Identification of Blast QTL in a Presidio/Oryza rufipogon rice advanced backcross population

Authors: Eizenga, Georgia; Jia, Melissa; TRAN, NHIEN - Cuu Long Delta Rice Research Institute; Jia, Yulin; Jackson, Aaron

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/31/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The wild ancestral species of cultivated rice, Oryza sativa are O. rufipogon and O. nivara, collectively referred to as the Oryza rufipogon Species Complex (ORSC) which includes Oryza spp. accessions. These accessions are a potential source of novel alleles for rice improvement. Blast disease caused by the fungal pathogen Magnaporthe oryzae, is a major threat to global rice production with more than 25 blast resistance genes molecularly characterized. The objectives of this study were to a) genotype a collection of 94 ORSC accessions with DNA markers targeting blast resistance genes, Pib, Piz, Pik and Pita, b) screen the ORSC collection for reaction to three virulent US blast races, and c) develop an advanced backcross (ABC) mapping population using one of the most resistant accessions as the donor parent and an adapted O. sativa cultivar as the recurrent parent to map the potential novel allele/gene for blast resistance. Based on DNA markers, the Pib resistance allele was in two of the 94 ORSC accessions, Piz in one accession, Pita was homozygous in 13 accessions and segregated in three accessions, and twelve accessions had a variate of one of the three Pik resistance genes (PikLeah, Pikm, Piks). Screening these accessions for reaction to leaf blast using the three of the most virulent US blast races, IA1, IB49 and IB33 using a 0 (resistant) to 9 (susceptible) rating scale where ratings < 2.0 were considered resistant, revealed 22 accessions were resistant to IB49, seven accessions resistant to IA1 and four accessions resistant to IB33. Considering Pi-gene presence and the blast ratings, five accessions were selected to cross with two US Midsouth long grain cultivars, Presidio and LaGrue. Based on the F1 seed produced from these crosses, the blast ratings and Pi-genes present, the Presidio/O. rufipogon (IRGC103404) cross was selected for developing an ABC mapping population. This O. rufipogon accession originated in Bangladesh, exhibited resistance to the three races, and segregated for Pi-ta. Presidio is a Texas semidwarf, long grain possessing Piz. The final population was comprised of 244 BC2F2 backcross inbred lines (BILs) which were genotyped with the 1K-Rice Custom Amplicon and 229 of the 1,000 SNP markers on the amplicon were polymorphic and well-distributed across the genome. An additional 20 polymorphic SSR markers were included to improve mapping in the regions with low SNP marker coverage. The population was screened for the same three races used to screen the ORSC accessions at the seedling stage and IB54 using the spot inoculation method. Screening with IB45 and IB54 at the seedling stage and IE1K using the spot inoculation is in progress. The frequency distribution of IB33, IA1 and IB49 ratings were negatively skewed, thus the results from QTL mapping were inconclusive. Surveying the ratings of the BILs for these three races revealed three BILs which rated as resistant to all three races. Examining the genotypes of these BILs identified the chromosome (chr.) 6 region (28.10 - 30.81 Mb) had overlapping O. rufipogon introgressions across the resistant BILs. The candidate gene, Pitq1 (29.02 Mb) was reported in this chr. 6 region. Compiling the results of screening with all six races should better define the source of the blast resistance discovered in this wild O. rufipogon accession.