Abstract
Rice blast, sheath blight and bacterial leaf blight are major rice diseases found worldwide. The development of resistant cultivars is generally perceived as the most effective way to combat these diseases. Plant disease resistance is a polygenic trait where a combinatorial effect of major and minor genes affects this trait. To locate the source of this trait, various quantitative trait loci (QTL) mapping studies have been performed in the past two decades. However, investigating the congruency between the reported QTL is a daunting task due to the heterogeneity amongst the QTLs studied. Hence, the aim of our study is to integrate the reported QTLs for resistance against rice blast, sheath blight and bacterial leaf blight and objectively analyze and consolidate the location of QTL clusters in the chromosomes, reducing the QTL intervals and thus identifying candidate genes within the selected meta-QTL. A total of twenty-seven studies for resistance QTLs to rice blast (8), sheath blight (15) and bacterial leaf blight (4) was compiled for QTL projection and analyses. Cumulatively, 333 QTLs associated with rice blast (114), sheath blight (151) and bacterial leaf blight (68) resistance were compiled, where 303 QTLs could be projected onto a consensus map saturated with 7633 loci. Meta-QTL analysis on 294 QTLs yielded 48 meta-QTLs, where QTLs with membership probability lower than 60% were excluded, reducing the number of QTLs within the meta-QTL to 274. Further, three meta-QTL regions (MQTL2.5, MQTL8.1 and MQTL9.1) were selected for functional analysis on the basis that MQTL2.5 harbors the highest number of QTLs; meanwhile, MQTL8.1 and MQTL9.1 have QTLs associated with all three diseases mentioned above. The functional analysis allows for determination of enriched gene ontology and resistance gene analogs (RGAs) and other defense-related genes. To summarize, MQTL2.5, MQTL8.1 and MQTL9.1 have a considerable number of R-genes that account for 10.21%, 4.08% and 6.42% of the total genes found in these meta-QTLs, respectively. Defense genes constitute around 3.70%, 8.16% and 6.42% of the total number of genes in MQTL2.5, MQTL8.1 and MQTL9.1, respectively. This frequency is higher than the total frequency of defense genes in the rice genome, which is 0.0096% (167 defense genes/17,272 total genes). The integration of the QTLs facilitates the identification of QTL hotspots for rice blast, sheath blight and bacterial blight resistance with reduced intervals, which helps to reduce linkage drag in breeding. The candidate genes within the promising regions could be utilized for improvement through genetical engineering.
Highlights
Rice blast (RB), sheath blight (SHB) and bacterial leaf blight (BLB) are the major rice diseases reported in rice
After careful examination of the quantitative trait loci (QTL), a total number of 333 QTLs associated with sheath blight, rice blast and bacterial leaf blight resistance were compiled and prepared as individual input files for each study and subjected to mapping, QTL projection and meta-QTL analysis
Based on the gene ontology mapping and annotation for these genes, we found that the oxidation-reduction process, electron transport chain, ethanol oxidation and interstrand crosslink repair were among the most enriched biological processes in MQTL2.5
Summary
Rice blast (RB), sheath blight (SHB) and bacterial leaf blight (BLB) are the major rice diseases reported in rice. Rice blast is the number one destructive disease, followed by sheath blight and bacterial leaf blight. For sheath blight, the reduction in yield can be up to 42% [2], and for bacterial leaf blight, the losses can be up to 60% [3]. While fungicides are the main method of controlling disease, their detrimental effects on the environment and the handlers cannot be discounted. This has caused the rice industry to be largely dependent on the generation of new resistant varieties as it is perceived to be the most efficient way by far
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