Identification of five new blast resistance genes in the highly blast-resistant rice variety IR64 using a QTL mapping strategy

Abstract

Rice progenies used for the construction of genetic maps permit exhaustive identification and characterization of resistance genes present in their parental cultivars. We inoculated a rice progeny derived from the cross IR64 x Azucena with different Magnaporthe grisea isolates that showed differential responses on the parental cultivars. By QTL mapping, nine unlinked loci conferring resistance to each isolate were identified and named Pi-24( t) to Pi-32( t). They could correspond to nine specific resistance genes. Five of these resistance loci (RLs) were mapped at chromosomal locations where no resistance gene was previously reported, defining new resistance genes. Using degenerate primers of the NBS (nucleotide binding site) motif found in many resistance genes, two resistance gene analogues (RGAs) IR86 and IR14 were identified and mapped closely to two blast RLs (resistance identified in this study, i.e. Pi-29(t) and Pi-30(t) respectively). These two RLs may correspond to the Pi-11 and Pi-a blast resistance genes previously identified. Moreover, the ir86 and ir14 genes have been identified "in silico" on the indica rice cultivar 93-11, recently sequenced by Chinese researchers. Both genes encodes NBS-LRR-like proteins that are characteristics of plant-disease resistance genes.

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

“…The population consists of 176 F 10 -F 12 lines developed by single seed descent and like many classic mapping populations, has been previously genotyped with only sparse SSR markers, 200 in the case of this population ). The population, or a doubled haploid population derived from the same parents, has already been used to dissect the genetic basis of several complex traits, including aluminum tolerance, root architecture, leaf width, plant ion concentration, and many other morphological and agronomic characteristics This et al 2010;Famoso et al 2011;Hemamalini et al 2000;Hittalmani et al 2003;Li et al 2003;Prasad et al 2000;Sallaud et al 2003;Stangoulis et al 2007). It is our hypothesis that by saturating the RIL population with dense SNP markers, we will be able to further capture additional QTL for agronomic traits of interest and better resolve the genetic architecture of the population, including regions of segregation distortion and recombination hot and cold spots.…”

Identification of a New Rice Blast Resistance Gene, Pid3, by Genomewide Comparison of Paired Nucleotide-Binding Site–Leucine-Rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes

“…Some of the genes have been successfully used in blast resistance breeding. When a map-based cloning strategy is used in the identification of R genes, resistance gene analog (RGA) markers that are designed according to the conserved NBS domain could be used to identify the corresponding candidate NBS-LRR resistance gene (Mago et al 1999;Chauhan et al 2002;Zhuang et al 2002;Lee et al 2003;Sallaud et al 2003;Chen et al 2004). In practice, however, successful examples of isolation of an NBS-LRR resistance gene with RGA markers have rarely been reported.…”

Screening of Rice Blast Resistance Genes from Aromatic Rice Germplasms with SNP Markers

“…Recently, more than 50 major blast resistance genes have been identified (Chauhan et al, 2002;Chen et al, 2002;Berruyer et al, 2003;Liu et al, 2004;Liu et al, 2005;Pan et al, 1999;Sallaud et al, 2003;Wu et al, 2003;Zhu et al, 2004). However, a number of blast resistance genes below have been mapped, which should be regarded as an essential starting point to isolate these important genes through map-based cloning approach.…”