Indian Journal of Agricultural Research

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Research Article

Indian Journal of Agricultural Research, volume 53 issue 3 (june 2019) : 277-283

Development of InDel marker for rice blast resistance gene Pi9

Z.A. Seman, S.F. AB Razak, M.B. AB Ghaffar, S.N. Misman, R.A. Redzuan, Y.S. Sew, M.R. Rashid
1Biotechnology and Nanotechnology Research Centre, MARDI Headquarters, Persiaran MARDI-UPM Serdang, Selangor Malaysia.
Cite article:- Seman Z.A., Razak AB S.F., Ghaffar AB M.B., Misman S.N., Redzuan R.A., Sew Y.S., Rashid M.R. (2019). Development of InDel marker for rice blast resistance gene Pi9. Indian Journal of Agricultural Research. 53(3): 277-283. doi: 10.18805/IJARe.A-346.

ABSTRACT

Pi9 is one of the major blast resistance genes which encodes a nucleotide-binding site-leucine-rich repeat (NBS-LRR) domain-containing protein. This gene was observed to show resistance against many pathotypes of the blast pathogen in Malaysia. Resistance allele Pi9 from rice variety 75-1-127 had previously been cloned using map-based cloning strategy. The gene sequence was used to design specific primers to amplify susceptible Pi9 allele from MR219 rice variety prior to cloning. The resistance and susceptible allele of Pi9 were 8.587kb and 8.785kb in length respectively. Allele mining was carried out by comparing between the susceptible and resistance allele of Pi9. One potential InDels polymorphism at position 590bp and 920bp was identified. Primer named as Pi9_InDel was designed targeting this region in such a way that the resistance and susceptible genotypes yielded 327 bp and 438 bp amplicon respectively.

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