Genetic and physical mapping of a new allele of Pik locus from japonica rice 'Liziangxintuanheigu'

The Chinese rice Liziangxintuanheigu (LTH) has been used as a universal susceptible background for the development of international monogenic blast differentials by the JIRCAS-IRRI network. Few reports on the occurrence of LTH incompatible blast isolates from the Philippines and India indicate that the genotype harbours unknown blast resistance gene(s). We report identification, mapping and physical delimitation of the chromosomal location of a new blast resistance gene from LTH. Preliminary linkage analysis of an F-2 mapping population generated from a cross between a susceptible cv. 'Dular' and LTH localized the blast resistance gene between simple sequence repeat (SSR) markers RM224 and RM6293 on the distal end of the long arm of chromosome 11. Further mapping with polymorphic SSR and sequence tagged site (STS) markers developed from the interval RM224-RM6293 delimited the resistance gene to a 2 cM interval flanked by STS markers STS-7 and STS-13. By aligning the sequences of linked markers on the sequence of cv. Nipponbare, a similar to 168.05 kb region at the telomeric end of long of chromosome 11 was delineated as the region of the blast resistance gene. Six putatively expressed NBS-LRR genes were identified in the target region by surveying the equivalent genomic region of Nipponbare and two of these, LOC_Os11g46200 and LOC_Os11g46210, were short-listed as a potential candidate for the resistance gene. The new blast resistance gene designated as Pik-l was inferred to be a new allele of Pik locus based on its genomic position and distinct resistance spectra compared to previously known Pik alleles.