A Chinese SCA36 pedigree analysis of NOP56 expansion region based on long-read sequencing.

Introduction: Spinocerebellar ataxias 36 (SCA36) is the neurodegenerative disease caused by the GGCCTG Hexanucleotide repeat expansions in NOP56, which is too long to sequence using short-read sequencing. Single molecule real time (SMRT) sequencing can sequence across disease-causing repeat expansion. We report the first long-read sequencing data across the expansion region in SCA36. Methods: We collected and described the clinical manifestations and imaging features of Han Chinese pedigree with three generations of SCA36. Also, we focused on structural variation analysis for intron 1 of the NOP56 gene by SMRT sequencing in the assembled genome. Results: The main clinical features of this pedigree are late-onset ataxia symptoms, with a presymptomatic presence of affective and sleep disorders. In addition, the results of SMRT sequencing showed the specific repeat expansion region and demonstrated that the region was not composed of single GGCCTG hexanucleotides and there were random interruptions. Discussion: We extended the phenotypic spectrum of SCA36. We applied SMRT sequencing to reveal the correlation between genotype and phenotype of SCA36. Our findings indicated that long-read sequencing is well suited to characterize known repeat expansion.

Irrigation Scheduling for Maize under Different Hydrological Years in Heilongjiang Province, China.

Appropriate irrigation schedules could minimize the existing imbalance between agricultural water supply and crop water requirements (ETc), which is severely impacted by climate change. In this study, different hydrological years (a wet year, normal year, dry year, and an extremely dry year) in Heilongjiang Province were calculated by hydrological frequency methods. Then, the single crop coefficient method was used to calculate the maize ETc, based on the daily meteorological data of 26 meteorological stations in Heilongjiang Province from 1960 to 2020. Afterward, the CROPWAT model was used to calculate the effective precipitation (Pe) and irrigation water requirement (Ir), and formulate the irrigation schedules of maize in Heilongjiang Province under different hydrological years. The results showed that ETc and Ir decreased first and then increased from west to east. The Pe and crop water surplus deficit index increased first and then decreased from west to east in Heilongjiang Province. Meanwhile, the average values of the Ir in were 171.14 mm, 232.79 mm, 279.08 mm, and 334.47 mm in the wet year, normal year, dry year, and extremely dry year, respectively. Heilongjiang Province was divided into four irrigation zones according to the Ir of different hydrological years. Last, the irrigation quotas for the wet year, normal year, dry year, and extremely dry year were 0~180 mm, 20~240 mm, 60~300 mm, and 80~430 mm, respectively. This study provides reliable support for maize irrigation practices in Heilongjiang Province, China.

Systemic regulation of nodule structure and assimilated carbon distribution by nitrate in soybean.

Background: The nitrate regulates soybean nodulation and nitrogen fixation systemically, mainly in inhibiting nodule growth and reducing nodule nitrogenase activity, but the reason for its inhibition is still inconclusive. Methods: The systemic effect of nitrate on nodule structure, function, and carbon distribution in soybean (Glycine max (L.) Merr.) was studied in a dual-root growth system, with both sides inoculated with rhizobia and only one side subjected to nitrate treatment for four days. The non-nodulating side was genetically devoid of the ability to form nodules. Nutrient solutions with nitrogen concentrations of 0, 100, and 200 mg L-1 were applied as KNO3 to the non-nodulating side, while the nodulating side received a nitrogen-free nutrient solution. Carbon partitioning in roots and nodules was monitored using 13C-labelled CO2. Other nodule responses were measured via the estimation of the nitrogenase activity and the microscopic observation of nodule ultrastructure. Results: Elevated concentrations of nitrate applied on the non-nodulating side caused a decrease in the number of bacteroids, fusion of symbiosomes, enlargement of the peribacteroid spaces, and onset of degradation of poly-ß-hydroxybutyrate granules, which is a form of carbon storage in bacteroids. These microscopic observations were associated with a strong decrease in the nitrogenase activity of nodules. Furthermore, our data demonstrate that the assimilated carbon is more likely to be allocated to the non-nodulating roots, as follows from the competition for carbon between the symbiotic and non-symbiotic sides of the dual-root system. Conclusion: We propose that there is no carbon competition between roots and nodules when they are indirectly supplied with nitrate, and that the reduction of carbon fluxes to nodules and roots on the nodulating side is the mechanism by which the plant systemically suppresses nodulation under nitrogen-replete conditions.

Melatonin improves nitrogen metabolism during grain filling under drought stress.

Drought affects the normal growth and development of soybeans. Melatonin reportedly alleviates drought stress-induced growth inhibition and plant injury, thus, its foliar application presumably has considerable potential in agriculture. However, few studies have investigated the mechanism responsible for its effects on soybean nitrogen metabolism. In this study, pot culture and plant physiological detection, qPCR, and other methods were used for analysis. The purpose of this study was to explore the effects of melatonin and melanin on glutathione metabolism. The results showed that drought stress led to an increase in soluble protein and proline content, concomitantly with a decrease in the activity of nitrogen metabolism-related key enzymes, an increase in inorganic nitrogen content, and a reduction in nitrogen accumulation and transport. Exogenous melatonin application under drought stress significantly increased the expression of key genes involved in nitrogen metabolism and the activity of key enzymes including, GOGAT, NR, Gs and GDH. Enhanced enzyme activity promotes the conversion of nitrate nitrogen in plants, increases proline, soluble protein, and ureide contents, and, consequently, nitrogen accumulation. Altogether, these changes were conducive to greater nitrogen assimilation and transport. Therefore, under drought stress, melatonin application upregulated key genes involved in nitrogen metabolism, thereby enhancing the activity of related enzymes and restoring growth, stable biomass production. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01219-y.

Integrated proteomics and metabolomics analysis of rice leaves in response to rice straw return.

Straw return is crucial for the sustainable development of rice planting, but no consistent results were observed for the effect of straw return on rice growth. To investigate the response of rice leaves to rice straw return in Northeast China, two treatments were set, no straw return (S0) and rice straw return (SR). We analyzed the physiological index of rice leaves and measured differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) levels in rice leaves by the use of proteomics and metabolomics approaches. The results showed that, compared with the S0 treatment, the SR treatment significantly decreased the dry weight of rice plants and non-structural carbohydrate contents and destroyed the chloroplast ultrastructure. In rice leaves of SR treatment, 329 DEPs were upregulated, 303 DEPs were downregulated, 44 DEMs were upregulated, and 71 DEMs were downregulated. These DEPs were mainly involved in photosynthesis and oxidative phosphorylation, and DEMs were mainly involved in alpha-linolenic acid metabolism, galactose metabolism, glycerophospholipid metabolism, pentose and gluconic acid metabolism, and other metabolic pathways. Rice straw return promoted the accumulation of scavenging substances of active oxygen and osmotic adjustment substances, such as glutathione, organic acids, amino acids, and other substances. The SR treatment reduced the photosynthetic capacity and energy production of carbon metabolism, inhibiting the growth of rice plants, while the increase of metabolites involved in defense against abiotic stress enhanced the adaptability of rice plants to straw return stress.

Systemic regulation of soybean nodulation and nitrogen fixation by nitrogen via isoflavones.

Nitrogen (N) inhibits soybean (Glycine max L.) nodulation and N2 fixation. Isoflavones secreted by soybean roots can stimulate signal transduction for symbiotic nodules, thus playing a key role in root nodule development and N2 fixation. The relationship between the inhibition of soybean nodulation, N2 fixation and isoflavones by N is still unclear. In this study, dual-root soybean plants were prepared by grafting, and N or isoflavones were supplied to unilateral roots. The number and dry weight of the soybean nodules, nitrogenase activity, isoflavone concentrations and relative changes in the level of expression of nodulation-related genes were measured to study the response relationship between the N systemic regulation the soybean nodule N2 fixation and changes in the concentrations of isoflavones in its roots. The results showed that N supply to one side of the dual-root soybeans systematically affected the N2 fixation of root nodules on both sides, and this effect began in the early stage of nodulation. Moreover, a unilateral supply of N systematically affected the concentrations of daidzein and genistein on both sides of the roots. The concentrations of isoflavones were consistent with the change trend of soybean root nodule and nodulation-related gene expression level. Treatment with unilateral N or isoflavones affected the soybean nodule N2 fixation and its nodulation-related genes, which had the same response to the changes in concentrations of root isoflavones. N regulates soybean nodulation and N2 fixation by systematically affecting the concentrations of isoflavones in the roots.

Physiology and Gene Expression Analysis of Potato (Solanum tuberosum L.) in Salt Stress.

The production of potato (Solanum tuberosum L.) faces a severe challenge due to the salinization of arable land worldwide. The cultivation of salt-tolerant potatoes is of great significance to ensure food security. In this study, two cultivars of 'Longshu 5' and 'Qingshu 9' were compared for physiological responses to salt stress, and then the salt tolerance of the two cultivars were assessed via principal component analysis. Furthermore, the Na+, K+, and Ca2+ flux of the cultivars under salt stress was recorded. Finally, the expression levels of ion transport-related genes and transcription factors in salt-tolerant cultivars were explored under NaCl stress. The results showed that the seven physiological indicators of salt tolerance were differed between the cultivars. Interestingly, soluble protein and sugar were early responsive to salt stress than proline in the salt-tolerance cultivar. Peroxidase and superoxide dismutase activity were significantly different in 'Longshu 5' under NaCl stress and without being significantly different in 'Qingshu9'. In addition, the salt tolerance of 'Longshu 5' was more tolerant than 'Qingshu 9' based on principal component evaluation. Meanwhile, the strong efflux of Na+, the stability of K+, and the high absorption of Ca2+ in 'Longshu 5' indicated salt adaption mechanisms in the salt-tolerant potato. In addition, we found that ion transport-related genes and transcription factors, such as StSOS1, StNHX4, StAKT1, StNAC24, and StCYP707A, played a role in the salt tolerance of 'Longshu 5'. In conclusion, the salt-tolerant potato can regulate physiological substances to adapt to salt stress, and ion transport related genes and transcription factors play a role in improving salt tolerance.

Proteome Analysis of the Soybean Nodule Phosphorus Response Mechanism and Characterization of Stress-Induced Ribosome Structural and Protein Expression Changes.

In agroecosystems, a plant-usable form of nitrogen is mainly generated by legume-based biological nitrogen fixation, a process that requires phosphorus (P) as an essential nutrient. To investigate the physiological mechanism whereby phosphorus influences soybean nodule nitrogen fixation, soybean root nodules were exposed to four phosphate levels: 1 mg/L (P stress), 11 mg/L (P stress), 31 mg/L (Normal P), and 61 mg/L (High P) then proteome analysis of nodules was conducted to identify phosphorus-associated proteome changes. We found that phosphorus stress-induced ribosomal protein structural changes were associated with altered key root nodule protein synthesis profiles. Importantly, up-regulated expression of peroxidase was observed as an important phosphorus stress-induced nitrogen fixation-associated adaptation that supported two nodule-associated activities: scavenging of reactive oxygen species (ROS) and cell wall growth. In addition, phosphorus transporter (PT) and purple acid phosphatase (PAPs) were up-regulated that regulated phosphorus transport and utilization to maintain phosphorus balance and nitrogen fixation function in phosphorus-stressed root nodules.

Integrated Proteomics and Metabolomics Analysis of Nitrogen System Regulation on Soybean Plant Nodulation and Nitrogen Fixation.

The specific mechanisms by which nitrogen affects nodulation and nitrogen fixation in leguminous crops are still unclear. To study the relationship between nitrogen, nodulation and nitrogen fixation in soybeans, dual-root soybean plants with unilateral nodulation were prepared by grafting. At the third trifoliate leaf (V3) to fourth trifoliate leaf (V4) growth stages (for 5 days), nitrogen nutrient solution was added to the non-nodulated side, while nitrogen-free nutrient solution was added to the nodulated side. The experiment was designed to study the effects of exogenous nitrogen on proteins and metabolites in root nodules and provide a theoretical reference for analyzing the physiological mechanisms of the interaction between nitrogen application and nitrogen fixation in soybean root nodules. Compared with no nitrogen treatment, exogenous nitrogen regulated the metabolic pathways of starch and sucrose metabolism, organic acid metabolism, nitrogen metabolism, and amino acid metabolism, among others. Additionally, exogenous nitrogen promoted the synthesis of signaling molecules, including putrescine, nitric oxide, and asparagine in root nodules, and inhibited the transformation of sucrose to malic acid; consequently, the rhizobia lacked energy for nitrogen fixation. In addition, exogenous nitrogen reduced cell wall synthesis in the root nodules, thus inhibiting root nodule growth and nitrogen fixation.

Study on the Regulatory Effects of GA3 on Soybean Internode Elongation.

Excessive plant height is an important factor that can lead to lodging, which is closely related to soybean yield. Gibberellins are widely used as plant growth regulators in agricultural production. Gibberellic acid (GA3), one of the most effective active gibberellins, has been used to regulate plant height and increase yields. The mechanism through which GA3 regulates internode elongation has been extensively investigated. In 2019 and 2020, we applied GA3 to the stems, leaves, and roots of two soybean cultivars, Heinong 48 (a high-stalk cultivar) and Henong 60 (a dwarf cultivar), and GA3 was also applied to plants whose apical meristem was removed or to girded plants to compare the internode length and stem GA3 content of soybean plants under different treatments. These results suggested that the application of GA3 to the stems, leaves, and roots of soybean increased the internode length and GA3 content in the stems. Application of GA3 decreased the proportion of the pith in the soybean stems and primary xylem while increasing the proportion of secondary xylem. The apical meristem is an important site of GA3 synthesis in soybean stems and is involved in the regulation of stem elongation. GA3 was shown to be transported acropetally through the xylem and laterally between the xylem and phloem in soybean stems. We conclude that the GA3 level in stems is an important factor affecting internode elongation.

Nitrate Transport and Distribution in Soybean Plants With Dual-Root Systems.

Nitrate absorbed by soybean (Glycine max L. Merr.) roots from the soil can promote plant growth, while nitrate transported to nodules inhibits nodulation and nodule nitrogen fixation activity. The aim of this study was to provide new insights into the inhibition of nodule nitrogen (N) fixation by characterizing the transport and distribution of nitrate in soybean plants. In this research, pot culture experiments were conducted using a dual root system of soybeans. In the first experiment, the distribution of 15N derived from nitrate was observed. In the second experiment, nitrate was supplied-withdrawal-resupplied to one side of dual-root system for nine consecutive days, and the other side was supplied with N-free solution. Nitrate contents in leaves, stems, petioles, the basal root of pealed skin and woody part at the grafting site were measured. Nitrate transport and distribution in soybean were analyzed combining the results of two experiments. The results showed that nitrate supplied to the N-supply side of the dual-root system was transported to the shoots immediately through the basal root pealed skin (the main transport route was via the phloem) and woody part (transport was chiefly related to the xylem). There was a transient storage of nitrate in the stems. After the distribution of nitrate, a proportion of the nitrate absorbed by the roots on the N-supply side was translocated to the roots and nodules on the N-free side with a combination of the basal root pealed skin and woody part. In conclusion, the basal root pealed skin and woody part are the main transport routes for nitrate up and down in soybean plants. Nitrate absorbed by roots can be transported to the shoots and then retranslocated to the roots again. The transport flux of nitrate to the N-free side was regulated by transient storage of nitrate in the stems.

Effect of straw retention on carbon footprint under different cropping sequences in Northeast China.

Inappropriate farm management practices can lead to increased agricultural inputs and changes in atmospheric greenhouse gas (GHG) emissions, impacting climate change. This study was initiated in 2012 to assess the potential for straw retention to mitigate the negative environmental impact of various cropping systems on the Songnen Plain using the life cycle assessment (LCA) method combined with field survey data. Straw retention (STR) and straw removal (STM) treatments were established in continuous corn (CC) and corn-soybean rotation (CS) systems in a split-plot experiment. The effects of straw retention on the carbon footprint (CF) of cropland under different cropping systems were compared. The CF under CC was 2434-2707 kg CO2 ha-1 year-1, 49-57% higher than that under CS. Nitrogen fertilizer produced the most CO2, accounting for 66-80% of the CF. The carbon balances of the CC and CS systems with STR were positive, with annual carbon sequestrations of 9633 and 2716 kg CO2 ha-1 year-1, respectively. The carbon balance (CB) of CC-STR was 255% higher than that of CS-STR. This study demonstrates that STR under CC cultivation is an environmentally friendly practice for agricultural production, can help achieve high-yield and low-carbon production in rainfed cropland, and can support the sustainable development of grain production in Northeast China.

Genome-scale analyses and characteristics of putative pathogenicity genes of Stagonosporopsis cucurbitacearum, a pumpkin gummy stem blight fungus.

Outbreaks of gummy stem blight (GSB), an emerging seed pumpkin disease, have increased in number and have become more widespread in recent years. Previously we reported that Stagonosporopsis cucurbitacearum (Sc.) is the dominant fungal cause of pumpkin seedling GSB in Northeast China, where it has greatly reduced crop yields in that region. Here, high-throughput whole-genome sequencing and assembly of the Sc. genome were conducted toward revealing pathogenic molecular regulatory mechanisms involved in fungal growth and development. Zq-1 as representative Sc. strain, DNA of Zq-1was prepared for genomic sequencing, we obtained 5.24 Gb of high-quality genomic sequence data via PacBio RS II sequencing. After sequence data was processed to filter out low quality reads, a hierarchical genome-assembly process was employed that generated a genome sequence of 35.28 Mb in size. A total of 9844 genes were predicted, including 237 non-coding RNAs, 1024 genes encoding proteins with signal peptides, 2066 transmembrane proteins and 756 secretory proteins.Transcriptional identification revealed 54 differentially expressed secretory proteins. Concurrently, 605, 130 and 2869 proteins were matched in the proprietary databases Carbohydrate-Active EnZymes database (CAZyme), Transporter Classification Database (TCDB) and Pathogen-Host Interactions database (PHI), respectively. And 96 and 36 DEGs were identified form PHI database and CAZyme database, respectively. In addition, contig00011.93 was an up-regulated DEG involving ATP-binding cassette metabolism in the procession of infection. In order to test relevance of gene predictions to GSB, DEGs with potential pathogenic relevance were revealed through transcriptome data analysis of Sc. strains pre- and post-infection of pumpkin. Interestingly, Sc. and Leptosphaeria maculans (Lm.) exhibited relatively similar with genome lengths, numbers of protein-coding genes and other characteristics. This work provides a foundation for future exploration of additional Sc. gene functions toward the development of more effective GSB control strategies.