting RSA. OsAS84 produces robust RSA with more crown roots, lateral roots and root hairs than OsAS83. Using comparative root transcriptome analysis of these cultivars, we identified genes related to root development and different physiological responses like abiotic stress responses, hormone signaling, and nutrient acquisition or transport. The two cultivars differ in their response to salinity/dehydration stresses, phosphate/nitrogen deficiency, and different phytohormones. Differential expression of genes involved in salinity or dehydration response, nitrogen (N) transport, phosphate (Pi) starvation signaling, hormone signaling and root development underlies more resistance of OsAS84 towards abiotic stresses, Pi or N deficiency and its robust RSA. Thus our study uncovers gene-network involved in root development and abiotic stress responses in rice.
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Alka
authors.initials: A
authors.lastname: Singh
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Pramod
authors.initials: P
authors.lastname: Kumar
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Vibhav
authors.initials: V
authors.lastname: Gautam
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Balakrishnan
authors.initials: B
authors.lastname: Rengasamy
authors.affiliation: Rice Research Station, Chinsurah, West Bengal 712101, India.
authors.forename: Bijan
authors.initials: B
authors.lastname: Adhikari
authors.affiliation: Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore 560065, India.
authors.forename: Makarla
authors.initials: M
authors.lastname: Udayakumar
authors.affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
authors.forename: Ananda K
authors.initials: AK
authors.lastname: Sarkar
mesh_terms: D015536:Down-Regulation; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D009584:Nitrogen / Q000172:deficiency / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics / Q000378:metabolism*; D010710:Phosphates / Q000172:deficiency / Q000378:metabolism; D010937:Plant Growth Regulators / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D013312:Stress, Physiological; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D010710:Phosphates; D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors; D009584:Nitrogen