Background: Asian rice (Oryza sativa L.) has been a model plant but its cultivation history is inadequately understood, and its origin still under debate. Several enigmas remain, including how this annual crop shifted its growth habit from its perennial ancestor, O. rufipogon, why genetic divergence between indica and japonica appears older than the history of human domestication, and why some domestication genes do not show signals of introgression between subgroups. Addressing these issues may benefit both basic research and rice breeding. Results: Gene genealogy-based mutation (GGM) analysis shows that history of Asian rice is divided into two phases (Phase I and II) of about equal lengths. Mutations occurred earlier than the partition of indica and japonica to Os genome mark Phase-I period. We diagnosed 91 such mutations among 101 genes sampled across 12 chromosomes of Asian rice and its wild relatives. Positive selection, detected more at 5′ regions than at coding regions of some of the genes, involved 22 loci (e.g., An-1, SH4, Rc, Hd3a, GL3.2, OsMYB3, OsDFR, and OsMYB15), which affected traits from easy harvesting, grain color, flowering time, productivity, to likely taste and tolerance. Phase-I mutations of OsMYB3, OsHd3a and OsDFR were experimentally tested and all caused enhanced functions of the genes in vivo. Phase-II period features separate cultivations, lineage-specific selection, and expanded domestication to more genes. Further genomic analysis, along with phenotypic comparisons, indicates that O. sativa is hybrid progeny of O. rufipogon and O. nivara, inherited slightly more genes of O. rufipogon. Congruently, modern alleles of the sampled genes are approximately 6% ancient, 38% uni-specific, 40% bi-specific (mixed), and 15% new after accumulating significant mutations. Results of sequencing surveys across modern cultivars/landraces indicate locus-specific usages of various alleles while confirming the associated mutations. Conclusions: Asian rice was initially domesticated as one crop and later separate selection mediated by human resulted in its major subgroups. This history and the hybrid origin well explain previous puzzles. Positive selection, particularly in 5′ regions, was the major force underlying trait domestication. Locus-specific domestication can be characterized and the result may facilitate breeders in developing better rice varieties in future.

Genes of metabolic pathways are individually or collectively regulated, often via unclear mechanisms. The anthocyanin pathway, well known for its regulation by the MYB/bHLH/WDR (MBW) complex but less well understood in its connections to MYC2, BBX21, SPL9, PIF3, and HY5, is investigated here for its direct links to the regulators. We show that MYC2 can activate the structural genes of the anthocyanin pathway but also suppress them (except F3′H) in both Arabidopsis and Oryza when a local MBW complex is present. BBX21 or SPL9 can activate all or part of the structural genes, respectively, but the effects can be largely overwritten by the local MBW complex. HY5 primarily influences expressions of the early genes (CHS, CHI, and F3H). TF-TF relationships can be complex here: PIF3, BBX21, or SPL9 can mildly activate MYC2; MYC2 physically interacts with the bHLH (GL3) of the MBW complex and/or competes with strong actions of BBX21 to lessen a stimulus to the anthocyanin pathway. The dual role of MYC2 in regulating the anthocyanin pathway and a similar role of BBX21 in regulating BAN reveal a network-level mechanism, in which pathways are modulated locally and competing interactions between modulators may tone down strong environmental signals before they reach the network.

Lamiophlomis rotata (Benth.) Kudo is a typical alpine medicinal plant. However, the mechanism underlying its adaptation to high altitudes remains incompletely understood. In this study, we integrated transcriptome and metabolome analyses. Specifically, we used third-generation sequencing for building a reference transcriptome and second-generation sequencing for differential gene expression analysis. Our findings revealed that the activation of the hydrogen sulfide signaling pathway and the reprogramming of amino acid metabolism are probable adaptation mechanisms. Different from previous reports, the hydrogen sulfide signaling may regulate the activity of cellulose synthase in addition to enhancement of antioxidant capacity and accumulation of osmolytes. By altering the agronomic traits of plants in a cell wall remodeling-dependent manner, it enables L. rotata to adapt to alpine stress. The accumulated amino acids not only store energy-efficient organic nitrogen as precursors for the synthesis of secondary metabolites but also act as signaling molecules to activate defense responses. Additionally, we propose a potential link between the hydrogen sulfide signaling pathway and amino acid metabolism. Overall, this study systematically explores the adaptation mechanism of L. rotata to high-altitude environments, offering a novel perspective for understanding the growth, development, stress responses, and secondary metabolic processes of alpine plants.

Wolfberry production has become a major agro-industry on the Qinghai–Tibetan Plateau, causing increased nitrogen (N) pollution and greenhouse gas (GHG) emissions. Appropriate N fertilizer rate and nitrification inhibitors may mitigate GHG emissions and improve N use efficiency. A 2-year field experiment was conducted to measure the effects of N application rate and nitrapyrin on GHG emissions, to reduce GHG emissions and N pollution. We used eight treatments: Control (CK), 667 kg·ha⁻¹ N (Con), 400 kg·ha⁻¹ N (N₄₀₀), 267 kg·ha⁻¹ N (N₂₆₇), 133 kg·ha⁻¹ N (N₁₃₃), 400 kg·ha⁻¹ N plus 2.00 kg·ha⁻¹ nitrapyrin (N₄₀₀I_2.00), 267 kg·ha⁻¹ N plus 1.33 kg·ha⁻¹ nitrapyrin (N₂₆₇I_1.33) and 133 kg·ha⁻¹ N plus 0.67 kg·ha⁻¹ nitrapyrin (N₁₃₃I_0.67). Compared with Con treatment, N₄₀₀ maintained fruit yield and increased net income, but saved 40% of N fertilizer and decreased the cumulative N₂O emission by 14–16%. Compared to N₄₀₀, N₂₆₇ and N₁₃₃ treatments, the cumulative N₂O emission of N₄₀₀I_2.00, N₂₆₇I_1.33 and N₁₃₃I_0.67 treatments was reduced by 28.5–45.1%, 26.6–29.9% and 33.8–45.9%, respectively. Furthermore, N₄₀₀I_2.00 resulted in the highest wolfberry yield and net income. The emissions of CH₄ and CO₂ were not significantly different among treatments. Moreover, the global warming potential (GWP) and the greenhouse gas emission intensity (GHGI) of N₄₀₀I_2.00 declined by 45.6% and 48.6% compared to Con treatment. Therefore, 400 kg·ha⁻¹ N combined with 2.00 kg·ha⁻¹ nitrapyrin was shown to be a promising management technique for maintaining wolfberry yield while minimizing GWP and GHGI.

The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice’s oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5′ or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5′ mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5′ region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5′ mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships.

Background: Lycium ruthenicum, commonly known as Black goji berry, is a shrub species native to western China and is rich in bioactive compounds that contribute to its nutritional and health-promoting effects. However, the transcriptional dynamics associated with fruit development and quality formation in black goji berry remain incompletely understood. This study aimed to investigate transcriptional dynamics during fruit development and identify candidate genes associated with sugar accumulation and fruit enlargement. Methods: Fruits were sampled at five developmental stages (S1–S5), and RNA-seq was performed to investigate the alterations in gene expression. Differential expression analysis, temporal expression-pattern analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed, followed by the integration of differential expression, temporal expression patterns, co-expression relationships, and functional annotation. Results: Fruit diameter, fresh weight, and total soluble sugar content increased markedly during the later developmental stages. Differential expression analysis revealed extensive transcriptional changes across successive developmental transitions, while temporal expression-pattern analysis identified distinct increasing and decreasing gene clusters. Functional enrichment analysis showed that the DEGs were mainly associated with carbohydrate metabolism, sugar transport, hormone-related processes, photosynthesis, and cell-wall modification. WGCNA identified 13 co-expression modules, among which MEyellow and MEbrown showed strong but opposite associations with developmental stage, total soluble sugar content, fruit diameter, and fruit fresh weight. The integrated analysis highlighted several candidate genes associated with sugar metabolism and transport during late fruit development. Conclusions: These findings provide a transcriptomic perspective on the coordinated changes in sugar accumulation and fruit enlargement during L. ruthenicum fruit development.