Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pik h )

Ramkumar, G.; Srinivasarao, Kommoju; Mohan, K. Madhan; Sudarshan, I.; Sivaranjani, A. K. P.; Gopalakrishna, K; Neeraja, C. N.; Balachandran, S. M.; Sundaram, R. M.; Prasad, M. S.; Rani, N. Shobha; Prasad, Ashish; Viraktamath, B. C.; Madhav, M. S.

doi:10.1007/s11032-010-9538-6

Cited by 83 publications

(63 citation statements)

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“…In addition, a 92 bp region was also deleted in RP2068-18-3-5 when compared with the third allele in the rice variety Phalguna carrying Gm2 (Sama et al 2014). Likewise, in the NBS-LRR-domain-containing protein coding for Pi54 lacked a 144 bp segment in an exon in the functional allele (Ramkumar et al 2011). We report here four separate deletions of 4, 16, 4 and 273 bp in the Abhaya allele at the untranslated region compared with the allele present in the susceptible parent, ISM.…”

Section: Discussionmentioning

confidence: 99%

“…While over 150 NBS-LRR encoding genes are reported in Arabidopsis thaliana (Meyers et al 2003), rice genome has 653 NBS-LRR genes (Marone et al 2013). Rice blast resistance genes Pi-ta, Pi9 and Pi54 encode NBS-LRR proteins (Bryan et al 2000;Qu et al 2006;Ramkumar et al 2011). Two bacterial blight (BB) resistance genes Xa1 and Xa26 are also members of the NBS-LRR family (Sun et al 2004).…”

Section: Introductionmentioning

confidence: 99%

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Cloning of a gene encoding LRR protein and its validation as candidate gall midge resistance gene, Gm4, in rice

et al. 2014

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The Asian rice gall midge, Orseolia oryzae, is an important pest of rice. Gm4, a major rice gall midge resistance gene in the indica rice variety Abhaya has been fine mapped within 0.3 Mb region with the flanking markers RM22551 and RM22562. Among the 70 putative candidate genes identified in the reference Nipponbare rice genome in this region, two genes coding for leucine rich repeat (LRR) proteins were shortlisted for further analysis.Polymorphisms was observed between the parents improved samba masuri (ISM) (susceptible parent) and Abhaya (resistant parent) and the recombinant inbred line (RIL)-derived near isogenic lines (preNILs) 482R (resistant line) and 489S (susceptible line) with one pair of the markers targeting the candidate genes. Polymorphism co-segregated with the trait in a larger mapping population consisting of 40 resistant and 40 susceptible RILs (F 10 generation). A major segment of this gene (LOC_Os08g09670.1), covering one of the two exons, was cloned and sequenced from both parents as well as from the two pre-NILs 482R and 489S. Data revealed a large deletion in the Abhaya fragment as compared to that of ISM. At least five amino acid substitutions were detected, between the alleles, that are likely to influence the protein function. Expression analysis of this putative candidate gene through reverse transcription real time PCR showed more than two fold increase in its expression levels in the resistant parent Abhaya and resistant line 482R at 24 h after gall midge infestation when compared with the uninfested controls. These results suggested the LRR coding gene to be the candidate for Gm4. In addition, the current work also identified a functional marker (LRR-del) for the detection of the gene for use in marker-assisted introgression of Gm4.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Cloning of a gene encoding LRR protein and its validation as candidate gall midge resistance gene, Gm4, in rice

et al. 2014

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“…This allele mining strategy can help trace the evolution of alleles, identify new useful haplotypes and guide the development of allele-specific markers for use in marker-assisted selection (MAS). For instance, following an allele mining approach several resistance gene homologues and functional resistance genes have been isolated in potato [31], wheat [32], rice [33,34], and barley [35].…”

Section: Mining Plant Diversity: From Genotype To Phenotypementioning

confidence: 99%

Next generation breeding

Barabaschi¹,

Tondelli²,

Desiderio³

et al. 2016

Plant Science

150

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“…The Pi54 blast resistance gene was mapped on chromosome 11L from the Vietnamese rice genotype, Tetep that conferred the resistance against predominant races of the pathogen in India (Sharma et al 2010). Tightly linked (Sharma et al 2005) and functional markers (Ramkumar et al 2010) are available for marker-assisted selection of the gene, and a few research groups in India have successfully introgressed Pi54 into varieties (Narayanan et al 2002;Joseph et al 2004;Sundaram et al 2008Sundaram et al , 2009 and parental lines (Basavaraj et al 2010;Singh et al 2011;Zhan et al 2012;Hari et al 2011Hari et al , 2013.…”

Section: Introductionmentioning

confidence: 99%

Marker-assisted introgression of bacterial blight and blast resistance into DRR17B, an elite, fine-grain type maintainer line of rice

et al. 2015

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DRR17A is a stable wild-abortive cytoplasmic male sterile line with medium-slender grain type. DRR17A and its maintainer line DRR17B are highly susceptible to two of the major rice diseases, bacterial blight (BB) and blast. To improve DRR17B for resistance against BB and blast, we have introgressed a major dominant gene each conferring resistance against BB (Xa21) and blast (Pi54) into CH Balachiranjeevi, S. Bhaskar Naik, V. Abhilash and R. M. Sundaram have contributed equally to this work.Electronic supplementary material The online version of this article (

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Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pik h )

Cited by 83 publications

References 16 publications

Cloning of a gene encoding LRR protein and its validation as candidate gall midge resistance gene, Gm4, in rice

Cloning of a gene encoding LRR protein and its validation as candidate gall midge resistance gene, Gm4, in rice

Next generation breeding

Marker-assisted introgression of bacterial blight and blast resistance into DRR17B, an elite, fine-grain type maintainer line of rice

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