Qianhua Yuan

Shanlan upland rice, is known for its nutritional attributes but is constrained by low yield potential under rainfed cultivation. Although flooded cultivation is known to enhance rice yield, its effects on grain quality, particularly nutritional quality, remain unclear. Here, we evaluated the feasibility of flooded cultivation by assessing grain yield, appearance and milling quality, and nutritional-related metabolites across 26 Shanlan upland rice varieties grown under rainfed and flooded conditions. Flooded cultivation increased grain yield and its yield components. It also improved appearance quality by reducing chalkiness and enhanced milling quality. In contrast, flooded cultivation reduced the accumulation of health-related metabolites, including γ-aminobutyric acid, vitamins, anthocyanins, and phenylpropanoids, indicating a decline in nutritional quality. These results provide metabolite-level evidence for a trade-off between productivity and nutritional value under contrasting water-management strategies. Optimized water management and varietal selection are therefore required to balance yield, appearance, and nutritional quality in Shanlan upland rice.

Plastic films are extensively utilized in agroecosystems, and their residues are accumulating in global soil at a worrying rate. Biodegradable films are employed as a substitute for polyethylene (PE) films due to their rapid degradation rate. Although the taxonomic diversity of soil microbiome in response to biodegradable films has been studied, its alterations in functional diversity remain unexplored. Here, we conduct a two-year field experiment in cherry tomato to address how PE and poly (butylene adipate-co-terephthalate) (PBAT) influences soil microbiota across multi-kingdom (bacteria, fungi, and protists) regarding its taxonomic and functional diversity. The results show that PBAT exposure reduces the taxonomic diversity while increasing functional diversity across multi-kingdom domains compared to PE exposure. We further find that the decreased taxonomic diversity under PBAT exposure reduces the complexity of microbial inter-kingdom and internal-kingdom networks. Conversely, PBAT exposure enhances microbial functional diversity (Shannon index) and average genome size, accompanied by elevated abundances of plastic-degrading genes as well as carbon, nitrogen, phosphorus, and sulphur cycling functional genes. Overall, our study indicates that environmental filtration induced by PBAT exposure changes the microbial life adaptive strategies and leads to a decoupling between taxonomic diversity and functional diversity.

The gene flow rate in rice (Oryza sativa L.) is a critical factor for establishing safe isolation distances between genetically modified (GM) and non-GM varieties and for ensuring varietal purity in rice breeding programs. This study refines existing gene flow models by disentangling two key components of rice pollen dynamics: quantitative pollen competition and genetic competitiveness. We define B as the proportion of GM pollen within mixed pollen, representing quantitative pollen competitiveness. The outcrossing parameter C_b reflects the likelihood of successful fertilization and seed development by foreign pollen, while the hybrid compatibility parameter C_p captures the relative fertilization success of GM versus non-GM pollen within the same pollen pool. Together, C_b and C_p characterize the genetic competitiveness of rice pollen. Our findings reveal a nonlinear relationship between B and the observed GM pollen rate G, which may exhibit either upward or downward curvature. A nonlinear model provides a significantly better fit to this relationship than a linear model, improving R² by 4.1–21.4% and reducing RMSE by 9.9–47.8%. The parameters C_b and C_p play central roles in determining gene flow; higher values correspond to stronger GM pollen competitiveness, resulting in higher gene flow rates and greater dispersal distances. Specifically, C_b sets the range of the B–G curve, while C_p determines its curvature.

As a drought-resistant and water-saving rice (Oryza sativa L.), the Shanlan upland rice germplasm can provide solutions to the food security problems caused by frequent water shortages. In most nitrogen (N) fertilizer management strategies targeting maximum rice yields, lodging (both root and stem) is often ignored. Hence, this study aimed to determine an optimal N fertilizer management strategy that balanced the trade-off between yield and lodging in Shanlan upland rice. Our research employed the “safety factor” (SF) technique to explore the root-lodging resistance (represented by SFr) and stem-lodging resistance (represented by SFs) of Shanlan upland rice using three N fertilizer methods, including conventional N fertilization (CNF), split–postponed N fertilization (SPNF), and controlled-release N fertilizer (CRNF), and three N application rates (80, 120, and 160 kg N ha⁻¹) for two consecutive years. Compared with CNF, the SFr improved by 14.9% for CRNF and 9.1% for SPNF. Likewise, the SFs increased by 22.7% for CRNF and 15.3% for SPNF. Moreover, Shanlan upland rice was found to be more prone to the risk of root lodging than stem lodging. At the same time, the grain yield and net benefit improved by 14.6% and 18.1% for CRNF, respectively, compared with CNF. Hence, employing the CRNF technique was more effective at reducing the lodging risk of Shanlan upland rice. Moreover, increasing the N application rate beyond 120 kg N ha⁻¹ did not significantly increase the grain yield for CRNF but the lodging resistance and net benefit were reduced. In conclusion, with an N application rate of 120 kg N ha⁻¹ for CRNF, Shanlan upland rice could achieve a relatively stable and high net income and can be recommended to growers for adoption.

Understanding the agronomic interventions that ensure higher crop yields and minimize their chances of failure is critical for meeting global nutritional demands. Rice is a staple food crop that is prone to lodging risk, particularly when higher yields are desired. The potential role of a combined application of Zinc (Zn) and Silicon (Si) in determining the grain yield and lodging resistance has been rarely investigated under field conditions. Thus, field trials were carried out to evaluate the grain yield and lodging resistance of rice at two different locations i.e., Qionghai and Wuzhishan, under three levels of Zn (0, 40, and 80 kg ha⁻¹) and Si (0, 120, and 240 kg ha⁻¹). The results showed that Zn application at the rates of 40 and 80 kg ha⁻¹ increased rice yield by 9% and 5% at Qionghai, and by 5% and 6% at Wuzhishan, respectively. The improved grain yield due to Zn application could be attributed to the increased panicles m⁻², splikelets m⁻², and aboveground biomass. Meanwhile, Zn failed to show any remarkable impact on stem and root lodging susceptibility. Conversely, no significant influence of applying Si on grain yield was observed, while its application at the rates of 120 and 240 kg Si ha⁻¹ enhanced the stem and root lodging resistance (denoted by their respective safety factors, for stem (SF_s) and for root (SF_r) by 32% and 22% at Qionghai, and by 11% and 34% at Wuzhishan, respectively, compared to zero Si application. The improved lodging resistance in terms of SF_s and SF_r could be ascribed to the increased stem bending strength and anchorage strength, while self-weight moment of whole plant decreased. In summary, a beneficial role of Si in lodging resistance and Zn in yield enhancement were evidenced in the present study across the two sites. It can be concluded that by combining 40 kg Zn ha⁻¹ with 120 kg Si ha⁻¹, both grain yield and lodging resistance could be simultaneously improved in rice crops.

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Background: Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported. Results: In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR. Conclusion: Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Shanlan upland rice is a kind of upland rice and is suitable for planting in the mountains and in hilly terrain. It is mainly found in China’s Hainan province. To discover the drought-resistant genes in Shanlan upland rice, two representative varieties—Baishanuo (BSN) and Dongfang Manpoxiang (MPX)—were selected for transcriptome sequencing, after which gene expression analysis was used to confirm their gene expression patterns. The results demonstrated that 2791 and 829 differentially expressed genes (DEGs) were identified for each variety, including 184 and 58 transcriptional factors, respectively. Expression analysis demonstrated that some genes with unknown functions, such as Os10g0505900, were highly expressed under drought stress treatment. The transcriptomic data and digital gene expression profiling data obtained in this study provide a basis for studying the drought-resistant mechanism in Shanlan upland rice.