Identification and fine mapping of Pi39(t), a major gene conferring the broad-spectrum resistance to Magnaporthe oryzae

Abstract

Blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most devastating diseases of rice worldwide. The Chinese native cultivar (cv.) Q15 expresses the broad-spectrum resistance to most of the isolates collected from China. To effectively utilize the resistance, three rounds of linkage analysis were performed in an F(2) population derived from a cross of Q15 and a susceptible cv. Tsuyuake, which segregated into 3:1 (resistant/susceptible) ratio. The first round of linkage analysis employing simple sequence repeat (SSR) markers was carried out in the F(2) population through bulked-segregant assay. A total of 180 SSR markers selected from each chromosome equally were surveyed. The results revealed that only two polymorphic markers, RM247 and RM463, located on chromosome 12, were linked to the resistance (R) gene. To further define the chromosomal location of the R gene locus, the second round of linkage analysis was performed using additional five SSR markers, which located in the region anchored by markers RM247 and RM463. The locus was further mapped to a 0.27 cM region bounded by markers RM27933 and RM27940 in the pericentromeric region towards the short arm. For fine mapping of the R locus, seven new markers were developed in the smaller region for the third round of linkage analysis, based on the reference sequences. The R locus was further mapped to a 0.18 cM region flanked by marker clusters 39M11 and 39M22, which is closest to, but away from the Pita/Pita(2) locus by 0.09 cM. To physically map the locus, all the linked markers were landed on the respective bacterial artificial chromosome clones of the reference cv. Nipponbare. Sequence information of these clones was used to construct a physical map of the locus, in silico, by bioinformatics analysis. The locus was physically defined to an interval of approximately 37 kb. To further characterize the R gene, five R genes mapped near the locus, as well as 10 main R genes those might be exploited in the resistance breeding programs, were selected for differential tests with 475 Chinese isolates. The R gene carrier Q15 conveys resistances distinct from those conditioned by the carriers of the 15 R genes. Together, this valuable R gene was, therefore, designated as Pi39(t). The sequence information of the R gene locus could be used for further marker-based selection and cloning.

Rice RING protein OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell wall defence

“…We did not observe the involvement of OsBBI1 in disease resistance against bacterial blight, indicating that OsBBI1-mediated resistance is likely specific to defence against blast fungus, consistent with its induction by BTH and M. oryzae but not by Xoo. In rice, several R genes/loci such as Pi5, Pi9, Pi21, Pi33, Pi39(t), and Pi40(t), have been identified to confer broad-spectrum blast resistance [9,10,[48][49][50][51]. However, molecular mechanisms by which these R genes provide broad-spectrum resistance remain elusive.…”

Evolutionary Dynamics of the Genomic Region Around the Blast Resistance Gene Pi-ta in AA Genome Oryza Species

“…First, other blast R genes in the Pi-ta region also introgressed into diverse elite rice cultivars. Other R genes such as Pi-ta 2 , Pi39, and Pi20(t) (Rybka et al 1997;Liu et al 2007;Li et al 2008) were also mapped at the Pi-ta region, but it was unknown if these and/or other unknown R genes were clustered in the Pi-ta region that have been introgressed as a large linkage block. Second, other components for the Pi-tamediated resistance reside within the 5-Mb region to form a superlocus.…”

Artificial introgression of a large chromosome fragment around the rice blast resistance gene Pi-ta in backcross progeny and several elite rice cultivars

“…A cluster of R genes including Pi-ta 2 was also mapped at the same region, and both of them were inseparable in 4000 F 2 individuals of a cross involving Katy with a breeding line RU9101001 (Chao et al, 1999;Jia, unpublished data). In addition, two blast R genes, Pi20(t) and Pi39(t) were recently mapped near the Pi-ta/Pi-ta 2 /Ptr(t) genes although their allelic relationship to Pi-ta/Pi-ta 2 /Ptr(t) is unclear (Liu et al, 2007;Li et al, 2008). It is also unknown if Pi20(t) and Pi39(t) confer resistance to the race IB49 of M. oryzae.…”