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Integrated omics analysis of root-preferred genes across diverse rice varieties including Japonica and indica cultivars
- Source :
- Journal of Plant Physiology. 220:11-23
- Publication Year :
- 2018
- Publisher :
- Elsevier BV, 2018.
-
Abstract
- Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44 K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles. The expression patterns of four candidate genes were confirmed in vivo by monitoring expression of β-glucuronidase under control of the candidate-gene promoters, providing new tools to manipulate agronomic traits associated with roots. We also utilized real-time PCR to examine the root-preferential expression of 14 genes across four rice varieties, including japonica and indica cultivars. Using a database of rice genes with known functions, we identified the reported functions of 39 out of the 684 candidate genes. Sixteen genes are directly involved in root development, while the remaining are involved in processes indirectly related to root development (i.e., soil-stress tolerance or growth retardation). This indicates the importance of our candidate genes for studies on root development and function. Gene ontology enrichment analysis in the ‘biological processes’ category revealed that root-preferred genes in rice are closely associated with nutrient transport-related genes, indicating that the primary role of roots is the uptake of nutrients from soil. In addition, predicted protein–protein interaction analysis suggested a molecular network for root development composed of 215 interactions associated with 44 root-preferred or root development-related genes. Taken together, our data provide an important foundation for future research on root development in rice.
- Subjects :
- 0106 biological sciences
0301 basic medicine
Candidate gene
Physiology
In silico
Plant Science
Biology
Real-Time Polymerase Chain Reaction
Plant Roots
01 natural sciences
Japonica
03 medical and health sciences
Gene Expression Regulation, Plant
Botany
Gene expression
Gene
Plant Proteins
Genetics
Microarray analysis techniques
Gene Expression Profiling
food and beverages
Oryza
Promoter
biology.organism_classification
030104 developmental biology
Agronomy and Crop Science
Genome, Plant
Function (biology)
010606 plant biology & botany
Subjects
Details
- ISSN :
- 01761617
- Volume :
- 220
- Database :
- OpenAIRE
- Journal :
- Journal of Plant Physiology
- Accession number :
- edsair.doi.dedup.....3d3809a0beae28125d1cf0ceaaf0ea4d