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

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

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

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

Development and validation of a genome-wide InDel marker set discriminating the alleles between the BB-genome Oryza species and rice (O. sativa)

Wild relatives of cultivated rice (Oryza sativa) belonging to the genus Oryza are regarded as ‘genetic reservoirs’ for rice improvement. Their genes are transferable to cultivated rice through crossing and they have been contributing significantly to rice variety improvement by introgression of their diverse valuable traits, especially biotic stress resistance. Moreover, active use of wild rice resources might be one of the ideal solutions to seek novel or superior alleles/genes to cope with climate change and stable high-yield rice production. DNA markers are essential tools for genetic analysis and breeding. However, to date, there are no suitable DNA marker sets for BB-genome species (O. punctata). In this study, we developed a genome genome-wide InDel marker set evenly distributed (∼2 Mb intervals) across the 12 chromosomes for BB-genome species. The markers were validated by PCR-agarose gel analysis with BB-genome containing species: four accessions each of O. punctata (BB) and O. minuta (BBCC). Out of the 191 InDel markers designed, 184 (96.3%) and 138 (72.2%) were able to differentiate the alleles between O. sativa and O. punctata and between O. sativa and O. minuta respectively. The same marker sets were also tested in other genome types species (CC, CCDD, EE, FF, GG, HHJJ, and KKLL) and one accession of Leersia perrieri (a sister genus to Oryza). The number of polymorphic markers (O. sativa vs other genome types) was drastically reduced in other genome types. In contrast, the number of markers showing no PCR amplification increased, especially in FF, GG, HHJJ, and KKLL species. This suggests that the development of genome type-specific marker sets would be more efficient rather than testing random InDel markers. The newly developed InDel markers maybe be useful for the identification of valuable genetic factors from the BB or BBCC-genome species and also for transferring the identified genes/QTLs into elite variety backgrounds