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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #326221
Title: Identification of a Pi9 containing rice germplasm with a newly developed robust marker

Author
item SCHEUERMANN, KLAUS - Epagri
item Jia, Yulin

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/30/2016
Publication Date: 7/1/2016
Citation: Scheuermann, K.K., Jia, Y. 2016. Identification of a Pi9 containing rice germplasm with a newly developed robust marker. Phytopathology. Phytopathology 106:871-876.

Interpretive Summary: Rice blast is a destructive rice disease that threatens staple rice production worldwide. There are many major blast resistance genes that provide some level of protection against the pathogen. However, deployed resistance genes can be rendered ineffective by the constantly evolving pathogen. Thus, identifying new sources of resistance that can be used by breeders to develop improved cultivars is important for food security. In the present study, we developed an effective means to incorporate a blast resistance gene Pi9 using marker assisted selection (MAS). We first developed a DNA marker from a specific region of the Pi9 gene. We then identified a publically available rice germplasm accessions carrying Pi9 for breeders to use as the Pi9 gene donor. The genetic method we developed should accelerate the development of blast resistant rice varieties using a MAS approach.

Technical Abstract: The Pi9 gene, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease (Magnaporthe oryzae). However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker assisted selection (MAS). In addition, no known Pi9 containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a functional Pi9 marker. A total of 29 DNA primers ranging from 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28 and KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9 specific blast reaction. Subsequently, a total of 201 genetically diverse mini core rice germplasm accessions from 114 countries were screened with KS28/KS6, and with pathogenicity assays. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9. This functional DNA marker derived from a portion of the Pi9 gene, and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach.