A Single-Tube, Functional Marker-Based Multiplex PCR Assay for Simultaneous Detection of Major Bacterial Blight Resistance GenesXa21, xa13 andxa5 in Rice

In marker-assisted breeding for bacterial blight (BB) resistance in rice, three major resistance genes, viz.,Xa21, xa13andxa5,are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed forxa13 andxa5,we have developed simple PCR-based functio...

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Published in:水稻科学（英文版） 2016, Vol.23 (3), p.144-151
Main Authors: S. K. HAJIRA, R. M. SUNDARAM, G. S. LAHA, A. YUGANDER, S. M. BALACHANDRAN, B. C. VIRAKTAMATH, K. SUJATHA, C. H. BALACHIRANJEEVI, K. PRANATHI, M. ANILA, S. BHASKAR, V. ABHILASH, H. K. MAHADEVASWAMY, M. KOUSIK, T. DILIPKUMAR, G. HARIKA, G. REKHA
Format: Article
Language:English
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Summary:In marker-assisted breeding for bacterial blight (BB) resistance in rice, three major resistance genes, viz.,Xa21, xa13andxa5,are routinely deployed either singly or in combinations. As efficient and functional markers are yet to be developed forxa13 andxa5,we have developed simple PCR-based functional markers for both the genes.Forxa13,we designed a functional PCR-based marker, xa13-prom targeting the InDel polymorphism in the promoter of candidate geneOs8N3 located on chromosome 8 of rice. With respect toxa5, a multiplex-PCR based functional marker system, named xa5FM, consisting of two sets of primer pairs targeting the 2-bp functional nucleotide polymorphism in the exon II of the geneTFIIA?5 (candidate forxa5), has been developed. Both xa13-prom and xa5FM can differentiate the resistant and susceptible alleles forxa13 andxa5, respectively, in a co-dominant fashion. Using these two functional markers along with the already reported functional PCR-based marker forXa21 (pTA248),we designed a single-tube multiplex PCR based assay for simultaneous detection of all the three major resistance genes and demonstrated the utility of the multiplex marker system in a segregating population.
ISSN:1672-6308