Siripar Korinsak

Rice blast, caused by Magnaporthe oryzae , is a devastating disease threatening global rice production. While Southeast Asia is a centre of origin, the pathogen's population dynamics in Thailand are not well understood. We analysed whole‐genome sequences from 191 M. oryzae isolates (60 from Thailand and 131 global) to investigate their genetic diversity, structure and pathogenicity. Phylogenomic analysis revealed that Thai isolates cluster with other Asian populations but exhibit greater within‐population diversity, forming two major genetic clusters. We found that Thai rice isolates from rain‐fed lowland and irrigated rice in the northeast and central regions cluster in World Group 3, while isolates from upland rice in northern Thailand cluster in World Group 1. This revised interpretation provides a more accurate representation of the population structure and highlights previously uncharacterised diversity. To link molecular data with phenotypes, we performed avirulence gene profiling and pathogenicity assays on 31 rice blast resistance near‐isogenic lines. A correlation analysis showed a strong relationship for key gene pairs, including AvrPik and AvrPi9 , highlighting their functional importance. In contrast, the correlation was low for Pii , Pizt and Pib due to the low frequency of their corresponding avirulence genes. The Avr‐Pita interaction displayed a complex, haplotype‐specific correlation. Our findings provide new insights into the genomic and pathogenic variation of M. oryzae in Thailand, establishing a robust link between avirulence gene profiles and observed pathogenicity phenotypes. This work offers a refined foundation for region‐specific resistance breeding and disease management strategies.

Magnaporthae oryzae (M. oryzae) is the most destructive disease of rice worldwide. In this study, one hundred and two isolates of M. oryzae were collected from rice (Oryzae sativa L.) from 2001 to 2017, and six rice varieties with resistance genes Pizt, Pish, Pik, Pib, and Pi2 were used in a genome-wide association study to identify pathogenicity loci in M. oryzae. Genome-wide association analysis was performed using 5338 single nucleotide polymorphism (SNPs) and phenotypic data of neck blast screening by TASSEL software together with haplotype block and SNP effect analysis. Twenty-seven significant SNPs were identified on chromosomes 1, 2, 3, 4, 5, 6, and 7. Many predicted genes (820 genes) were found in the target regions of six rice varieties. Most of these genes are described as putative uncharacterized proteins, however, some genes were reported related to virulence in M. oryzae. Moreover, this study revealed that R genes, Pik, Pish, and Pi2, were broad-spectrum resistant against neck blast disease caused by Thai blast isolate. Haplotype analysis revealed that the combination of the favorable alleles causing reduced virulence of isolates against IRBLz5-CA carrying Pi2 gene contributes 69% of the phenotypic variation in pathogenicity. The target regions and information are useful to develop marker-specific genes to classify blast fungal isolates and select appropriate resistance genes for rice cultivation and improvement.

Rice blast disease is found worldwide leading to economic losses. Use of resistance gene is effective to improve rice resistance variety. Therefore, to deploy genomic regions harbouring resistance genes, a population of 587 F_2:6 recombinant inbred lines (RILs) was developed from a cross between Jao Hom Nin, a Thai black rice variety with broad-spectrum resistance to blast disease, and Kao Dawk Mali 105, a susceptible Thai jasmine variety. The RILs were challenged with 17 blast isolates collected from Thailand and Laos PDR. Quantitative trait locus analysis identified genomic regions associated with broad-spectrum quantitative resistance (qBSRLs) and race-specific quantitative resistance (qRSRLs). Two qBSRLs were detected on chromosomes 1 and 11, and two qRSRLs were detected on chromosomes 8 and 12. The two qBSRLs were introgressed into two new genetic backgrounds through marker-assisted selection (MAS). Twelve breeding lines were tested for their spectra of resistance against 35 blast isolates. The results indicated that both qBSRLs were effective in new genetic backgrounds. The flanking markers and qBSRLs identified in the large mapping population showed high selection accuracy and effectiveness, suggesting the routine deployment of MAS technique in rice breeding programmes.

Rice blast disease, caused by the filamentous fungus Pyricularia oryzae , is one of the most destructive diseases in rice worldwide. Breeding of resistant rice cultivars remains a cost‐effective and environment‐friendly means for controlling blast disease, but the resistance tends to break down over time because of the pathogen's rapid adaptation. In this study, AVRPiz‐t gene sequences of 46 rice blast isolates were evaluated using a Southern blot analysis. The AVRPiz‐t gene was present in 24 of 46 (52.2%) rice blast isolates. The pathogenicity assay showed that all blast isolates were avirulent against Japanese rice cv. Toride 1, which carries several rice blast resistance genes including Piz‐t , Pii , Pi37 , and Pi‐ta . Screening for the Piz‐t gene in Thai rice germplasm revealed that less than 20% of rice varieties harbour the Piz‐t gene. Therefore, the Toride 1 rice variety could serve as an effective donor of rice blast resistance to be used in rice breeding programmes in Thailand. This study provides evidence for co‐evolution between the rice blast resistance gene Piz‐t and the rice blast fungal avirulence gene AVRPiz‐t . Understanding this relationship will facilitate the sustainable development of breeding for rice blast resistance in the future.

Bacterial leaf blight (BLB) is a serious disease affecting global rice agriculture caused by Xanthomonas oryzae pv. oryzae (Xoo). Most resistant rice lines are dependent on single genes that are vulnerable to resistance breakdown caused by pathogen mutation. Here we describe a genome-wide association study of 222 predominantly Thai rice accessions assayed by phenotypic screening against 20 Xoo isolates. Loci corresponding to BLB resistance were detected using >142,000 SNPs. We identified 147 genes according to employed significance thresholds across chromosomes 1–6, 8, 9 and 11. Moreover, 127 of identified genes are located on chromosomal regions outside estimated Linkage Disequilibrium influences of known resistance genes, potentially indicating novel BLB resistance markers. However, significantly associated SNPs only occurred across a maximum of six Xoo isolates indicating that the development of broad-spectrum Xoo strain varieties may prove challenging. Analyses indicated a range of gene functions likely underpinning BLB resistance. In accordance with previous studies of accession panels focusing on indica varieties, our germplasm displays large numbers of SNPs associated with resistance. Despite encouraging data suggesting that many loci contribute to resistance, our findings corroborate previous inferences that multi-strain resistant varieties may not be easily realised in breeding programs without resorting to multi-locus strategies.