Title

Genome-wide analyses of rice root development QTLs and development of an online resource, Rootbrowse

Authors

Pala Surya Priya¹, A. Snehalatha¹, U. Kayalvili¹, A.R.Krishna¹, Sukpal Singh¹ and K. Ulaganathan^1, *

Affiliation

¹Centre for Plant Molecular Biology, Osmania University, Hyderabad 500 007, India

Email

kulaganathan123@gmail.com; * Corresponding author

Article Type

Database

Date

received December 11, 2008; revised December 19, 2008; accepted December 29, 2008; published January 12, 2009

Abstract

Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles. Intensive data mining of literature resulted in the identification 861 root development QTLs and associated microsatellite markers located on different chromosomes. The QTL and marker data generated and the genome sequence of rice were used for construction of a relational database, Rootbrowse, using MySQL relational database management system and Bio::DB::GFF schema. The data is viewed using GBrowse visualization tool. It graphically displays a section of the genome and all features annotated on it including the QTLs. The QTLs can be displayed along with SSR markers, protein coding genes and/or known root development genes for prediction of probable candidate genes.

Keywords

root development; rice; QTLs; candidate genes; auxin metabolism;

Citation

Priya et al., Bioinformation 3(6): 279-281 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.