In silico Identification of Resistance and Defense Related Genes for Bacterial Leaf Blight (BLB) in Rice

Abstract

Bacterial leaf blight (BLB) disease is a rice disease caused by Xanthomonas oryzae pv.oryzae (Xoo). This disease causes devastating losses in the rice industry. To date research has been directed towards identifying QTLs and disease resistance genes that will afford resistance against Xoo. The rice plantations in different parts of the world are attacked by various strains of Xoo and thence the varieties that exhibit resistance to these strains may vary from one geographical location to another. In this paper we have analysed a QTL that has been recurrent in various rice backgrounds making it one of the three main QTLs responsible for BLB resistance in rice. qBBR11-1, a QTL found in chromosome eleven of rice is a good candidate for defense and resistance analysis towards BLB due to the various reports on the presence of multiple resistance genes in this QTL. Through the utilisation of bioinformatics tools we (1) identified and classified defense genes to functional groups, (2) identified and classified resistance genes according to the relevant domains, and finally, (3) mapped the relationship between defense related and resistance genes to build a defense model against BLB. A total of 21 defense genes have been classified according to functional groups such as chitinase activity, transduction signal and response to stress. A total of 37 putative resistance genes have been found and classified according to related domains such as nucleotide binding sites (NBS), trans membrane domains (Trd), WRKY domains and Ser / Thr Kin without LRR. Collectively all this information is used to provide a graphical representation of the interaction between the dense and the resistance gene systems. The key genes identified may be developed into markers for breeding or used in plant transformation works.

Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice (Oryza sativa L.)

“…Rice blast, sheath blight and bacterial leaf blight are the major rice diseases reported in rice. Kumar et al mapped the relationship between defense related and resistance genes to build a defense model for diseases in rice [7]. The major R-genes found in specific QTLs can be utilized in developing resistant cultivars [8].…”

Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens

“…Fungal diseases are rather difficult to control as the spores disperse easily and their presence in soil and air persist despite the application of chemical controls. While breeding for resistance through quantitative trait locus (QTL) identification [4,5,6], application of fungicide and improved agricultural practices are current methods utilized to control plant diseases, the understanding of the fungal pathogen itself is crucial in establishing effective defense.…”

Dissection of Quantitative Trait Loci (QTL), annotation of Single Nucleotide Polymorphism (SNP), and Identification of Candidate Genes for Grain Yield in Triticum turgidum L. var durum

“…Some genes of this large family under abiotic stress may be over or underexpressed depending on the stress [36]. As for the candidate gene coding for the Hydroxyproline-rich glycoprotein-like identified in the QTLs detected in the dry and cold environments: RF, INC, and EP (Supplementary: Table S1), this gene was associated with drought tolerance in barley [37] and with the resistance to bacterial pathogen in rice [38].…”