Mapping quantitative trait loci conferring blast resistance in upland indica rice (Oryza sativa L.)

Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis

Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS-LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.

Selection of Candidate Genes Conferring Blast Resistance and Heat Tolerance in Rice through Integration of Meta-QTLs and RNA-Seq

Due to global warming, high temperature is a significant environmental stress for rice production. Rice (Oryza sativa L.), one of the most crucial cereal crops, is also seriously devastated by Magnaporthe oryzae. Therefore, it is essential to breed new rice cultivars with blast and heat tolerance. Although progress had been made in QTL mapping and RNA-seq analysis in rice in response to blast and heat stresses, there are few reports on simultaneously mining blast-resistant and heat-tolerant genes. In this study, we separately conducted meta-analysis of 839 blast-resistant and 308 heat-tolerant QTLs in rice. Consequently, 7054 genes were identified in 67 blast-resistant meta-QTLs with an average interval of 1.00 Mb. Likewise, 6425 genes were obtained in 40 heat-tolerant meta-QTLs with an average interval of 1.49 Mb. Additionally, using differentially expressed genes (DEGs) in the previous research and GO enrichment analysis, 55 DEGs were co-located on the common regions of 16 blast-resistant and 14 heat-tolerant meta-QTLs. Among, OsChib3H-c, OsJAMyb, Pi-k, OsWAK1, OsMT2b, OsTPS3, OsHI-LOX, OsACLA-2 and OsGS2 were the significant candidate genes to be further investigated. These results could provide the gene resources for rice breeding with excellent resistance to these 2 stresses, and help to understand how plants response to the combination stresses of blast fungus and high temperature.

Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop

Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.

Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): current status and future considerations

Rice blast disease, which is caused by the fungal pathogen Magnaporthe oryzae, is a recurring problem in all rice-growing regions of the world. The use of resistance (R) genes in rice improvement breeding programmes has been considered to be one of the best options for crop protection and blast management. Alternatively, quantitative resistance conferred by quantitative trait loci (QTLs) is also a valuable resource for the improvement of rice disease resistance. In the past, intensive efforts have been made to identify major R-genes as well as QTLs for blast disease using molecular techniques. A review of bibliographic references shows over 100 blast resistance genes and a larger number of QTLs (∼500) that were mapped to the rice genome. Of the blast resistance genes, identified in different genotypes of rice, ∼22 have been cloned and characterized at the molecular level. In this review, we have summarized the reported rice blast resistance genes and QTLs for utilization in future molecular breeding programmes to introgress high-degree resistance or to pyramid R-genes in commercial cultivars that are susceptible to M. oryzae. The goal of this review is to provide an overview of the significant studies in order to update our understanding of the molecular progress on rice and M. oryzae. This information will assist rice breeders to improve the resistance to rice blast using marker-assisted selection which continues to be a priority for rice-breeding programmes.