Available cloned genes and markers for genetic improvement of biotic stress resistance in rice

Abstract

Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.

Map-Based Cloning and Characterization of a Major QTL Gene, FfR1, Which Confers Resistance to Rice Bakanae Disease

“…Firstly, its genetic effect will be quite reliable because it was functionally validated by using transgenic approaches, including complementation tests and gene editing. Secondly, because the exact physical location of the gene has been identified, it enables a precision marker-assisted introgression of the target gene without linkage drag caused by the neighboring genes [ 57 ]. Therefore, breeders will be able to precisely introduce the FfR1 gene into other elite rice varieties to develop BD-resistant varieties.…”

“…Therefore, breeders will be able to precisely introduce the FfR1 gene into other elite rice varieties to develop BD-resistant varieties. Moreover, pyramiding of resistance genes (two or more) in one background is usually used in a breeding program to achieve durable and broad-spectrum resistance [ 57 ]. Therefore, it is necessary to identify more BD-resistant QTLs and genes by using map-based cloning or other methods, and develop their gene-based markers, which will be used in pyramiding BD-resistant genes, including FfR1 .…”

Recent Advances in the Genetic and Biochemical Mechanisms of Rice Resistance to Brown Planthoppers (Nilaparvata lugens Stål)

“…The Bph37 that from SE382, Bph25, bph29, Bph32 and bph4 were present on chromosome 6S between 0.21 and 1.47 Mb [22,[48][49][50][51]. The Bph43 and Bph28(t) genes were clustered between 16.79 and 16.96 Mb of chromosome 11L [23,52]. Some regions of these genes in the same cluster might overlap, indicating that these genes were not the same but were tightly linked, or that they were the same gene.…”

“…Bph1, the first BPH-resistance gene identified from Mudgo, was mapped on chromosome 12 [21]. In recent decades, more than 49 BPH-resistance genes/QTLs have been detected due to the development of molecular marker technology and methods for evaluating the resistance of rice to BPHs [2,3,[22][23][24]. Among these 49 genes/QTLs, 33 (Bph37 from IR64; Bph38(t), Bph33(t), bph19, Bph31, Bph44(t), qBph4.3, Bph33, Bph30, Bph41, Bph40, qBph4.1, Bph3, and qBph4.2 from IR65482-17, qBph4.4, Bph17, and qBph4.2 from Rathu Heenati; Bph27(t), Bph6, Bph44, Bph42, Bph25, and Bph37 from SE382; Bph32, bph4, Bph43, Bph28(t), bph2, bph7, and Bph9 from Kaharamana; and Bph1, Bph26, and Bph9 from Pokkali) were derived from traditional cultivated rice species; the rest were derived from wild rice varieties, including Bph13(t), bph11, qBph3, Bph14, qBph4, and Bph15 from O. officinalis; Bph12 from O. latifolia; Bph35, Bph36, Bph27, and bph29 from O. rufipogon; Bph21 and Bph20(t) from O. minuta; Bph34 from O. nivara; and Bph18 and Bph10 from O. australiensis (Table 1).…”

“…The salicylic acid (SA) signaling pathway was activated and callose deposition was induced in phloem during BPH feeding on plants expressing Bph14 [34]. Additional studies have shown that BPH14 interacts with the transcription factors (TFs) OsWRKY46 and OsWRKY72 and activates the expression of the receptor-like cytoplasmic kinase gene RLCK281 and the callose synthase gene LOC_Os01g67364.1 in rice [23].…”