Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.

Rice blast caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases in rice production worldwide. Information on rice varieties with the blast disease resistance gene is important for rice cultivar development. This study identified rice blast resistant genes in 226 rice cultivars including 203 Thai landrace rice cultivars (19 upland rice cultivars from the North, 99 lowland rice cultivars from the Northeast, 45 floating rice cultivars from the Northeast and 40 cultivars from the South), 21 recommended rice varieties and two susceptible varieties ‘KDML105’ and ‘Nipponbare’ by using gene-specific markers for the blast resistant genes Pid3, Pi54 and Pigm. Results showed that 159 cultivars have at least one resistant gene and four cultivars have all three resistant genes. These results indicate that Thai landrace rice is a valuable source of rice blast resistant genes for rice breeding programmes.

Rice blast disease, caused by Magnaporthe oryzae, is one of the most damaging diseases of rice worldwide. Cultivation of rice varieties carrying resistance genes is the most economic and successful strategy to control the disease. In this study, 451 rice varieties from around the world including 363 Thai landrace rice varieties, 21 Thai improved rice varieties, 43 Japanese rice varieties and 24 worldwide rice varieties were screened by PCR technique using gene-specific markers for 10 rice blast resistance genes: Pi9, Piz-t, Pi50, Pigm(t), Pid2, Pid3, Pia, Pik, Pi54 and Pita. The results showed that 382 (99.48%) Thai rice varieties have at least one resistance gene and two rice varieties, ‘Hom’ and ‘Bak muay’, contained eight out of ten screened rice blast resistance genes. 320 rice varieties (83.33%) contained three or more rice blast resistance genes. The frequency of the rice blast resistance gene ranges from 87.76–9.64 per cent, of which the Pid3 gene has the highest frequency and the Pi54 gene has the lowest frequency. Two major resistance genes, found in Japanese rice varieties, are the Pik gene (76.74%) and the Pi9 gene (72.09%). While two major resistance genes, found in the international rice varieties are the Pi9 gene (66.67%) and the Pi54 gene (62.50%). The disease resistance gene profile of each rice variety obtained from this study will benefit the rice blast resistant breeding programme in the future.

InDel markers are commonly used to assess genetic relationships among populations. In this study, we employed a whole-genome sequence comparison method to identify and develop InDel markers for the rice blast fungus Pyricularia oryzae. We analyzed 152 whole-genome sequences of P. oryzae isolates from diverse global regions, including Brazil, Burundi, China, Colombia, Côte d'Ivoire, France, Ghana, Hungary, India, Japan, Korea, Laos, Madagascar, Mali, Morocco, Nepal, the Philippines, Portugal, Spain, Suriname, Thailand, the UK, the USA, and Zambia. Our analysis identified a total of 233,595 InDel loci distributed across the seven chromosomes of P. oryzae. From these, 82 loci were selected based on their high polymorphism across the 152 genome sequences. The effectiveness of these 82 loci was assessed by analyzing the genetic diversity of 47 Thai rice blast isolates alongside two reference isolates, GUY11 (France) and KJ201 (Korea). Of the 82 InDel loci, 33 exhibited polymorphisms, with 2–4 alleles per locus and polymorphic information content (PIC) scores ranging from 0.04 to 0.67. Principal coordinate and structure analyses revealed two genetic subgroups among the Thai rice blast isolates, categorized according to host specificity. Genetic relationships highlighted disparities among rice blast populations based on their respective hosts: rice and grassy weeds. This finding suggests a correlation between genetic relatedness and the plant hosts susceptible to rice blast disease. The newly developed InDel markers provide a valuable resource for future research in this field.

Fragrance and cooking quality are pivotal traits in the development of aromatic and soft-textured rice varieties, which are highly favored by consumers. This study aimed to validate these attributes in seven improved rice lines that were developed for resistance to blast disease and tolerance to submergence. These lines were derived from a cross between HomWarin, a recipient variety conferring submergence tolerance, and RD75, a donor variety for blast resistance, through marker-assisted backcrossing. The presence of the badh2, Wxb, and SSIIa-TT genes, associated with grain fragrance, low amylose content, and low gelatinization temperature, was confirmed using Aromarker, Waxy, and SNP2340-41 markers, respectively. The grain fragrance and cooking qualities, including amylose content, gel consistency, and gelatinization temperature of the seven improved lines, were evaluated through sensory testing, colorimetric analysis, gel consistency measurements, and alkali tests, respectively. The results demonstrated that these lines exhibited notable grain fragrance, low amylose content (15.60–16.32%), soft gel consistency (91.33–120.67 mm), and low gelatinization temperature (alkali spreading value [ASV] 6.7–7.0). Furthermore, these improved lines, which are resistant to blast and tolerant to submergence, were comparable to the widely cultivated KDML105 variety. These aromatic, soft-textured, and low gelatinization temperature rice lines will undergo further selection for superior agronomic traits, and evaluate for yield performance and stability in intra-, inter-, and farmer-level trials.

Phosphorus (P) is a critical nutrient for rice (Oryza sativa L.) growth and productivity. This study investigated the effects of varying P fertilizer rates on grain yield, yield components, phosphorus use efficiency (PUE), and economic returns for the HomWarin rice variety cultivated in low-fertility sandy soil. A field experiment was conducted using a randomized complete block design (RCBD) with three replications and five P application rates: 0, 4, 8, 12, and 16 kg P2O5 per rai. All treatments received uniform applications of nitrogen (18 kg N/rai) and potassium (15 kg K2O/rai) in three split doses at establishment, tillering, and panicle initiation stages. Results revealed significant differences (p≤0.05) in grain yield and yield components among P rates, while plant height, tiller number per hill, panicle number per hill, panicle length, 1,000-grain weight, and straw yield were unaffected. The highest grain yield (635.25 kg/rai) and spikelet number per panicle (131.01) were achieved with 16 kg P2O5/rai, but these results were statistically similar to the yield at 12 kg P2O5/rai (618.36 kg/rai). Phosphorus use efficiency declined with increasing P application rates, with the highest efficiency (8.97 kg grain/kg P) observed at 4 kg P2O5/rai, followed by 12 kg P2O5/rai (8.02 kg grain/kg P). The marginal rate of return was maximized (217.83%) at 12 kg P2O5/rai, which also provided the optimal balance between high yield, phosphorus use efficiency, and economic returns. These findings suggest that applying P fertilizer at 12 kg P2O5/rai is the most effective rate for maximizing grain yield phosphorus use efficiency and economic benefits in HomWarin rice grown under low-fertility sandy soil conditions.