Abstract
The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.
Highlights
Rice (Oryza sativa) is one of the most important food crops of the world and its yield is constantly affected by several diseases [1]
We used a data set of 61250 rice cDNA and identified 786-R gene models in rice genome of japonica species, which is 1.16% of the total number of the gene models predicted in rice (S1 Table)
Of the total R-genes predicted in rice genome, 24% of the genes have homology to leucine rich repeat (LRR)-transmembrane domains (TM) category
Summary
Rice (Oryza sativa) is one of the most important food crops of the world and its yield is constantly affected by several diseases [1]. The severity and significance of damage caused by pathogens in rice have necessitated the development of effective disease management strategies to minimize the crop losses. Among such new strategies, the exploitation of host resistance appears to be the most reliable method of disease management. Plants will be resistant to the pathogens when compatible R- and Avr-genes are present in host-pathogen systems [4]. This gene-for-gene interaction is very specific and important in getting resistance phenotypes [5]. Various molecular mechanism like gene duplication, unequal crossing over, ectopic recombination, and diversifying selection have been proposed to contribute to the structure of R-gene clusters and the evolution of resistance specificities [10]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
