Rice brown spot (BS) disease, caused by Bipolaris oryzae, is a significant threat to rice production worldwide. In this study, a major quantitative trait locus (QTL), qBS11, associated with resistance to BS in rice, was identified and fine-mapped. A recombinant inbred line (RIL) population from a cross between the susceptible variety Zhenshan97 and the resistant variety C309 was used for QTL mapping. Using composite interval mapping (CIM) and bulked segregant analysis sequencing (BSA-seq), qBS11 was narrowed to a 244.6 kb interval on chromosome 11, explaining up to 47.7% of the phenotypic variance. Fine mapping identified several potential candidate genes, including LOC_Os11g41170 and LOC_Os11g41210, encoding disease resistance proteins. The resistance exhibited by qBS11 was found to be partially dominant, with heterozygotes showing medium resistance. High broad-sense heritability (89.2%) confirmed the dominance of genetic factors in BS resistance. Additionally, regulatory region variations in the candidate genes suggest a gene dosage effect, which may explain the partial dominance observed for qBS11. This study provides valuable insights into the genetic basis of BS resistance and offers a foundation for breeding BS-resistant rice varieties through molecular marker-assisted selection (MAS). The findings also pave the way for future functional studies of the identified genes.

Introduction: Lodging is a significant challenge in rice production, particularly for high-yielding cultivars. Previous research has shown that stem characteristics, such as internode length and diameter, are key determinants of lodging resistance. However, the genetic mechanisms controlling these traits remain poorly understood. Methods: To investigate the genetic basis of lodging-related stem traits, a recombinant inbred line (RIL) population was developed from a cross between Zhenshan 97 and C309, two rice varieties with contrasting stem architectures. A high-density genetic linkage map was constructed using 3,307 bin markers generated by next-generation sequencing. Comprehensive phenotypic analysis was conducted for heading date, internode length, and diameter. Results: A total of 54 quantitative trait loci (QTLs) were identified across the genome. Importantly, 15 pleiotropic QTLs were detected, each affecting multiple internode-related traits. These pleiotropic loci include well-known functional genes such as SCM2 and Gn1a , as well as several novel loci potentially involved in regulating stem strength and lodging resistance. Additionally, RNA-Seq analysis was performed to identify candidate genes associated with these traits. Among the 1,263 expressed genes within the 15 pleiotropic QTL regions, 183 differentially expressed genes were identified. LOC_Os06g11130 was highlighted as a key gene for further investigation. Haplotype analysis and linkage disequilibrium analysis revealed significant haplotype variation in LOC_Os06g11130 , further confirming its potential role in lodging resistance. Discusssion: This study enhances our understanding of the genetic architecture of internode traits associated with lodging resistance in rice. The identification of pleiotropic and major-effect QTLs provides valuable genetic resources for marker-assisted selection and genomic breeding, with the potential to improve lodging resistance in high-yielding rice cultivars. These findings contribute to the development of rice varieties that balance high yield potential with enhanced lodging resistance.

Shanlan upland rice is a unique genetic resource from the mountainous regions of Hainan, China, yet its genetic diversity and agronomic potential remain poorly characterized. This study systematically evaluated 114 Shanlan upland rice landraces using phenotypic assessment and 38 genome-wide Insertion/Deletion (InDel) markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, and yield components. The molecular analysis revealed a moderate level of genetic diversity (average PIC = 0.43) and consistently grouped the landraces into three distinct genetic subpopulations. To facilitate efficient germplasm management, we developed a DNA fingerprinting system using a reduced set of 19 core InDel markers, which was integrated with a phenotypic QR code database. Furthermore, a network-based strategy identified a core collection of 54 accessions, streamlining the resource for future breeding and conservation efforts. These findings provide a robust molecular framework for the conservation and genetic improvement of Shanlan upland rice.

Upland rice, particularly Shanlan upland rice from the mountainous regions of south China, represents an important genetic resource for improving rice productivity and resilience, especially in the face of climate change and environmental stress. However, understanding its genetic diversity and agronomic potential remains limited. This study systematically analyzed the genetic diversity and agronomic traits of 114 Shan-lan upland rice landraces, primarily collected from the mountainous regions of Hai-nan, China, using both phenotypic evaluation and Insertion/Deletion (InDel) molec-ular markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, panicle length, grain shape, and yield-related traits. The 38 InDel markers used in this study exhibited an average polymorphism information content (PIC) of 0.43, suggesting moderate-to-low genetic diversity, likely due to geographic isolation and localized selection. Pairwise simple matching coeffi-cient (SMC) analysis revealed substantial germplasm redundancy, with 7.9% of com-parisons showing high similarity (SMC ≥ 0.85). Phylogenetic and K-means clustering analyses consistently grouped the landraces into three distinct genetic subpopulations. A DNA fingerprinting system was successfully developed using a reduced set of 19 core InDel markers, which was coupled with a QR code database linking molecular profiles with phenotypic data for efficient germplasm management. A network-based strategy identified a core collection of 54 accessions, streamlining the resource for fu-ture breeding and conservation efforts. These findings may provide a valuable mo-lecular framework for breeding programs aimed at enhancing yield, lodging re-sistance, and stress tolerance in Shanlan upland rice.