Rice blast (the causative agent the fungus Magnaporthe oryzae) represents a major constraint on the productivity of one of the world’s most important staple food crops. Genes encoding resistance have been identified in both the Xian and Geng subspecies genepools, and combining these within new cultivars represents a rational means of combating the pathogen. In this research, deeper allele mining was carried out on Pid2, Pid3, and Pid4 via each comprehensive FNP marker set in three panels consisting of 70 Xian and 58 Geng cultivars. Within Pid2, three functional and one non-functional alleles were identified; the former were only identified in Xian type entries. At Pid3, four functional and one non-functional alleles were identified; once again, all of the former were present in Xian type entries. However, the pattern of variation at Pid4 was rather different: here, the five functional alleles uncovered were dispersed across the Geng type germplasm. Among all the twelve candidate functional alleles, both Pid2-ZS and Pid3-ZS were predominant. Furthermore, the resistance functions of both Pid2-ZS and Pid3-ZS were assured by transformation test. Profiting from the merits of three comprehensive FNP marker sets, the study has validated all three members of the Pid family as having been strictly diverged into Xian and Geng subspecies: Pid2 and Pid3 were defined as Xian type resistance genes, and Pid4 as Geng type. Rather limited genotypes of the Pid family have been effective in both Xian and Geng rice groups, of which Pid2-ZS_Pid3-ZS has been central to the Chinese rice population.

Background: Rice blast (causative agent the fungus Pyricularia oryzae) represents a major constraint over the productivity of one of the world’s most important staple foods. Genes encoding resistance have been identified in both the indica and japonica subspecies genepools and combining these within new cultivars represents a rational means of combating the pathogen.Results: In this research, a deeper allele mining was carried out on Pid-2, Pid-3, and Pid-4 by each of comprehensive FNP marker set in the three panels consisting of 70 indica and 58 japonica cultivars. Within Pid-2, three functional and one non-functional alleles were identified; the former were only identified in indica type entries. At Pid-3, four functional and one non-functional alleles were identified, and once again, all of the formers were present in indica type entries. However, the pattern of variation at Pid-4 was rather different: here, the five functional alleles uncovered were dispersed across the japonica type germplasm. Among all the 12 candidate functional alleles, both Pid2-ZS and Pid3-ZS were predominant. Furthermore, the resistance functions of both Pid2-ZS and Pid3-ZS were assured by transformation test. Conclusions: Profiting from merits of three comprehensive FNP marker sets, the study has validated that all three members of the Pid family have been strictly diverged into indica and japonica subspecies: Pid-2 and Pid-3 were defined as indica type resistance genes, and Pid-4 as japonica one. Rather limited genotypes of the Pid family have been effective in both indica and japonica rice groups, of which Pid2-ZS+Pid3-ZS has been central to the Chinese rice population.