Association mapping of resistance to rice blast in upland field conditions

Abstract

BackgroundRice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers.ResultsThe contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance.ConclusionsIt was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0131-4) contains supplementary material, which is available to authorized users.

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

“…The few indica accessions included in the panel, although much less numerous than the other groups, showed a generally higher level of resistance: the median disease scores were 1.33 in the growth chamber (compared to 2.00 and 4.00 for tropical and temperate japonica, respectively) and 2.25 in the field (6.50 and 8.75 for tropical and temperate japonica, respectively). This observation is in agreement with evidence that several donors for qualitative Pi R genes conferring high levels of vertical resistance belong to the indica group(Sharma et al 2012;Liao et al 2016;Raboin et al 2016). these loci should be considered effective in governing both single and multiple strain resistance and can be suggested as useful targets for blast resistance breeding.…”

“…Moreover, a search for blast R genes within a panel of 227 japonica genotypes was recently conducted with a low coverage of SSR markers, allowing the identification of 13 significant associations, eight of them ascribable to previously mapped blast R genes (Guo et al 2016). A rice diversity panel of 150 tropical japonica and 190 indica accessions evaluated for blast resistance in field conditions allowed the identification of three significant associations, on chromosomes 1 and 12 for the japonica panel and chromosome 8 for the indica panel, and candidate genes were discovered on chromosomes 1 and 8 (Raboin et al 2016). A GWAS for blast resistance in rice was also recently applied using a rice diversity panel including 420 accessions representative of the five major O. sativa subpopulations that were challenged respectively with five different blast isolates under a growth chamber assay (Kang et al 2016) and in field conditions in three major rice production areas of China (Zhu et al 2016).…”

Quantitative Resistance: More Than Just Perception of a Pathogen

“…Similarly, mapping of large-effect loci in wheat identified a novel kinase (Fu et al, 2009). Supporting these observations that medium-to-large effect loci appear to function in perception and/or signaling are the large number of studies that investigated the quantitative genetics of rice resistance to rice blast (Magnaporthe oryzae; Ballini et al, 2008;Miah et al, 2013;Kang et al, 2016;Raboin et al, 2016). The vast majority of cloned loci encode RLKs or NLRs, suggesting that the majority of causal loci are in genes controlling the detection of the pathogen.…”

Association mapping in rice: basic concepts and perspectives for molecular breeding

“…These secondary traits may be utilized, provided they are more heritable and highly correlated with the trait of interest like yield. Some notable exceptions were studies to specifically identify loci associated with field blast resistance (Raboin et al, 2016;Zhu et al, 2016). The challenge is that high priority complex traits for breeders (e.g.…”