Genetic analysis of durable resistance to Magnaporthe oryzae in the rice accession Gigante Vercelli identified two blast resistance loci

Abstract

Rice cultivars exhibiting durable resistance to blast, the most important rice fungal disease provoking up to 30 % of rice losses, are very rare and searching for sources of such a resistance represents a priority for rice-breeding programs. To this aim we analyzed Gigante Vercelli (GV) and Vialone Nano (VN), two temperate japonica rice cultivars in Italy displaying contrasting response to blast, with GV showing a durable and broad-spectrum resistance, whereas VN being highly susceptible. An SSR-based genetic map developed using a GV × VN population segregating for blast resistance identified two blast resistance loci, localized to the long arm of chromosomes 1 and 4 explaining more than 78 % of the observed phenotypic variation for blast resistance. The pyramiding of two blast resistance QTLs was therefore involved in the observed durable resistance in GV. Mapping data were integrated with information obtained from RNA-seq expression profiling of all classes of resistance protein genes (resistance gene analogs, RGAs) and with the map position of known cloned or mapped blast resistance genes to search candidates for the GV resistant response. A co-localization of RGAs with the LOD peak or the marker interval of the chromosome 1 QTL was highlighted and a valuable tool for selecting the resistance gene during breeding programs was developed. Comparative analysis with known blast resistance genes revealed co-positional relationships between the chromosome 1 QTL with the Pi35/Pish blast resistance alleles and showed that the chromosome 4 QTL represents a newly identified blast resistance gene. The present genetic analysis has therefore allowed the identification of two blast resistance loci in the durable blast-resistant rice cultivar GV and tools for molecular selection of these resistance genes.

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

“…The 277 rice accessions evaluated under growth chamber conditions were arti cially inoculated with a mixture of three Italian blast isolates (IT02, IT03, IT10), showing a broad pattern of virulence towards several blast R genes (Roumen et al 1997;Urso et al 2016). Based on a 1-5 scoring system on leaves (where accessions with a blast disease score equal to-or below 2 were considered as resistant and the remaining as susceptible), 59 varieties (21.3%) were resistant ( Fig.…”

“…The accessions were high-throughput genotyped by SNP markers and genotypic data associated with the rice blast phenotypic scores and the SNP genotypes were then used for a GWAS for eld blast resistance. With the same purpose, a largely overlapping panel (257 accessions in common with the panel evaluated in eld conditions) was also evaluated in growth chamber conditions using a mixture of three highly virulent Italian P. oryzae isolates (IT02, IT03, IT10; Roumen et al 1997;Faivre-Rampant et al 2011;Urso et al 2016). A total of 14 signi cant associations were highlighted either in eld or growth chamber conditions (3 regions were detected as common in both systems), with three associations putatively representing previously unidenti ed blast resistance loci.…”

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions

“…To identify new sources of blast resistance within the japonica background,the resistance to blast of a panel of 279 japonica rice accessions was evaluated in field conditions under natural P. oryzae inoculum for two years and a GWAS study was conducted for blast resistance. A largely overlapping panel (257 accessions in common with the panel evaluated in field conditions) was also evaluated in growth chamber conditions using a mixture of three highly virulent Italian P. oryzae isolates (IT02, IT03, IT10; Roumen et al 1997;Faivre-Rampant et al 2011;Urso et al 2016). A total of 14 significant associations were highlighted either in field or growth chamber conditions (3 regions were detected as common in both systems).…”

“…A total of 110 mapped SSR markers (McCouch et al 2002) listed in the Gramene markers database (http://www.gramene.org/marker) were also tested for polymorphisms between Salvo and Maratelli.The polymorphic SSRs were analyzed in the segregant population using the M13-tailed primer method(Zhou et al 2002) to label amplicons. PCRs were carried out in a 10 µL reaction volume as described inUrso et al (2016). Amplicons were separated using an ABI 3130xl Genetic Analyzer sequencer (Applied Biosystems), GeneScan ROX 500 was used as size standard.…”

“…Jefferson (tropical japonica) has resistant alleles at most of the MTAs; Gigante Vercelli carries resistant alleles at BRF04 and BRF10. The BRF04 resistant allele is most frequently identified in field conditions and its position (31,257,415 to 32,476,401 bp) is adjacent to a QTL for durable blast resistance qBDR4(32,499,412 to 32,887,572 bp) identified in a cross between the durable resistant Gigante Vercelli and the susceptible Vialone Nano(Urso et al 2016). This locus, putatively conferring durable resistance, appears to have been selected in several temperate and tropical japonica, as well as in indica accessions, adapted to temperate conditions.…”