Comparative transcriptome and metabolome analyses provide new insights into the molecular mechanisms underlying taproot thickening in Panax notoginseng.

BACKGROUND: Taproot thickening is a complex biological process that is dependent on the coordinated expression of genes controlled by both environmental and developmental factors. Panax notoginseng is an important Chinese medicinal herb that is characterized by an enlarged taproot as the main organ of saponin accumulation. However, the molecular mechanisms of taproot enlargement are poorly understood. RESULTS: A total of 29,957 differentially expressed genes (DEGs) were identified during the thickening process in the taproots of P. notoginseng. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment revealed that DEGs associated with "plant hormone signal transduction," "starch and sucrose metabolism," and "phenylpropanoid biosynthesis" were predominantly enriched. Further analysis identified some critical genes (e.g., RNase-like major storage protein, DA1-related protein, and Starch branching enzyme I) and metabolites (e.g., sucrose, glucose, fructose, malate, and arginine) that potentially control taproot thickening. Several aspects including hormone crosstalk, transcriptional regulation, homeostatic regulation between sugar and starch, and cell wall metabolism, were identified as important for the thickening process in the taproot of P. notoginseng. CONCLUSION: The results provide a molecular regulatory network of taproot thickening in P. notoginseng and facilitate the further characterization of the genes responsible for taproot formation in root medicinal plants or crops.

Illumina-based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after-ripening process.

Panax notoginseng (Burk) F.H. Chen is an economically and medicinally important plant of the family Araliacease, with seed dormancy being a key factor limiting the extended cultivation of P. notoginseng. The seeds belong to the morphophysiological dormancy (MPD) group, and it has also been described as the recalcitrant seed. To date, the molecular mechanism of dormancy release in the recalcitrant seed of P. notoginseng is unknown. In the present study, the transcript profiles of seeds from different after-ripening stages (0, 20, 40 and 60 days) were investigated using Illumina Hiseq 2500 technology. 91 979 946 clean reads were generated, and 81 575 unigenes were annotated in at least one database. In addition, the differentially expressed genes (DEGs) were identified by the pairwise comparisons. We screened out 2483 DEGs by the three key groups of 20 days vs 0 d, 40 d vs 0 d and 60 d vs 0 d. The DEGs were analyzed by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Meanwhile, we obtained 78 DEGs related to seeds dormancy release at different after-ripening stages of P. notoginseng, of which 15 DEGs were associated with abscisic acid and gibberellin. 26 DEGs that encode late embryogenesis abundant protein and antioxidant enzyme were correlated with desiccation tolerance in seeds. In summary, the results obtained here showed that PECTINESTERASE-2-LIKE, GA-INSENSITIVE, ENT-KAURENE SYNTHASE, PROTEIN PHOSPHATASE 2C, GIBBERELLIN 2-BETA-DIOXYGENASE, SUPEROXIDE DISMUTASE, L-ASCORBATE PEROXIDASE, CATALASE, LATE EMBRYOGENESIS ABUNDANT PROTEIN DC3 and DEHYDRIN 9 were potentially involved in dormancy release and desiccation sensitivity of P. notoginseng seeds. The data might provide a basis for researches on MPD.

[A semimicroquality evaluation method on Panax notoginseng and its application in analysis of continuous cropping obstacles research samples].

Panax notoginseng is a commonly used traditional Chinese medicine with blood activating effect while has continuous cropping obstacle problem in planting process. In present study, a semimicroextraction method with water-saturated n-butanol on 0.1 g notoginseng sample was established with good repeatability (RSD<2.5%) and 9.6%-20.6% higher extraction efficiency of seven saponins than the conventional method. A total of 16 characteristic peaks were identified by LC-MS-IT-TOF, including eight 20(S)-protopanaxatriol (PPT) type saponins and eight 20(S)-protopanaxadiol (PPD) type saponins. The established method was utilized to evaluate the quality of notoginseng samples cultivated by manual intervened methods to overcome continuous cropping obstacles.As a result, HPLC fingerprint similarity, content of Fa and ratio of notoginsenoside K and notoginsenoside Fa (N-K/Fa) were found out to be as valuatable markers of the quality of samples in continuous cropping obstacle research, of which N-K/Fa could also be applied to the analysis of notoginseng samples with different growth years.Notoginseng samples with continuous cropping obstacle had HPLC fingerprint similarity lower than 0.87, in consistent with normal sample, and had significant lower content of notoginsenoside Fa and significant higher N-K/Fa (2.35-4.74) than normal group (0.45-1.33). All samples in the first group with manual intervention showed high similarity with normal group (>0.87), similar content of common peaks and N-K/Fa (0.42-2.06). The content of notoginsenoside K in the second group with manual intervention was higher than normal group. All samples except two displayed similarity higher than 0.87 and possessed content of 16 saponins close to normal group. The result showed that notoginseng samples with continuous cropping obstacle had lower quality than normal sample. And manual intervened methods could improve their quality in different levels.The method established in this study was simple, fast and accurate, and the markers may provide new guides for quality control in continuous cropping obstacle research of notoginseng.

[Wild resources survey of Marsdenia tenacissima in Honghe, Yunnan].

To ascertain current situation of wild Marsdenia tenacissima resources in Honghe, Yunnan province, the distribution, habitat characteristic and resources reserves of M. tenacissima were surveyed based on interviews and investigation. The results showed that M. tenacissima was found in 7 counties such as Jinping, Mengzi etc, and distributed mainly on the mountainsides from 800 m to 1 200 m. And distribution was affected by many factors, such as light, heat, topography, soil, and vegetation. M. tenacissima grew well in distribution areas. M. tenacissima had averagely a weight of 2.8 kg per plant. Resources reserve of M. tenacissima in Honghe was estimated to 1 300 tons by now but it reduced rapidly in resent years, the wild resources reserve may not meet demand of market. Resources protection and wildlife tending would be conducted to deal with increasing medication requirements.

[Effects of intercropping and nitrogen application on soil microbial metabolic functional diversity in maize cropping soil.] / çŽ‰ç±³é—´ä½œå’Œæ–½æ°®å¯¹åœŸå£¤å¾®ç”Ÿç‰©ä»£è°¢åŠŸèƒ½å¤šæ ·æ€§çš„å½±å“.

Soil microorganism is an important indicator of soil health and plays a critical role in biogeochemical processes. We collected soil samples from a multi-year in-situ field experiment with two cropping modes (maize monocropping and maize-potato intercropping) subjected to four nitrogen (N) levels (N0, 0 kg·hm-2; N125, 125 kg·hm-2; N250, 250 kg·hm-2; N375, 375 kg·hm-2). By using the Biolog-ECO microplate method, soil microbial metabolic activity, diversity and utilization of six carbon groups were analyzed. The results showed that N application significantly increased the average well color development (AWCD) values, Simpson and Shannon indices, with the highest value at N250 in mono- and inter-cropped soils. Moreover, N application promoted the utilization of amino acids, amines and phenolic compounds, but decreased the utilization of polymers. Compared with monocropping at the same N level, intercropping improved the AWCD values, Simpson and Shannon indices, with a maximal improvement at N250. Intercropping and nitrogen application significantly affected the metabolic activities of the six carbon-source groups. In addition, intercropping improved the utilization of labile carbon sources, such as amino acids and carbohydrates. Results of the redundancy analysis and linear regression showed that intercropping and N application elevated AWCD values by increasing soil temperature, water content, and soil organic carbon content. Therefore, the changes in soil physicochemical properties after intercropping were the main reason for the enhancement of microbial metabolic activity under N application.

[Effects of intercropping on soil nitrification and nitrogen supply in potato field.] / 间作对马铃薯种植土壤硝化作用和硝态氮供应的影响.

Nitrate supply in soils is essential to meet nitrogen (N) demand of crops. However, how intercropping would affect soil nitrate supply and the underlying mechanisms remain unclear. Based on a field experiment of mono- and inter-cropped potato amended with four N application rates (N0, 0 kg·hm-2; N1, 62.5 kg·hm-2; N2, 125 kg·hm-2; N3, 187.5 kg·hm-2), we analyzed the differences in soil nitrate content and intensity, nitrification potential, and ammonia oxidation gene abundance. We further explored the mechanisms underlying the effects of intercropping on nitrate supply and N regulation. The results showed that both content and intensity of soil nitrate increased with N application rate. Under the same N level, nitrate content in intercropping soil was lower than that in monocropping soil. Nitrogen application increased soil nitrification potential, with stronger effects in monocropping than that of intercropping. The amoA gene abundance of AOB in soil was greater than that of AOA. The abundance of amoA gene for both AOA and AOB were increased firstly and then decreased with increasing N application rate when potato intercropped with maize. Under the same N application rate, AOA gene and AOB gene in all treatments (except N2) in intercropping were lower than those in the monocropping. The amoA gene abundance of soil AOB and AOA decreased and nitrification potential was weakened when potato intercropped with maize, resulting in a decrease of soil nitrate content and intensity. Therefore, intercropping led to a reduction of soil nitrate supply, which was related to the microbial process of soil N transformation. Much attention should be paid to soil N supply under the condition of potato and maize intercropping.

[Effects of light intensity on photosynthetic capacity and light energy allocation in Panax notoginseng.] / å ‰å¼ºå¯¹ä¸‰ä¸ƒå ‰åˆèƒ½åŠ›åŠèƒ½é‡åˆ†é çš„å½±å“.

To explore the effects of light intensity on photosynthetic characteristics and light adaptation of the shade-demanding species Panax notoginseng, the responses of photosynthesis to photosynthetic photon flux density, CO2 and sunflecks in the two-year-old Panax notoginseng were investigated under different levels of light intensity (29.8%, 9.6%, 5.0%, 1.4% and 0.2% of full sunlight). Meanwhile, chlorophyll a fluorescence parameter and light energy partitioning were also recorded and calculated in the responsive process. P. notoginseng grown under 29.8% full sunlight (FL) had a lower apparent quantum yield (AQY), potential photochemical quantum yield (Fv/Fm) and potential photochemical activity (Fv/Fo), however, it had a higher maximum net photosynthetic rate (Pn max), maximum electron transport rate (Jmax), F/Fm', electron transport rate (ETR), photochemical quenching (qP) and the proportion of light energy allocated to photochemistry dissipation (ΦPS2), but the non-photochemical quenching (NPQ) was not the highest. There were no significant differences in Pn max, light compensation point (LCP), light saturation point (LSP), dark respiration rate (Rd) among 9.6%FL and 5.0% FL treatments, but these treatments had relatively higher values of NPQ, AQY, carboxylation efficiency (CE), maximum carboxylation rate (Vc max), Fv/Fm and Fv/Fo. In addition, the Pn max, CE, Vc max, Jmax, ETR,F/Fm', qP, NPQ and ΦPSII decreased with the decrease in light intensity from 5.0%FL to 0.2%FL, and the proportion of light energy allocated to fluorescent dissipation (Φf,d) were increased. Under 500 µmol·m-2·s-1 light-flecks inducting, the ΦPSⅡof P. notoginseng increased slowly with the extension of time except for the treatment of less than 5.0%FL, and under the circumstance of 1.4%FL and 0.2%FL, ΦPSⅡreached significantly a perfect result, moreover, Φf,dincreased rapidly. These results suggested that the enhancement in photosynthetic electron transport to use the light energy and the moderate photoinhibition of PS2 might avoid the irreversible oxidative damage of photosynthetic organization in P. notoginseng under high levels of light intensity. Moderate shading was beneficial to maintain its higher non-photochemical quenching ability. However, its photosynthetic capacity depressed and the proportion of light energy allocated to non-photochemical pathway increased obviously in excessive shading, and it easily caused a light oxidative damage.

Unigene-based RNA-seq provides insights on drought stress responses in Marsdenia tenacissima.

Marsdenia tenacissima is a well-known anti-cancer medicinal plant used in traditional Chinese medicine, which often grows on the karst landform and the water conservation capacity of land is very poorly and drought occurrences frequently. We found M. tenacissima has strong drought resistance because of continuousdrought16 d, the leaves of M. tenacissima were fully curly and dying. But the leaves were fully almost recovering after re-watering 24h. The activity of SOD and POD were almost doubled under drought stress. The content of osmotic regulating substance proline and soluble sugar were three times than control group. But after re-watering, these indexes were declined rapidly. Three cDNA libraries of control, drought stress, and re-watering treatments were constructed. There were 43,129,228, 47,116,844, and 42,815,454 clean reads with Q20 values of 98.06, 98.04, and 97.88respectively.SRA accession number of raw data was PRJNA498187 on NCBI. A total of 8672, 6043, and 6537 differentially expressed genes (DEGs) were identified in control vs drought stress, control vs re-watering, and drought stress vs re-watering, respectively. In addition, 1039, 1016, and 980 transcription factors (TFs) were identified, respectively. Among them, 363, 267, and 299 TFs were identified as DEGs in drought stress, re-watering, and drought stress and re-watering, respectively. These differentially expressed TFs mainly belonged to the bHLH, bZIP, C2H2, ERF, MYB, MYB-related, and NAC families. A comparative analysis found that 1174 genes were up-regulated and 2344 were down-regulated under drought stress and this pattern was the opposite to that found after re-watering. Among the up-regulated genes, 64 genes were homologous to known functional genes that directly protect plants against drought stress. Furthermore, 44 protein kinases and 38 TFs with opposite expression patterns under drought stress and re-watering were identified, which are possibly candidate regulators for drought stress resistance in M. tenacissima. Our study is the first to characterize the M. tenacissima transcriptome in response to drought stress, and will serve as a useful resource for future studies on the functions of candidate protein kinases and TFs involved in M. tenacissima drought stress resistance.

[Contribution of nutrient uptake and utilization on yield advantage in maize and potato intercropping under different nitrogen application rates]. / ä¸åŒæ°®æ°´å¹³ä¸‹ä½œç‰©å »åˆ†å¸æ”¶ä¸Žåˆ©ç”¨.

Intercropping of maize and potato, as an important intercropping planting pattern, has a prominent advantage of resource utilization and yield. However, contribution of nutrient uptake and utilization to crop yield advantage and its response to N application rates remain unclear. Through a 2-year plot experiment, including maize monoculture, potato monoculture and maize intercropping with potato at 4 N-fertilized levels of N0(0 kg·hm-2), N1(125 kg·hm-2), N2(250 kg·hm-2) and N3(375 kg·hm-2), nutritional contribution of yield advantage of intercropping was studied. The results showed that weighted average uptake of nitrogen, phosphorus and potassium was gradually increased with N application rate in monocultures, but increase followed by a decrease in intercropping. Compared with monoculture at the same N level, nutrient uptake advantage of intercropping was the highest at N1, which increased nitrogen, phosphorus and potassium uptake by 14.9%, 38.6% and 27.8%, respectively. However, the nutrient use efficiencies were highest in intercropping at N0 and N3 with increment of 3.5%-14.3% for nitrogen, 3.5%-18.5% for phosphorus and 10.6%-31.6% for potassium. Maize and potato intercropping had a significant yield advantage at N0 and N1. Yield advantage in intercropping attributed to improvement of nutrient use efficiency at N0 while to increase of nutrient uptake at N1. To utilize the yield advantage from nutrient uptake, controlling input of nitrogen fertilizer is necessary in intercropping.

[Effect of Different Nitrogen Rates on the Nitrification Potential and Abundance of Ammonia-oxidizer in Intercropping Maize Soils].

The objectives of this study were to explore the effects of different nitrogen rates on the nitrification potential in intercropping maize soils. The experiment included two plantation types (maize monocropping and intercropping maize and potato) and four nitrogen levels (N0: no fertilizer treatment, N1: 1/2 conventional fertilizer treatment, N2: conventional fertilizer treatment, N3: 3/2 conventional fertilizer treatment). Abundance of AOA and AOB was analyzed with real-time quantitative PCR (Q-PCR) and soil properties were also measured. Results of this study suggested that the PNF of soils, the abundance of AOA and AOB were increased with increasing N fertilization in conventional fertilizer range, and there was no significant difference between N2 and N3 treatments. The influences of intercropping on PNF, AOA and AOB were associated with N application rates and crop growth period, as well as the benefits of ammonia oxidizer and nitrification of intercropping on N1 level. Fertilization was obviously the main driving force of the PNF, correlation analysis indicated that water content was the main environmental factor affecting the nitrification potential. Nitrification potential in maize and potato intercropping soils exhibited significant positive correlations with AOA and AOB amoA gene abundance. Maize and potato intercropping could decrease the abundance of AOA and AOB, but it resulted in dominance of AOB among nitrification bacteria in these soils. In conclusion, N fertilizer and intercropping could affect both soil nitrogen internal cycling process and the abundance of AOA and AOB, which further affected soil environmental quality.

Photosynthesis, light energy partitioning, and photoprotection in the shade-demanding species Panax notoginseng under high and low level of growth irradiance.

Partitioning of light energy into several pathways and its relation to photosynthesis were examined in a shade-demanding species Panax notoginseng (Burkill) F.H.Chen ex C.Y.Wu & K.M.Feng grown along a light gradient. In fully light-induced leaves, the actual efficiency of PSII photochemistry (ΔF/Fm'), electron transport rate (ETR), non-photochemical quenching (NPQ) and photochemical quenching (qP) were lower in low-light-grown plants; this was also the case in fully dark-adapted leaves under a simulated sunfleck. In response to varied light intensity, high-light-grown plants showed greater quantum yields of light-dependent non-photochemical quenching (ΦNPQ) and PSII photochemistry (ΦPSII) and smaller quantum yields of fluorescence and constitutive thermal dissipation (Φf,d). Under the simulated sunfleck, high-light-grown plants showed greater ΦPSII and smaller Φf,d. There were positive relationships between net photosynthesis (Anet) and ΦNPQ+f,d and negative relationships between Anet and ΦPSII in fully light-induced leaves; negative correlations of Anet with ΦNPQ+f,d and positive correlations of Anet with ΦPSII were observed in fully dark-adapted leaves. In addition, more nitrogen was partitioned to light-harvesting components in low-light-grown plants, whereas leaf morphology and anatomy facilitate reducing light capture in high-light-grown plants. The pool of xanthophyll pigments and the de-epoxidation state was greater in high-light-grown plants. Antioxidant defence was elevated by increased growth irradiance. Overall, the evidences from P. notoginseng suggest that in high-light-grown shade-demanding plants irradiated by high light more electrons were consumed by non-net carboxylative processes that activate the component of NPQ, that low-light-grown plants correspondingly protect the photosynthetic apparatus against photodamage by reducing the efficiency of PSII photochemistry under high light illumination, and that during the photosynthetic induction, the ΔpH-dependent (qE) component of NPQ might dominate photoprotection, but the NPQ also depresses the enhancement of photosynthesis via competition for light energy.

Analysis of the transcriptome of Erigeron breviscapus uncovers putative scutellarin and chlorogenic acids biosynthetic genes and genetic markers.

BACKGROUND: Erigeron breviscapus (Vant.) Hand-Mazz. is a famous medicinal plant. Scutellarin and chlorogenic acids are the primary active components in this herb. However, the mechanisms of biosynthesis and regulation for scutellarin and chlorogenic acids in E. breviscapus are considerably unknown. In addition, genomic information of this herb is also unavailable. PRINCIPAL FINDINGS: Using Illumina sequencing on GAIIx platform, a total of 64,605,972 raw sequencing reads were generated and assembled into 73,092 non-redundant unigenes. Among them, 44,855 unigenes (61.37%) were annotated in the public databases Nr, Swiss-Prot, KEGG, and COG. The transcripts encoding the known enzymes involved in flavonoids and in chlorogenic acids biosynthesis were discovered in the Illumina dataset. Three candidate cytochrome P450 genes were discovered which might encode flavone 6-hydroase converting apigenin to scutellarein. Furthermore, 4 unigenes encoding the homologues of maize P1 (R2R3-MYB transcription factors) were defined, which might regulate the biosynthesis of scutellarin. Additionally, a total of 11,077 simple sequence repeat (SSR) were identified from 9,255 unigenes. Of SSRs, tri-nucleotide motifs were the most abundant motif. Thirty-six primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism. The result revealed that 34 (94.40%) primer pairs were successfully amplified and 19 (52.78%) primer pairs exhibited polymorphisms. CONCLUSION: Using next generation sequencing (NGS) technology, this study firstly provides abundant genomic data for E. breviscapus. The candidate genes involved in the biosynthesis and transcriptional regulation of scutellarin and chlorogenic acids were obtained in this study. Additionally, a plenty of genetic makers were generated by identification of SSRs, which is a powerful tool for molecular breeding and genetics applications in this herb.