Mapping blast resistance genes in rice varieties ‘Pecos’ and ‘M205’

Authors: Jia, Melissa; Lin, Michael; McClung, Anna; Jia, Yulin

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 1/11/2023
Publication Date: 1/30/2024
Citation: Jia, M.H., Lin, M.J., Mcclung, A.M., Jia, Y. 2024. Mapping blast resistance genes in rice varieties ‘Pecos’ and ‘M205’. Rice Technical Working Group Meeting Proceedings, Hot Springs, Arkansas, February 20-23, 2024. p94.

Interpretive Summary:

Technical Abstract: Rice blast caused by the fungal pathogen Magnaporthe oryzae is one of the most devastating diseases of rice worldwide. Disease resistance is most durable when varieties possess both non-race specific, quantitative resistance, and race specific resistance due to the presence of major (Pi) genes. More research has been conducted on identifying Pi genes that convey resistance to a number of blast races commonly found in the US and deploying these in new varieties. Much less is understood about the contribution and inheritance of field (dilatory) blast resistance. However, a few US and global varieties that lack any known Pi gene have been identified as having relatively slow development of blast disease symptoms. Pecos is medium grain variety released in 1983 that possesses no Pi genes but demonstrates dilatory resistance to common races of blast found in the US. As a means to evaluate the inheritance of this resistance, a cross was made between Pecos and M205 by Carl Johnson at the California Rice Research Foundation, Biggs, California in 1998. M205 is a variety that possesses only the Pi-ks gene which confers resistance to just the IB54 pathotype and it is highly susceptible to all other races of blast common to the US. The F2 seed of the cross was provided to USDA-ARS for genotypic and phenotypic analysis. The F3 generation (n=315) was evaluated for resistance (1=resistant, 9=very susceptible) after inoculation with a mixture of blast races in a nursery setting at Beaumont, T. Pecos (22 replications) was rated as 4 whereas M205 (16 replications) was rated as 9 indicating a clear difference in resistance and, although the Pi-ks gene was present in M205, it was not affecting resistance to the races present in this setting. A continuous distribution of reactions was observed among the progeny with ratings of <3, 4, 5, 6, 7, 8, and 9 representing 0.5, 17, 21, 37, 18, 5, and 1.5% of the population, respectively. The population was subsequently advanced to the F6 generation and 211 progeny were evaluated against six blast isolates: IB54 (3 replications), IE1, IE1K, IA1, IA45, and IB1 (1 replication each) under greenhouse conditions at Stuttgart, AR. The population was genotyped with 122 SSR and indel markers. Utilizing Inclusive Composite Interval Mapping (ICIM) QTL mapping software, a map was developed that spanned 1420.28 cM. Subsequently, QTL analysis was performed using ICIM mappers ICIM-Add portion of the BIP function. We identified a major QTL on chromosome 11 that colocalizes with the Pi-ks locus ranging from a LOD score of 8.5-16.2 in response to the blast isolate IB54. No QTL were identified with the other blast isolates. More markers will be developed to fill in chromosomal gaps and additional replications of phenotyping will be performed using the five pathotypes that have only one replication completed so far. In addition, subsequent studies will be conducted to determine disease progress curves during the four weeks following seedling inoculation with scoring performed visually and using digital imaging. These results will be used to identify QTL associated with dilatory resistance due to quantitative inheritance as well as due to the presence of the Pi-ks gene in response to isolates other than IB54.