Resistance in rice cultivars to the rice blast fungus Magnaporthe oryzae is complex and is controlled by both major genes and quantitative trait loci (QTLs). We undertook a genome-wide association study (GWAS) using the rice diversity panel 1 (RDP1) that was genotyped using a high-density (700 000 single nucleotide polymorphisms) array and inoculated with five diverse M. oryzae isolates. We identified 97 loci associated with blast resistance (LABRs). Among them, 82 were new regions and 15 co-localized with known blast resistance loci. The top 72 LABRs explained up to 98% of the phenotypic variation. The candidate genes in the LABRs encode nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance proteins, receptor-like protein kinases, transcription factors and defence-related proteins. Among them, LABR_64 was strongly associated with resistance to all five isolates. We analysed the function of candidate genes underlying LABR_64 using RNA interference (RNAi) technology and identified two new resistance alleles at the Pi5 locus. We demonstrate an efficient strategy for rapid allele discovery using the power of GWAS, coupled with RNAi technology, for the dissection of complex blast resistance in rice.
BackgroundRice is a temperature-sensitive crop and its production is severely affected by low temperature in temperate and sub-tropical regions. To understand the genetic basis of cold tolerance in rice, we evaluated the cold tolerance at the seedling stage (CTS) of 295 rice cultivars in the rice diversity panel 1 (RDP1), these cultivars were collected from 82 countries.ResultsThe evaluations revealed that both temperate and tropical japonica rice cultivars are more tolerant to cold stress than indica and AUS cultivars. Using the cold tolerance phenotypes and 44 K SNP chip dataset of RDP1, we performed genome-wide association mapping of quantitative trait loci (QTLs) for CTS. The analysis identified 67 QTLs for CTS that are located on 11 chromosomes. Fifty-six of these QTLs are located in regions without known cold tolerance-related QTLs.ConclusionOur study has provided new information on the genetic architecture of rice cold tolerance and has also identified highly cold tolerant cultivars and CTS-associated SNP markers that will be useful rice improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0133-2) contains supplementary material, which is available to authorized users.
High temperature stress (HTS), an increasingly important problem in rice production, significantly reduces rice yield by reducing seed set percentage (SSP). Breeding rice varieties with tolerance to HTS at the flowering stage is therefore essential for maintaining rice production as the climate continues to warm. In this study, two quantitative trait loci (QTL) underlying tolerance to HTS were identified using the recombinant inbred lines (RILs) derived from a cross between the HTS-tolerant rice cultivar 996 and the sensitive cultivar 4628. SSP was used as the heattolerance indicator for the lines, which were subjected to HTS at the flowering stage in both field and growth chamber experiments. Two major QTL that affected SSP in both conditions were detected in the interval between RM5687 and RM471 on chromosome 4, and between RM6132 and RM6100 on chromosome 10. The QTL located on chromosome 4 explained 21.3% in field and 25.8% in growth chamber of the total phenotypic variation in SSP, and increased the SSP of plants subjected to HTS by 9.1% in field and by 9.3% in growth chamber. The second QTL located on chromosome 10 explained 11.5% in field and 11.6% in growth chamber of the total phenotypic variation in SSP, and increased the SSP of plants subjected to HTS by 7.2% in field and 7.0% in growth chamber. The positive additive effects of the two QTL were derived from the 996 alleles. The two major QTL identified in this study could be useful for further fine mapping and cloning of these genes and for molecular marker-aided breeding of heat-tolerant rice cultivars.
Rice diseases caused by fungi, bacteria and viruses are one of the major constraints for sustainable rice (Oryza sativa L.) production worldwide. The use of resistant cultivars is considered the most economical and effective method to control rice diseases. In the last decade, a dozen resistance genes against the fungal pathogen Magnaporthe grisea and the bacterial pathogen Xanthomonas oryzae pv.
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