GENOMIC CHARACTERIZATION OF RICE GERMPLASM
Location: Dale Bumpers National Rice Research Center
Title: Mapping of a genetic component required for Pi-ta-mediated signal recognition
Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: February 1, 2008
Publication Date: March 1, 2008
Citation: Costanzo, S., Jia, M.H., Jia, Y. 2008. Mapping of a genetic component required for Pi-ta-mediated signal recognition. In: Proceedings of the 32nd Rice Technical Working Group Meetings, February 18-21, 2008, San Diego, CA. 2008. CDROM.
A large deletion population of rice plants using an adapted US tropical japonica cultivar, Katy, was developed during 2001-2005 to identify mutants with “interesting” phenotypes. These mutants can be used to screen for specific changes at a gene of interest or to discover single or multiple genes regulating a particular plant phenotype. Among this material, a rice mutant ‘2354’, derived from Katy irradiated with fast neutrons, lost its resistance to all races of Magnaporthe oryzae, including race IB49, indicating the loss of Pi-ta-mediated resistance. However, it was shown that Pi-ta is intact and was expressed in 2354. To investigate the genetic components affected by this mutation, we have developed and analyzed an F2 segregating population from a cross between ‘2354’ and an indica cultivar ‘Te Qing’ from China that is resistant to IB-49 (isolate ZN61) and has Pi-ta intact and expressed. Results of artificial inoculations with isolate ZN61, confirmed the presence of a single dominant gene that segregates with a ratio of 3:1 (resistant: susceptible) in the F2 population. This result suggests that the genetic component defected in 2354 was complemented by the allele from Te Qing. We designated this new locus as Ptr (t) referencing Pi-ta required temporary.
Pi-ta and its critical component(s) co-segregated in several mapping populations. The genomic region responsible for resistance is delimited within a 9 Mb region spanning the Pi-ta locus of the centromere of chromosome 12. To isolate Ptr (t) a few available polymorphic Simple Sequence Repeat (SSR) markers in this region were not sufficient for high resolution mapping. To generate new molecular markers, a total of 16 chromosomal regions were selected based on publicly available rice genome sequences (www.tiger.gov), and primers were designed to amplify approximately 1.8 kb fragments from the genomic DNA of both parents. DNA sequences of these fragments were analyzed and new primers designed in the presence of Single Nucleotide Polymorphism (SNP) or Insertion and Deletions (InDels) sites to obtain dominant markers specific to one of the two parents. A total of 7 new markers were developed positioned approximately 1.3 Mb from each other spanning a 9 Mb region. Identified SSR markers and these new dominant markers are being used to genotype 600 blast susceptible plants. The initial results obtained from this work will be presented.