Isolation and Manipulation of Quantitative Trait Loci for Disease Resistance in Rice Using a Candidate Gene Approach

Abstract

Bacterial blight caused by Xanthomonas oryzae pv. oryzae and fungal blast caused by Magnaporthe grisea result in heavy production losses in rice, a main staple food for approximately 50% of the world's population. Application of host resistance to these pathogens is the most economical and environment-friendly approach to solve this problem. Quantitative trait loci (QTLs) controlling quantitative resistance are valuable sources for broad-spectrum and durable disease resistance. Although large numbers of QTLs for bacterial blight and blast resistance have been identified, these sources have not been used effectively in rice improvement because of the complex genetic control of quantitative resistance and because the genes underlying resistance QTLs are unknown. To isolate disease resistance QTLs, we established a candidate gene strategy that integrates linkage map, expression profile, and functional complementation analyses. This strategy has proven to be applicable for identifying the genes underlying minor resistance QTLs in rice-Xoo and rice-M. grisea systems and it may also help to shed light on disease resistance QTLs of other cereals. Our results also suggest that a single minor QTL can be used in rice improvement by modulating the expression of the gene underlying the QTL. Pyramiding two or three minor QTL genes, whose expression can be managed and that function in different defense signal transduction pathways, may allow the breeding of rice cultivars that are highly resistant to bacterial blight and blast.

Unraveling the Complex Trait of Crop Yield With Quantitative Trait Loci Mapping in Brassica napus

“…Cloning such QTL via fine mapping may be unlikely, but the application of bioinformatics (such as meta-analysis, comparative genomics, and haplotype association mapping) and/or transcriptomics to narrow QTL/QTG (quantitative trait genes) without fine mapping seems promising (Price 2006;Burgess-Herbert et al 2008;Norton et al 2008). Recently, four minor QTL for disease resistance in rice, each explaining ,5% of the phenotypic variation, have been isolated successfully by a strategy involving candidate genes that integrated expression profiling, bioinformatics, and functional complementation analysis (Hu et al 2008). In other words, a minor QTL might be a major QTL if the variability of the parental alleles is sufficiently large and/or the environment allows the induction of differential expression of the two alleles.…”

Rice RING protein OsBBI1 with E3 ligase activity confers broad-spectrum resistance against Magnaporthe oryzae by modifying the cell wall defence

“…The OsBBI1 gene (Os06g03580) is located in a region of chromosome 6, in which a number of blast resistance QTLs have been identified [52][53][54][55]. The features of Os-BBI1-mediated basal and partial resistance suggest that OsBBI1 might be a QTL against M. oryzae, such as other rice defence genes [56].…”

A CCCH-Type Zinc Finger Nucleic Acid-Binding Protein Quantitatively Confers Resistance against Rice Bacterial Blight Disease

“…According to an analysis using the strategy of validation and functional analysis of the QTL (Hu et al, 2008), we argue that C3H12 contributes to a minor resistance QTL against Xoo. This inference can be supported by the following evidence.…”

“…Although a large number of resistance QTLs have been identified, only a limited number of QTLs have been characterized recently, because of the genetic complexity of this type of resistance (Hayashi et al, 2010;Fu et al, 2011). A strategy of validation and functional analysis of the QTLs has been established to characterize resistance QTLs in rice; this strategy integrates the linkage map, expression profile, functional complementation analysis, and allele comparison and has provided the approach to characterize the genes underlying minor resistance QTLs (Hu et al, 2008;Kou and Wang, 2012).…”