Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.

Heat tolerance (HT) of rice at anthesis is a key trait that ensures high and stable yields under heat stress. Finding the quantitative trait loci (QTLs) and gene loci controlling HT is crucial. We used relative spikelet fertility (RSF) as a measure of HT. The phenotypic values of RSF in 173 rice accessions were investigated in two environments and showed abundant variations. We performed a genome-wide association study on RSF using 1.2 million single nucleotide polymorphisms (SNPs). Five QTLs were significantly associated with RSF were identified, four were found in previously reported QTLs/genes, and one was novel. The novel QTL qRSF9.2 was mapped into the 22,059,984-22,259,984 bp region, which had 38 positional candidate genes. By combining the linkage disequilibrium analysis, the QTL region was narrowed to 22,110,508–22,187,677 bp, which contained 16 candidate genes. Among them, only gene LOC_Os09g38500 contained nonsynonymous SNPs that were significantly associated with RSF. In addition, accessions with large and small RSF values had corresponding respective high and low gene expression levels. Furthermore, the RSF of the CC allele was significantly higher than that of the TT allele. Hap 2 and Hap 3 can increase heat tolerance by 7.9 and 11.3%, respectively. Our results provide useful information that recommends further cloning of qRSF9.2 and breeding heat-tolerant rice varieties by marker-assisted selection.

Rice blast caused by Magnaporthe oryzae poses significant threaten to rice production. For breeding and deploying resistant rice varieties, it is essential to understand the frequencies and genetic variations of avirulence (AVR) genes in the pathogen populations. In this study, 444 isolates were collected from Hunan Province, China in 2012, 2015, and 2016, and their pathogenicity was evaluated by testing them on monogenic rice lines carrying resistance genes Pita, Pizt, Pikm, Pib, or Pi9. The frequencies of corresponding AVR genes AVRPizt, AVRPikm, AVRPib, AVRPi9, and AVRPita were characterized by amplification and sequencing these genes in the isolates. Both Pi9 and Pikm conferred resistance to >75% of the tested isolates, while Pizt, Pita, and Pib were effective against 55.63, 15.31, and 3.15% of the isolates, respectively. AVRPikm and AVRPi9 were detected in 90% of the isolates and AVRPita, AVRPizt, and AVRPib were present in 26.12, 66.22, and 79% of the isolates, respectively. Sequencing of AVR genes showed that most mutations were single nucleotide polymorphisms, transposon insertions, and insertion mutations. The variable sites of AVRPikm and AVRPita were mainly located in the coding sequence regions (CDS), and most were synonymous mutations. A 494-bp Pot2 transposon sequence insertion was found at the 87 bp position upstream of the start codon in AVRPib. Noteworthy, although no mutations were found in CDS of AVRPi9, a GC-rich inserted sequence of ∼200 bp was found at the 1,272 bp position upstream of the start codon in three virulent isolates. As AVRPikm and AVRPi9 were widely distributed with low genetic variation in the pathogen population, Pikm and Pi9 should be promising genes for breeding rice cultivars with blast resistance in Hunan.

Introduction: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking. Methods: In this study, metagenomic, metaproteomic, and non-targeted GC–MS analyses of Zaopei , along with HS-SPME-GC–MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation. Results: The Wuliangye -specific variety Dajiugu , with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis , Enterobacter , and Klebsiella . Functional genera such as Saccharopolyspora , Pediococcus , and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu. Discussion: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.