Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

To enhance the yield potential of an elite indica rice cultivar, an introgression (BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar, IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT. To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading (DTH), culm length (CL), flag leaf length (FLL), flag leaf width (FLW), and filled spikelet number per panicle (FSN). Six putative QTL were detected: four on chromosome 4 (for CL, FLL, FLW, and FSN) and two on chromosome 2 (for DTH and FLL). All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes 2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic effects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars

Estimation of genes in blast resistance in elite indica-type rice (Oryza sativa L.) varieties-bred at the International Rice Research Institute

The presence of blast resistance genes in the elite Indica-type rice (Oryza sativa L.) varieties bred at the International Rice Research Institute (IRRI) was estimated based on a differential system using Philippines isolates of the rice blast fungus Pyricularia grisea (Cooke) Sacc., according to the gene-for-gene theory. Based on the presence of the three resistance genes, Pi20, Pita and one of the Pik alleles (other than Pik-s), the 42 varieties were classified into seven groups. A group that did not harbor these three genes contained seven varieties derived from the progenies of the hybrids with IR24 as a parental variety. The largest group harboring Pita consisted of 17 varieties, including IR36 and its sister lines or progenies. The group harboring by Pi20 had seven varieties that included IR8, IR24 and their hybrid progenies. Thus, most of the IRRI varieties were classified into these three groups that included IR8, IR24, IR36 or their hybrid progenies in their pedigree. The presence of a total of seven resistance genes Pib, Pita, Piz-t, Pi20, Pik-s, one of the Pik alleles (other than Pik-s) and one of the two genes, Pii or Pi3, was estimated in these varieties. In some cases, the presence of genes like Pib, Pik-s and Piz-t could not be confirmed due to the masking effect of Pita, Pik allele, or Pi20. The number and kind of blast resistance genes in IRRI varieties were limited compared with previously reported blast resistance genes. Since the presence of Pik-s and another Pik allele was estimated in 17 varieties belonging to five groups, and that of Pib in 38 varieties belonging to four groups, it appeared that these genes were widely distributed in IRRI-bred varieties

Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia

Abstract A critical step to maximize the usefulness of genome-wide association studies (GWAS) in plant breeding is the identification and validation of candidate genes underlying genetic associations. This is of particular importance in disease resistance breeding where allelic variants of resistance genes often confer resistance to distinct populations, or races, of a pathogen. Here, we perform a genome-wide association analysis of rice blast resistance in 500 genetically diverse rice accessions. To facilitate candidate gene identification, we produce de-novo genome assemblies of ten rice accessions with various rice blast resistance associations. These genome assemblies facilitate the identification and functional validation of novel alleles of the rice blast resistance genes Ptr and Pia. We uncover an allelic series for the unusual Ptr rice blast resistance gene, and additional alleles of the Pia resistance genes RGA4 and RGA5. By linking these associations to three thousand rice genomes we provide a useful tool to inform future rice blast breeding efforts. Our work shows that GWAS in combination with whole-genome sequencing is a powerful tool for gene cloning and to facilitate selection of specific resistance alleles for plant breeding

Co-evolved plant and blast fungus ascorbate oxidases orchestrate the redox state of host apoplast to modulate rice immunity

Apoplastic ascorbate oxidases (AOs) play a critical role in reactive oxygen species (ROS)-mediated innate host immunity by regulating the apoplast redox state. To date, little is known about how apoplastic effectors of the rice blast fungus Magnaporthe oryzae modulate the apoplast redox state of rice to subvert plant immunity. In this study, we demonstrated that M. oryzae MoAo1 is an AO that plays a role in virulence by modulating the apoplast redox status of rice cells. We showed that MoAo1 inhibits the activity of rice OsAO3 and OsAO4, which also regulate the apoplast redox status and plant immunity. In addition, we found that MoAo1, OsAO3, and OsAO4 all exhibit polymorphic variations whose varied interactions orchestrate pathogen virulence and rice immunity. Taken together, our results reveal a critical role for extracellular redox enzymes during rice blast infection and shed light on the importance of the apoplast redox state and its regulation in plant-pathogen interactions