Research Article: A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population

Date Published: February 12, 2019

Publisher: Public Library of Science

Author(s): Suk-Man Kim, Russell F. Reinke, Raman Meenakshi Sundaram.

http://doi.org/10.1371/journal.pone.0211775

Abstract

Bacterial blight (BB) caused by the Xanthomonas oryzae pv. oryzae (Xoo) pathogen is a significant disease in most rice cultivation areas. The disease is estimated to cause annual rice production losses of 20–30 percent throughout rice-growing countries in Asia. The discovery and deployment of durable resistance genes for BB is an effective and sustainable means of mitigating production losses. In this study QTL analysis and fine mapping were performed using an F2 and a BC2F2 population derived from a cross with a new R-donor having broad spectrum resistance to Korean BB races. The QTL qBB11 was identified by composite interval mapping and explained 31.25% of the phenotypic variation (R2) with LOD values of 43.44 harboring two SNP markers. The single major R-gene was designated Xa43 (t). Through dissection of the target region we were able to narrow the region to within 27.83–27.95 Mbp, a physical interval of about 119-kb designated by the two flanking markers IBb27os11_14 and S_BB11.ssr_9. Of nine ORFs in the target region two ORFs revealed significantly different expression levels of the candidate genes. From these results we developed a marker specific to this R-gene, which will have utility for future BB resistance breeding and/or R-gene pyramiding using marker assisted selection. Further characterization of the R-gene would be helpful to enhance understanding of mechanisms of BB resistance in rice.

Partial Text

Rice bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of major diseases causing severe production losses in most rice cultivation areas. The disease poses a continuous threat to rice production especially in South and Southeast Asia [1,2]. Developing resistant lines or cultivars is the most effective and economical way to control this disease, while minimizing use of chemical disease control and the attendant environmental concerns [3].

The bacterial leaf blight (BB) caused by Xoo is one of the most widespread and devastating diseases in most rice cultivation areas. To date about 42 BB resistance genes have been identified and these are commonly used in breeding for BB resistance [20]. Given the relatively common breakdown of BB resistance caused by occurrence of a new BB pathotype or change of Xoo population it is necessary to find new resistance genes and combine these with known R-genes in order to develop durable and sustainable resistant lines.

In this study we confirmed the location of a novel BB resistance gene on chromosome 11 using QTL analysis and fine mapping. The QTL detected, qBB11, was renamed Xa43(t) and the physical location delimited to an approximately 119-Kbp segment by PCR based DNA markers IBb27os11_14 and S_BB11.ssr_9 on chromosome 11. Through qRT-PCR analysis two ORFs (Os11g0687700, and Os11g 0688000) demonstrated significant up-regulation of expression levels, noted in the resistant variety P8 in comparison with the susceptible variety Ilpum. Considering the propensity of R-genes to break down, and the need to counter race differentiation in disease resistance breeding, we hope this result will contribute to increasing the spectrum of R-genes available, the identification of new and durable R-genes, and facilitate development of combinations of R-genes using MAS. In particular, we suggest the PCR-based DNA marker may find practical use for MAS breeding programs to improve BB resistance in rice, with the combination of multiple sources of resistance contributing to more durable resistance, leading to greater stability of rice production in areas afflicted by bacterial blight.

 

Source:

http://doi.org/10.1371/journal.pone.0211775

 

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