Identification of a major rice blast quantitative trait Loci containing Pita/Pi39(t)/Ptr in USA Blackhull Awn Weedy Rice

Authors: OSAKINA, ARON - Washington University; GOAD, DAVID - Washington University; Jia, Melissa; OLSEN, KENNETH - Washington University; Jia, Yulin

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2025
Publication Date: 9/15/2025
Citation: Osakina, A., Goad, D., Jia, M.H., Olsen, K.M., Jia, Y. 2025. Identification of a major rice blast quantitative trait Loci containing Pita/Pi39(t)/Ptr in USA Blackhull Awn Weedy Rice. Phytopathology. https://doi.org/10.1094/PHYTO-02-25-0051-R.
DOI: https://doi.org/10.1094/PHYTO-02-25-0051-R

Interpretive Summary: Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating diseases and is estimated to account for 10-30% annual global losses in rice production. An effective way to control blast disease is through deployment of resistance genes. Quantitative trait loci (QTLs) for resistance against blast disease are more durable, and their continued discovery is therefore of paramount importance. Weedy rice (Oryza sativa L.), unwanted weeds have novel blast resistance genes. To evaluate blast resistance genes, a cross was made between the Black Hull Awn weedy rice and aus-196 rice variety. A total of 183 recombinant inbred lines (RILs) were obtained. Five blast races IB33, IB49, IG1, IE1K and ICI7 were used to access the disease score of (RILs) and parental lines under greenhouse conditions. Except for the race IB49, both parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance. The population was genotyped by genotyping by sequencing. A linkage map of 3066.1 cM was constructed using inclusive composite interval and QTL mapping analysis. A total of 24 resistance QTLs were mapped, including the major effect QTL on chromosome 12, three new minor QTLs on chromosomes 4, 7 and 11. Several other minor QTLs that were previously mapped in the same vicinity were also detected on chromosomes 5, 9 and 11. These findings are useful for the development of blast resistant rice varieties using a marker-assisted selection approach.

Technical Abstract: Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating diseases and is estimated to account for 10-30% annual global losses in rice production. Since rice supplies more than one-third of humanity’s calories, its losses due to the rice blast pandemic poses great concern to food security. A rice blast mitigation strategy is therefore urgently required. An effective way to control rice blast disease is through deployment of resistance genes. Although quantitative trait loci (QTLs) for resistance against blast disease have been identified, many more resistance QTLs remain unknown, and their continued discovery is therefore of paramount importance. In this study, we assessed disease scores of 183 F5 and F6 recombinant inbred lines (RILs) derived from a biparental mapping population and their respective parental lines, the Black Hull Awn weedy rice (PI 653431, RR14) and aus-196 rice variety, using five blast races IB33, IB49, IG1, IE1K and ICI7 under greenhouse conditions. Except for the race IB49, both parental lines were resistant all blast races; however, RILs showed a wide degree of variation in resistance. A linkage map of 3066.1 cM was constructed using inclusive composite interval mapping. A total of 24 resistance QTLs were mapped, including the major effect QTL on chromosome 12, three new minor QTLs on chromosomes 4, 7 and 11. Several other minor QTLs that were previously mapped in the same vicinity were detected on chromosomes 5, 9 and 11. These findings are useful for the development of blast resistant rice varieties using a marker-assisted selection approach.