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

Abstract

Background Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. Results The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11–2 and BRGC11–3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. Conclusions We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.

Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection

“…Vialone Nano is a traditional and renowned Italian variety, grown on several thousands of hectares and also having a Protected Geographical Indication (in Italy, denominated IGP). Nonetheless, it is one of the most blast-susceptible Italian cvs [ 8 , 59 ]. Although treated with fungicides during the growing season, Vialone Nano often suffers a serious yield penalty when exposed to moderate pathogen pressure, making the sustainability of this cultivation very uncertain.…”

“…It causes lesions to all aerial parts of the plant, mainly leaves and panicles, resulting in yield losses, sometimes up to 100% under favorable environmental conditions [ 4 ] and equivalent to the food of 60 million people annually [ 5 ]. Most of the current European varieties show intermediate or low resistance to blast in field conditions; in particular, some traditional renowned Italian varieties currently cultivated, such as Carnaroli and Vialone Nano, are highly susceptible [ 6 , 7 , 8 ].…”

Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene, Pb2, Encoding NLR Protein

“…Research on panicle blast is difficult due to factors such as heavy workload, long research period and uncontrollable environmental conditions. Many rice blast resistance loci have been identified by GWAS [ 31 , 32 , 33 , 34 , 35 ]. However, there is no report for the identification of panicle blast resistance loci by GWAS.…”

“…Five rice blast resistance loci including the cloned gene Pita were first identified by GWAS, which verified the feasibility of identifying rice blast resistance loci by GWAS [ 28 ]. To date, in total more than 230 rice blast resistance-related loci distributed in all 12 chromosomes were identified by GWAS [ 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. Among them, 16 resistance loci were identified through naturally occurring resistance phenotypes in the blast nurseries, which can resist the invasion of various strains [ 31 ].…”

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

“…Over the years, substantial progress has been made in these methods in relation to almost all organelles, cells, tissues, and organs of rice. Rice genomics led to the discovery and functional characterization of pivotal genes that play crucial roles in improving rice productivity (Yano et al, 2016;Tang et al, 2019;Volante et al, 2020). The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions (Takehisa et al, 2012;Kumar and Dash, 2019;Sun et al, 2019).…”