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In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes

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Title In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes
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Creator Yasala AK, Rawat N, VSAK Sama, Himabindu K, Sundaram RM and Bentur JS
 
Subject Candidate gene
Gene annotation
Genome sequence
Linked markers
Physical position
Resistance gene
 
Description Not Available
So far, 11 gall midge resistance genes (Gm1 through Gm11) have been identified in rice though classical inheritance studies and several of these have been mapped through linked markers. Nevertheless, the exact identity of these genes is still eluding. Hence, the present study aimed to identify the potential candidate genes involved in rice-gall midge interactions by in silico analysis for gene content of 4.02 Mb genomic regions containing the gall midge R genes. The candidate genes were identified in terms of common genes among the different gall midge resistance regions, transcriptomics data analysis from earlier studies and, reported genes widely implicated in defense against plant-pathogen interactions. Results revealed, of the 375 annotated genes, five genes with one or more copy number were common among these regions such as the genes encoding NBS-LRR class proteins, no apical meristem protein, Fbox family protein, pentatricopeptide repeat containing protein and SET domain containing protein. Further, 15 genes from these regions have been reported in earlier transcriptomics studies covering in incompatible (9 genes) and compatible (6 genes) rice-gall midge interactions and 22 genes are known to be implicated in different plant-pathogen interactions. From the present study, we have shortlisted 24 genes and developed 33 primer pairs. These primers are ready to use for conducting real time PCR validation.
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Date 2024-06-11T14:15:19Z
2024-06-11T14:15:19Z
2012-06
 
Type Article
 
Identifier Yasala, Arun & Rawat, Nidhi & Sama, VSArun & Himabindu, Kudapa & Sundaram, Raman & Bentur, Jagadish. (2012). In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes. Plant Omics. 5. 405-413.
ISSN:1836-3644
http://krishi.icar.gov.in/jspui/handle/123456789/83534
 
Language English
 
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Publisher Not Available