Abstract
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
Highlights
Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice
One of the major approaches followed for dissecting complex traits such as drought and salt tolerance is the identification of Quantitative trait loci (QTL) by preliminary genetic mapping followed by fine mapping and identification of the candidate gene(s)
Microarray generally identifies a large number of differentially expressed genes (DEGs) even in closely related individuals such as isogenic lines contrasting for a single trait [12]
Summary
Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. One of the major approaches followed for dissecting complex traits such as drought and salt tolerance is the identification of QTLs by preliminary genetic mapping followed by fine mapping and identification of the candidate gene(s). Though this is a robust approach, it is laborious and time-consuming. One of the proven and effective ways to dissect complex traits is to combine genetic mapping with genomewide transcriptome profiling of the parental genotypes which can help to narrow down the candidate gene(s) underlying the functional polymorphism in the QTL [13]. When huge numbers of genes from different biological materials are implicated in expression of a trait, meta-analysis provides a cost effective way to identify robust candidate gene(s) for trait improvement through breeding
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