Objectives: To provide insights for breeding high-quality rice varieties, we analyzed local rice (Oryza sativa L.) germplasm from Yunnan Province, China, focusing on the relationships among Waxy gene alleles, indica–japonica differentiation, and amylose content (AC). Methods: We examined 201 local rice accessions. Two functional molecular markers for the Waxy gene were used to detect four alleles (Wx^a, Wx^b, Wxⁱⁿ, Wx^mw). Additionally, 33 InDel markers were employed to classify indica–japonica attributes, and AC was measured according to GB/T 15683-2008. Results: We detected 175 accessions with Wx^a, 20 with Wx^b, 4 with Wxⁱⁿ, and 2 with Wx^mw, indicating Wx^a dominance and a diverse genetic basis at the Waxy locus. Indica–japonica classification identified 180 indica-type, 19 japonica-type, and 2 intermediate-type accessions, confirming predominant indica differentiation in Yunnan rice. Integrating Waxy allele detection, indica–japonica attributes, and AC showed that Wx^a occurred primarily in indica rice with higher AC (mean 22.55%), comparable to Wxⁱⁿ (mean 24.33%); Wx^b was mainly found in japonica rice with lower AC (mean 13.46%), similar to Wx^mw (mean 15.65%). Conclusions: Local Yunnan rice exhibits Wx^a predominance at the Waxy locus and clear indica differentiation. The observed associations between Waxy alleles, subspecies attributes, and AC provide useful references for marker-assisted breeding of premium rice and for exploiting indica–japonica heterosis.

Biological control is an effective and environmentally friendly strategy for managing plant diseases. In this study, a broad-spectrum antagonistic bacterium, designated strain AN6, was isolated from rice plants and exhibited potent inhibitory activity against a variety of phytopathogens. In Oxford cup assays, AN6 suppressed the growth of Xanthomonas oryzae pv. oryzae (Xoo) by 73.60%, and its cell-free culture filtrate caused pronounced morphological deformation in the bacterial cells. Further in vitro assays, including dual-culture assays, volatile organic compound (VOC) assays, and cell-free supernatant (CFS) assays, demonstrated that AN6 also exerted strong antifungal effects against several pathogenic fungi. In addition, the strain was found to produce proteases and siderophores, which may contribute to its antagonistic capabilities. Taxonomic identification based on morphological traits, 16S rRNA and gyrA gene sequencing, average nucleotide identity (ANI), in silico DNA–DNA hybridization (isDDH), and phylogenetic analysis classified strain AN6 as Bacillus velezensis. Whole-genome sequencing revealed that AN6 harbors a 3,929,788 bp genome comprising 4025 protein-coding genes with a GC content of 46.50%. Thirteen biosynthetic gene clusters (BGCs) associated with the production of secondary metabolites—such as nonribosomal peptides, polyketides, and dipeptide antibiotics—were identified. The pot experiment further validated the biocontrol potential of AN6, achieving an 80.49% reduction in rice bacterial blight caused by Xanthomonas oryzae pv. oryzae. Collectively, these results indicate that B. velezensis AN6 is a promising candidate for development as a highly effective biocontrol agent for the integrated management of diverse plant diseases.

Two-line hybrid rice breeding relies on photoperiod-/thermosensitive genic male sterile (P/TGMS) lines with reliable fertility transition across different environments. The fertility of japonica P/TGMS lines is intricately regulated by photoperiod and temperature, making it more challenging to breed japonica sterile lines with stable sterility than indica sterile lines. This complexity is one of the primary reasons the breeding and promotion of two-line japonica hybrid rice has lagged behind that of indica hybrid rice. Here, we report on Yun1032S, a novel japonica P/TGMS line bred in the low-latitude plateau. It was bred by crossing Peiai 64S, the famous P/TGMS line with the largest application area in China, with Yungengyou 1, a plateau japonica variety noted for its excellent cold tolerance and disease resistance. Yun1032S exhibited stable sterility and female-parent traits favorable for two-line seed production. The elite combination YLY7706 (Yunliangyou7706), derived from a cross between Yun1032S and Yungenghui7501, showed a stable and competitive yield and strong disease resistance in the 2022–2023 Yunnan provincial regional trials. To analyze the genetic basis of phenotypes, we performed whole-genome resequencing and functional loci analysis of the parents and found that they carry a great number of superior alleles, which account for their yield and disease-resistant performance. To assess the breeding value of Yun1032S, we analyzed heterosis of a new batch of combinations derived from Yun1032S and identified a new combination, Jian3, with greater yield potential than YLY7706. These findings not only enhance the breeding of japonica P/TGMS lines but also provide direction for future pairing of two-line hybrid combination breeding. The study presents innovative concepts that further integrate genomics with traditional breeding techniques. Ultimately, Yun1032S marks a significant milestone in japonica P/TGMS line breeding technology, opening new avenues for the development of the two-line system.

Fertilizer management plays a critical role in regulating both yield and aroma quality in fragrant rice. However, the combined effects of functional fertilizers on these traits across different varieties and ecological conditions remain poorly understood. In this study, field experiments were conducted at two sites (Fumin and Dali) using two japonica fragrant rice varieties (Yunjing 37 and Liuxiangzi 1) under four fertilization treatments: T1 (conventional fertilization); T2 (compound fertilizer + silicon fertilizer); T3 (compound fertilizer + magnesium ammonium phosphate + amino acid-chelated calcium); and T4 (compound fertilizer + bio-organic fertilizer + zinc + amino acid water-soluble fertilizer). Compared with T1, silicon application (T2) significantly increased grain yield by 8.58–15.08%, primarily through synergistic increases in effective panicles and grains per panicle. Treatments T3 and T4 significantly enhanced grain 2-acetyl-1-pyrroline (2-AP) content by 18.32–32.67% and increased the diversity of volatile compounds. Correlation analysis revealed that 2-AP content was positively correlated with ketones (r = 0.373, p < 0.05) and alcohols (r = 0.363, p < 0.05), and negatively correlated with aldehydes and esters. Multifactor ANOVA showed no significant variety × treatment interaction for yield or 2-AP content (p > 0.05), indicating consistent responses across varieties. These results provide preliminary evidence that silicon fertilizer serves as an effective strategy for yield improvement, while combined application of calcium, magnesium, and amino acids enhances aroma quality by promoting the accumulation of 2-APm ketones, and alcohols. However, because treatments T3 and T4 contained multiple components, the individual contributions of Ca, Mg, or amino acids cannot be isolated. Multi-year trials are required to confirm the stability of these effects, featuring a differentiated fertilization strategy—silicon for yield and medium/trace elements for aroma—applicable across varieties, with site-specific variety selection further optimizing performance.