Waterlily (Nymphaeaceae), a diploid dicotyledon, is an ornamental aquatic plant. In 2020, the complete draft genome for the blue-petal waterlily (Nymphaea colorata) was made available in GenBank. To date, the genome-wide mining of microsatellites or simple sequence repeats (SSRs) in waterlily is still absent. In the present study, we investigated the characteristics of genome-wide microsatellites for N. colorata and developed polymorphic SSR markers across tropical and hardy waterlilies. A total of 238,816 SSRs were identified in 14 N. colorata chromosomes with an average density of 662.60 SSRs per Mb, and the largest number of SSRs were present on chromosome 1 (n = 30,426, 705.94 SSRs per Mb). The dinucleotide was the most common type, and AT-rich repeats prevail in the N. colorata genome. The SSR occurrence frequencies decreased as the number of motif repeats increased. Among 2442 protein-coding region SSRs, trinucleotides, accounting for 63.84%, were the most abundant. Gene ontology terms for signal transduction (e.g., GO: 0045859 and GO: 0019887) and the lipoic acid metabolism (ko00785,) were overrepresented in GO and KEGG enrichment analysis, respectively. In addition, 107,152 primer pairs were identified, and 13 novel polymorphism SSR markers were employed to distinguish among nine waterlily cultivars, of which Ny-5.2 and Ny-10.1 were the most informative SSR loci. This study contributes the first detailed characterization of SSRs in N. colorata genomes and delivers 13 novel polymorphism markers, which are useful for the molecular breeding strategies, genetic diversity and population structure analysis of waterlily.

The effective management of water and nitrogen is crucial in the artificial cultivation of medicinal plants. Sophora alopecuroides, a perennial herbaceous plant in the Fabaceae family, is extensively used in medicine, with alkaloids as its primary bioactive constituents. Nevertheless, there remains a significant knowledge gap regarding how rhizospheric microbial communities respond to varying water and nitrogen conditions and their intricate relationships with soil environments and the growth of S. alopecuroides. In this study, two-year-old S. alopecuroides were used in a two-factor, three-level water-nitrogen interaction experiment. The irrigation levels included W1 (30–35% of maximum water holding capacity), W2 (50–55%), and W3 (70–75%), while nitrogen levels comprised N1 (32 mg/kg), N2 (64 mg/kg), and N3 (128 mg/kg). The study assessed plant growth indicators, total alkaloid content, and rhizospheric soil physicochemical parameters of S. alopecuroides. High-throughput sequencing (16S rRNA and ITS) was employed to analyze variations in rhizospheric microbial community composition and structure. The results showed that Proteobacteria and Ascomycota are the predominant bacterial and fungal phyla in the rhizosphere microbial community of S. alopecuroides. The highest biomass and alkaloid accumulation of S. alopecuroides were observed under the N1W3 treatment (50% nitrogen application and 70–75% of maximum water holding capacity). Specifically, six bacterial genus-level biomarkers (TRA3_20, MND1, env_OPS_17, SBR1031, Haliangium, S0134_terrestrial_group) and six fungal genus-level biomarkers (Pseudeurotium, Rhizophagus, Patinella, Pseudeurotium, Patinella, Rhizophagus) were identified under the N1W3 treatment condition. In the partial least squares path modeling (PLS-PM), water and nitrogen treatments demonstrated markedly positive direct effects on soil physicochemical parameters (p < 0.01), while showing significant negative direct impacts on alkaloid accumulation and plant growth indicators (p < 0.05). Soil physicochemical parameters, in turn, significantly negatively affected the rhizosphere fungal community (p < 0.05). Additionally, the rhizosphere fungal community exhibited highly significant negative direct effects on both the plant growth indicators and total alkaloid content of S. alopecuroides (p < 0.01). This study provides new insights into the interactions among rhizosphere soil environment, rhizosphere microbiota, plant growth, and alkaloid accumulation under water and nitrogen regulation, offering a scientific basis for the water and nitrogen management in the cultivation of S. alopecuroides.

Drought is a major limiting factor in the cultivation of Sophora alopecuroides in China’s arid and semi-arid regions. This study aimed to identify drought-resistant S. alopecuroides ecotypes and explore key drought tolerance indicators during germination by simulating drought conditions with a 10% PEG-6000 solution, using pure water as a control. Determination of seven germination indicators for S. alopecuroides, including germination rate (GR), germination energy (GE), germination index (GI), vigor index (VI), promptness index (PI), fresh weight (FW), and dry weight (DW), was conducted. Principal component analysis (PCA), membership function, cluster analysis, and linear regression were employed to comprehensively evaluate the drought resistance of thirty-five S. alopecuroides ecotypes. The results showed that drought stress caused reductions in six of the seven indicators across all ecotypes, except for DW, compared to the control. Correlation analysis revealed varying relationships among the indicators, with most showing significant or highly significant correlations. PCA reduced the seven indicators to two independent comprehensive factors, with a cumulative contribution rate of 83.99%. Based on the D-value and cluster analysis, the thirty-five ecotypes were ranked for drought resistance and classified into four categories. The top five drought-tolerant genotypes during the germination stage were identified as Yutian, Alar, Jinghe, Baoding, and Guyuan. Moreover, the stepwise regression model was established and demonstrated that GR, GE, PI, FW, and DW are key indicators for screening and identifying drought-resistant S. alopecuroides ecotypes. This study offers a comprehensive and reliable method for evaluating drought resistance in S. alopecuroides ecotypes and provides a reference for selecting ecotypes for artificial cultivation in Northwestern China.

Introduction: Sophora alopecuroides L., a perennial leguminous herb native to northwest China, holds medicinal, ecological, and forage value. However, intensified human activities have caused a sharp decline in its wild populations and genetic diversity.Methods: To assess its genetic structure and diversity, we analyzed 65 wild populations using SNP markers and seed phenotypic traits.Results: The coefficient of variation for eight seed traits ranged from 2.87% to 7.94%, with diversity indices (H) from 1.639 to 1.767, indicating rich phenotypic variation. Clustering based on phenotypic traits and SNP data both divided populations into two main groups. Genetic diversity was relatively low (He = 0.22; Ho = 0.17; Pi = 0.19), and AMOVA showed that variation was mainly among individuals (132.83%), with low population differentiation (F_ST = 0.00-0.04). Redundancy analysis revealed that phenotypic traits were largely influenced by mean temperature of the driest quarter and annual wind speed, while genetic diversity was shaped by precipitation and thermal variables.Conclusions: Our results provide a foundation for understanding the genetic variation of S. alopecuroides, offering valuable insights for its conservation and breeding programs.