RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

BMC Bioinformatics

Database

Tilak Raj Sharma¹  Amolkumar U. Solanke¹  Amitha Mithra S. V.¹  Chandra Prakash¹  V. Sureshkumar²  Maninder Sandhu³  Trilochan Mohapatra⁴  Rekha Dixit⁵ 

[1] ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, 110012, New Delhi, India;ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, 110012, New Delhi, India;Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, 641003, Coimbatore, India;ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, 110012, New Delhi, India;Shobhit University, Modipuram, 250110, Meerut, Uttar Pradesh, India;Indian Council of Agricultural Research, Krishi Bhawan, 110001, New Delhi, India;Shobhit University, Modipuram, 250110, Meerut, Uttar Pradesh, India;Current address: Department of biotechnology, Keralverma faculty of science, Swami Vivekanand Subharti University, 250005, Meerut, Uttar Pradesh, India;

关键词: Rice;    Meta-analysis;    Salinity;    Drought;    DNA markers;   

DOI  :  10.1186/s12859-017-1846-y

 received in 2016-12-27, accepted in 2017-09-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundGenome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice.ResultsRiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search.ConclusionsThe aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype.Database URL: http://14.139.229.201

【 授权许可】

CC BY   
© The Author(s). 2017