The response of N₂O emissions to nitrogen (N) addition is usually positive, but its response to phosphorus (P) addition varies, and the underlying mechanisms for the changes in N₂O emissions remain unclear.  We conducted field studies to examine the response of N₂O emissions to N and P addition over two years in three typical alpine grasslands, alpine meadow (AM), alpine steppe (AS), and alpine cultivated grassland (CG) on the Qinghai-Tibet Plateau (QTP).  Our results showed consistent increases in N₂O emissions under N addition alone or with P addition, and insignificant change in N₂O emissions under P addition alone in all three grasslands.  N addition increased N₂O emissions directly in AM, by lowering soil pH in AS, and by lowering abundance of denitrification genes in CG.  N and P co-addition increased N₂O emissions in AM and AS but only showed an interactive effect in AM.  P addition enhanced the increase in N₂O emissions caused by N addition mainly by promoting plant growth in AM.  Overall, our results illustrate that short-term P addition cannot alleviate the stimulation of N₂O emissions by N deposition in alpine grassland ecosystems, and may even further stimulate N₂O emissions.

Invasive alien ants (IAAs) are among the most aggressive, competitive, and widespread invasive alien species (IAS) worldwide.  Wasmannia auropunctata, the greatest IAAs threat in the Pacific region and listed in “100 of the world’s worst IAS”, has established itself in many countries and on islands worldwide.  Wild populations of W. auropunctata were recently reported in southeastern China, representing a tremendous potential threat to China’s agricultural, economic, environmental, public health, and social well-being.  Estimating the potential geographical distribution (PGD) of W. auropunctata in China can illustrate areas that may potentially face invasion risk.  Therefore, based on the global distribution records of W. auropunctata and bioclimatic variables, we predicted the geographical distribution pattern of W. auropunctata in China under the effects of climate change using an ensemble model (EM).  Our findings showed that artificial neural network (ANN), flexible discriminant analysis (FDA), gradient boosting model (GBM), Random Forest (RF) were more accurate than categorical regression tree analysis (CTA), generalized linear model (GLM), maximum entropy model (MaxEnt) and surface distance envelope (SRE).  The mean TSS values of ANN, FDA, GBM, and RF were 0.820, 0.810, 0.843, and 0.857, respectively, and the mean AUC values were 0.946, 0.954, 0.968, and 0.979, respectively.  The mean TSS and AUC values of EM were 0.882 and 0.972, respectively, indicating that the prediction results with EM were more reliable than those with the single model.  The PGD of W. auropunctata in China is mainly located in southern China under current and future climate change.  Under climate change, the PGD of W. auropunctata in China will expand to higher-latitude areas.  The annual temperature range (bio7) and mean temperature of the warmest quarter (bio10) were the most significant variables affecting the PGD of W. auropunctata in China.  The PGD of W. auropunctata in China was mainly attributed to temperature variables, such as the annual temperature range (bio7) and the mean temperature of the warmest quarter (bio10).  The populations of W. auropunctata in southern China have broad potential invasion areas.  Developing strategies for the early warning, monitoring, prevention, and control of W. auropunctata in southern China requires more attention.

The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in wheat.  Characterizing the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach.  ‘Kenong 9204’ (KN9204) is a candidate foundation parent characterized by ideotype, high yield potential, and particularly high nitrogen fertilizer utilization.  To better understand the genetic basis of its high yield potential, high throughput whole-genome re-sequencing (10×) was performed on KN9204, its parental lines and its derivatives.  A high-resolution genetic composition map of KN9204 was constructed, which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci (QTL) from a bi-parental mapping population.  Xiaoyan 693 (XY693), a wheat–Thinopyrum ponticum partial amphidiploid, contributed a great deal to the high yield potential of KN9204, and three major stable QTLs from XY693 were fine mapped.  The transmissibility of key genomic segments from KN9204 to its derivatives were delineated, indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by breeders.  Evidence for selection sweeps in the breeding programs was identified.  This study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.

Global food security is threatened by the impacts of the spread of crop pests and changes in the complex interactions between crops and pests under climate change.  Schrankia costaestrigalis is a newly-reported potato pest in southern China.  Early-warning monitoring of this insect pest could protect domestic agriculture as it has already caused regional yield reduction and/or quality decline in potato production.  Our research aimed to confirm the potential geographical distributions (PGDs) of S. costaestrigalis in China under different climate scenarios using an optimal MaxEnt model, and to provide baseline data for preventing agricultural damage by S. costaestrigalis.  Our findings indicated that the accuracy of the optimal MaxEnt model was better than the default-setting model, and the minimum temperature of the coldest month, precipitation of the driest month, precipitation of the coldest quarter, and the human influence index were the variables significantly affecting the PGDs of S. costaestrigalis.  The highly- and moderately-suitable habitats of S. costaestrigalis were mainly located in eastern and southern China.  The PGDs of S. costaestrigalis in China will decrease under climate change.  The conversion of the highly- to moderately-suitable habitat will also be significant under climate change.  The centroid of the suitable habitat area of S. costaestrigalis under the current climate showed a general tendency to move northeast and to the middle-high latitudes in the 2030s.  The agricultural practice of plastic film mulching in potato fields will provide a favorable microclimate for S. costaestrigalis in the suitable areas.  More attention should be paid to the early warning and monitoring of S. costaestrigalis in order to prevent its further spread in the main areas in China’s winter potato planting regions.

Inversion tillage with straw amendment is widely applied in northeastern China, and it can substantially increase the storage of carbon and improve multiple subsoil functions. Soil microorganisms are believed to be the key to this process, but research into their role in subsoil amelioration is limited. Therefore, a field experiment was conducted in 2018 in a region in northeastern China with Hapli-Udic Cambisol using four treatments: conventional tillage (CT, tillage to a depth of 15 cm with no straw incorporation), straw incorporation with conventional tillage (SCT, tillage to a depth of 15 cm), inversion tillage (IT, tillage to a depth of 35 cm) and straw incorporation with inversion tillage (SIT, tillage to a depth of 35 cm). The soils were managed by inversion to a depth of 15 or 35 cm every year after harvest. The results indicated that SIT improved soil multi-nutrient cycling variables and increased the availability of key nutrients such as soil organic carbon, total nitrogen, available nitrogen, available phosphorus and available potassium in both the topsoil and subsoil. In contrast to CT and SCT, SIT created a looser microbial network structure but with highly centralized clusters by reducing the topological properties of average connectivity and node number, and by increasing the average path length and the modularity. A Random Forest analysis found that the average path length and the clustering coefficient were the main determinants of soil multi-nutrient cycling. These findings suggested that SIT can be an effective option for improving soil multi-nutrient cycling and the structure of microbial networks, and they provide crucial information about the microbial strategies that drive the decomposition of straw in Hapli-Udic Cambisol.

Lignin metabolism plays a pivotal role in plant defense against pathogens and is always positively correlated as a response to pathogen infection.  Thus, understanding resistance genes against pathogens in plants depends on a genetic analysis of lignin response.  In the study, eight upland cotton lines were used to construct a multi-parent advanced generation intercross (MAGIC) population (n=280), which exhibited peculiar characteristics from the convergence of various alleles coding for advantageous traits.  To measure the lignin response to Verticillium wilt (LRVW), artificial disease nursery (ADN) and rotation nursery (RN) were prepared for MAGIC population planting in four environments.  The stem lignin contents were collected, and the LRVW was measured with the lignin value of ADN/RN in each environment, which showed great variation.  A total of 9323 high-quality single-nucleotide polymorphism (SNP) markers obtained from the Cotton-SNP63K array were employed for genotyping the MAGIC population.  The SNPs were distributed through the whole genome with 4.78 SNP/Mb density, ranging from 1.14 (ChrA06) to 10.08 (ChrD08).  A genome-wide association study was performed using a mixed linear model (MLM) for LRVW, and three stable quantitative trait loci (QTLs), qLRVW-A04, qLRVW-A10 and qLRVW-D05, were identified in more than two environments.  Two key candidate genes, Ghi_D05G01046 and Ghi_D05G01221, were selected within the QTLs through the combination of variations in the coding sequence, induced expression patterns, and function annotations, both of which presented nonsynonymous mutations in coding regions and were strongly induced by Verticillium dahliae. Ghi_D05G01046 encodes a leucine-rich extensin (LRx) protein, which is involved in Arabidopsis cell wall biosynthesis and organization.  Ghi_D05G01221 encodes a transcriptional co-repressor novel interactor of jaz (NINJA), which functions in the jasmonic acid (JA) signaling pathway.  In summary, the study creates valuable genetic resources for breeding and QTL mapping and opens up a new perspective to uncover the genetic basis of VW resistance in upland cotton.

Linoleic acid is an essential polyunsaturated fatty acid that cannot be synthesized by humans or animals themselves and can only be obtained externally.  The amount of linoleic acid present has an impact on the quality and flavour of meat and indirectly affects consumer preference.  However, the molecular mechanisms influencing the deposition of linoleic acid in organisms are not clear.  As the molecular mechanisms of linoleic acid deposition are not well understood, to investigate the main effector genes affecting the linoleic acid content, this study aimed to screen for hub genes in slow-type yellow-feathered chickens by transcriptome sequencing (RNA-Seq) and weighted gene coexpression network analysis (WGCNA).  We screened for candidate genes associated with the linoleic acid content in slow-type yellow-feathered broilers.  A total of 399 Tiannong partridge chickens were slaughtered at 126 days of age, fatty acid levels were measured in pectoral muscle, and pectoral muscle tissue was collected for transcriptome sequencing.  Transcriptome sequencing results were combined with phenotypes for WGCNA to screen for candidate genes.  KEGG enrichment analysis was also performed on the genes that were significantly enriched in the modules with the highest correlation.  A total of 13 310 genes were identified after quality control of transcriptomic data from 399 pectoral muscle tissues.  WGCNA was performed, and a total of 26 modules were obtained, eight of which were highly correlated with the linoleic acid content.  Four key genes, namely, MDH2, ATP5B, RPL7A and PDGFRA, were screened according to the criteria |GS|>0.2 and |MM|>0.8.  The functional enrichment results showed that the genes within the target modules were mainly enriched in metabolic pathways.  In this study, a large-sample-size transcriptome analysis revealed that metabolic pathways play an important role in the regulation of the linoleic acid content in Tiannong partridge chickens, and MDH2, ATP5B, RPL7A and PDGFRA were screened as important candidate genes affecting the linoleic acid content.  The results of this study provide a theoretical basis for selecting molecular markers and comprehensively understanding the molecular mechanism affecting the linoleic acid content in muscle, providing an important reference for the breeding of slow-type yellow-feathered broiler chickens.

Early maturity, complete defoliation and boll opening are essential for the efficient machine harvesting of cotton.  Chemical topping, involving one extra application of mepiquat chloride (MC) in addition to its traditional multiple-application strategy, may be able to replace manual topping.  However, it is not known whether this chemical topping technique will influence maturity or cotton responses to harvest aids.  In this 2-yr field study, we determined the effects of the timing of chemical topping using various rates of MC on boll opening percentage (BOP) before application of harvest aids (50% thidiazuron·ethephon suspension concentrate, referred to as TE), and the defoliation percentage (DP) and BOP 14 days after TE application.  The results indicated that late chemical topping (near the physiological cutout, when the nodes above white flower is equal to 5.0) significantly decreased BOP before TE by 5.9–11.2% compared with early (at peak bloom) or middle (seven days after peak bloom) treatments in 2019, which was a relatively normal year based on crop condition.  Also, a high MC rate (270 g ha^–1) showed a significantly lower (22.0%) BOP before TE than low (90 g ha^–1) or medium (180 g ha^–1) rates.  In 2020, which was characterized by stronger vegetative growth in the late season, the late chemical topping reduced the number of leaves before TE application relative to early or middle treatments, but had lower DP (23.2–27.2%) 14 days after TE application.  The high MC rate showed a leaf count before TE application that was similar to the low and medium rates, but it showed the most leaves after TE and much lower (15.0–21.7%) DP in 2020.  These results suggest that late timing of chemical topping and a high MC rate decreased the sensitivity of leaves to harvest aids.  Further analysis indicated that the late chemical topping mainly affected the leaf drop from the mainstem and fruiting branches where the late regrowth occurred, and the high MC rate reduced leaf shedding from these parts and also from the vegetative branches.  In conclusion, chemical topping with MC during the bloom period affected cotton maturity and responses to harvest aids in different ways according to the crop condition.  To avoid the risks of delayed maturity and poor defoliation after the application of harvest aids, chemical topping should not be performed too late (i.e., near the physiological cutout) by using MC at more than 180 g ha^–1.  The optimum timing of chemical topping probably varies from peak bloom to around seven days later, and the safest MC rates for chemical topping should be less than 180 g ha^–1.

In maize, two root epidermis-expressed ammonium transporters ZmAMT1;1a and ZmAMT1;3 play major roles in high-affinity ammonium uptake.  However, the transcriptional regulation of ZmAMT1s in roots for ensuring optimal ammonium acquisition remains largely unknown.  Here, using a split root system we showed that ZmAMT1;1a and ZmAMT1;3 transcript levels were induced by localized ammonium supply to nitrogen-deficient roots.  This enhanced expression of ZmAMT1s correlated with increases in ¹⁵NH₄⁺ influx rates and tissue glutamine concentrations in roots.  When ammonium was supplied together with methionine sulfoximine, an inhibitor of glutamine synthase, ammonium-induced expression of ZmAMT1s disappeared, suggesting that glutamine rather than ammonium itself regulated ZmAMT1s expression.  When glutamine was supplied to nitrogen-deficient roots, expression levels of ZmAMT1s were enhanced, and negative feedback regulation could subsequently occur by supply of glutamine at a high level.  Thus, our results indicated an ammonium-dependent regulation of ZmAMT1s at transcript levels, and a dual role of glutamine was suggested in the regulation of ammonium uptake in maize roots.

Although returning crop residue to fields is a recommended measure for improving soil carbon (C) stocks in agroecosystems, the response of newly formed soil C (NFC) to the integrated supply of residue and nutrients and the microbial mechanisms have not been fully understood. Therefore, an 84-day incubation experiment was conducted to ascertain the microbial mechanisms that underpin the NFC response to inputs of residue and nitrogen (N), phosphorus (P), and sulfur (S) in two black soils. The results showed that adding residue alone accelerated microbial nutrient mining, which was supported by decreases of 8–16% in the ratios of C:N and C:P enzyme activities (relative to soils with nutrient inputs). The NFC amounts increased from 1155.9 to 1722.4 mg kg⁻¹ soil in Gongzhuling and increased from 725.1 to 1067.5 mg kg⁻¹ soil in Hailun as the levels of nutrient supplementation increased. Boosted regression tree analysis suggested that β-glucosidase (BG), acid phosphatase (AP), microbial biomass C (MBC), and Acidobacteria accounted for 27.8, 18.5, 14.7, and 8.1%, respectively, of the NFC in Gongzhuling and accounted for 25.9, 29.5, 10.1, and 13.9%, respectively, of the NFC in Hailun. Path analysis determined that Acidobacteria positively influenced NFC both directly and indirectly by regulating BG, AP, and MBC, in which MBC acquisition was regulated more by AP. The intensity of NFC was lower in Hailun soil than in Gongzhuling soil and was directly affected by AP, thereby indicating the importance of soil status (e.g., SOC and pH) in determining NFC. Overall, our results reveal the response of NFC to supplementation by N, P, and S, which depends on Acidobacteria and Proteobacteria, and their investment in BG and AP in residue-amended soil.

Embryo rescue technology plays an important role in seedless grape breeding.  However, the efficiency of embryo rescue, including the embryo formation, germination, and seedling rates, is closely related to the parental genotypes, degree of abortion, growth medium, and plant growth regulators.  In this study, we investigated the effects of different concentrations of paclobutrazol (PAC), a plant growth regulator, and embryo collection times on the embryo formation, germination, and seedling rates for different hybrid combinations of grape breeding varieties used for their aroma and cold-resistance traits.  The results showed that the different PAC concentrations had varying impacts on the development of ovules and embryos from the different grape varieties.  The embryo formation rates of the ‘Sultanina Rose’בBeibinghong’ and ‘Kunxiang Seedless’בTaishan-2’ crosses were the highest under the 5.1 μmol L^–1 PAC treatment.  The 1.0 μmol L^–1 PAC treatment was optimal for the germination and seedling development of the ‘Sultanina Rose’בBeibinghong’ embryos, whereas the 0.2 μmol L^–1 PAC treatment induced the highest germination rate for the ‘Sultanina Rose’בKunxiang Seedless’ cross.  The optimal sampling times for each cross varied as 39 d after pollination (DAP) for the ‘Flame Seedless’בMuscat Hamburg’ cross, 46 DAP for the ‘Kunxiang Seedless’בBeibinghong’ cross, and 41 DAP for the ‘Ruby Seedless’בBeibinghong’ and ‘Fantasy Seedless’בShuangyou’ crosses.  Moreover, the medium modified with 0.5 g L^–1 of indole-3-butyric acid allowed the malformed seedlings to develop into plantlets and achieve larger progenies.  This study provides a useful basis for further studies into grape embryo rescue and could improve breeding efforts for new seedless grape varieties.

To address the relationships between the amount of nitrogen fertilizer application and the yield of double cropping rice systems, we investigated the effects of a cultivation pattern of strong seedlings with increased planting density and reduced nitrogen application (SDN) on the morphological and physiological characteristics of double cropping rice.  Our results indicated that the effects of SDN on the morphological characteristics of the single plant roots of double cropping rice were not significant, but the morphological characteristics of the population roots were largely different.  Specifically, SDN significantly increased the morphological indexes of the root population such as root fresh weight, root volume, root number, root length and root dry weight.  The effects of SDN on the total root absorption areas and root active absorption areas of the single plants were non-significant, but it dramatically enhanced the total root absorption areas and root active absorption areas of the plant population during the tillering, heading and mature stages.  In addition, SDN significantly increased the root bleeding intensity and elevated the soluble sugar and free amino acid contents of root bleeding sap.  Compared to the traditional cultivation pattern (CK), SDN significantly increased root bleeding intensity at the heading stage by 4.37 and 8.90% for early and late rice, respectively.  Meanwhile, SDN profoundly enhanced the soluble sugar contents of root bleeding sap by 12.85 and 10.41% for early and late rice, respectively.  In addition, SDN also significantly enhanced free amino acid content of root bleeding sap by 43.25% for early rice and by 37.50% for late rice systems compared to CK.  Furthermore, SDN increased the actual yield of double cropping rice mainly due to the higher effective panicle number and the larger seed-setting rate.  The actual yields of early rice under SDN were higher than CK by 9.37 and 5.98% in 2016 and 2017, and the actual yields of late rice under SDN were higher than CK by 0.20 and 1.41% in 2016 and 2017, respectively.  Correlation analysis indicated that the significant positive correlations were observed between the majority of the root indexes and the actual yield across the four different growth stages.

Single-step genomic best linear unbiased prediction (ssGBLUP) is now intensively investigated and widely used in livestock breeding due to its beneficial feature of combining information from both genotyped and ungenotyped individuals in the single model.  With the increasing accessibility of whole-genome sequence (WGS) data at the population level, more attention is being paid to the usage of WGS data in ssGBLUP.  The predictive ability of ssGBLUP using WGS data might be improved by incorporating biological knowledge from public databases.  Thus, we extended ssGBLUP, incorporated genomic annotation information into the model, and evaluated them using a yellow-feathered chicken population as the examples.  The chicken population consisted of 1 338 birds with 23 traits, where imputed WGS data including 5 127 612 single nucleotide polymorphisms (SNPs) are available for 895 birds.  Considering different combinations of annotation information and models, original ssGBLUP, haplotype-based ssGHBLUP, and four extended ssGBLUP incorporating genomic annotation models were evaluated.  Based on the genomic annotation (GRCg6a) of chickens, 3 155 524 and 94 837 SNPs were mapped to genic and exonic regions, respectively.  Extended ssGBLUP using genic/exonic SNPs outperformed other models with respect to predictive ability in 15 out of 23 traits, and their advantages ranged from 2.5 to 6.1% compared with original ssGBLUP.  In addition, to further enhance the performance of genomic prediction with imputed WGS data, we investigated the genotyping strategies of reference population on ssGBLUP in the chicken population.  Comparing two strategies of individual selection for genotyping in the reference population, the strategy of evenly selection by family (SBF) performed slightly better than random selection in most situations.  Overall, we extended genomic prediction models that can comprehensively utilize WGS data and genomic annotation information in the framework of ssGBLUP, and validated the idea that properly handling the genomic annotation information and WGS data increased the predictive ability of ssGBLUP.  Moreover, while using WGS data, the genotyping strategy of maximizing the expected genetic relationship between the reference and candidate population could further improve the predictive ability of ssGBLUP.  The results from this study shed light on the comprehensive usage of genomic annotation information in WGS-based single-step genomic prediction.

Pakchoi (Brassica campestris L. ssp. chinensis) is an important leafy vegetable.  Various light spectra, especially red and blue light, play vital roles in the regulation of nitrate metabolism.  Information on the effects of red and blue light on nitrate metabolism at the transcriptome level in pakchoi is still limited, so this study used RNA sequencing technology to explore this molecular mechanism.  Through pairwise comparisons with white LED light, 3 939 and 5 534 differentially expressed genes (DEGs) were identified under red and blue light, respectively.  By Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses, these unigenes were found to be involved in nitrate assimilation, plant–pathogen interaction, biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis.  The differential effects of light spectra on the nitrate concentration and metabolism-related enzyme activities were also confirmed at the physiological level.  Several signal transduction modules, including Crys/Phys-COP1-HY5/HY5-like, were found to be involved in red and blue light-induced nitrate metabolism, and the transcript levels for this complex were consistent with the observed degree of nitrate assimilation.  The expression patterns of 15 randomly selected DEGs were further validated using qPCR.  Taken together, the results of this study could help improve our understanding of light spectrum-regulated nitrate metabolism in pakchoi at the transcriptome level.

Mechanized grain harvest of maize becomes increasingly important with growing land plot size in Northeast China.  Grain moisture is an important factor affecting the performance of mechanized grain harvest.  However, it remains unclear what influences grain dehydration rate.  In this study, maize grain dehydrating process was investigated in a two-year field experiment with five hybrids under two planting densities in 2017 and 2018.  It was found that damaged-grain ratio was the main factor affecting mechanized harvest quality, and this ratio was positively correlated with grain moisture content at harvest (R²=0.6372, P<0.01).  To fulfill the national standard of <5% damaged-grain ratio for mechanized grain harvest, the optimal maize grain moisture content was 22.3%.  From silking to physiological maturity, grain dehydrating process was mostly dependent on the thermal time (growing degree days, GDDs) (r=–0.9412, P<0.01).  The average grain moisture content at physiological maturity was 29.4%.  Thereafter, the linear relationship between GDDs and grain moisture still existed, but the correlation coefficient became smaller (r=–0.8267, P<0.01).  At this stage, grain dehydrating process was greatly affected by genotypes.  Grain dehydrated faster when a hybrid has a smaller husk area (r=0.6591, P<0.05), larger ear angle (r=–0.7582, P<0.05), longer ear peduncle (r=–0.9356, P<0.01) and finer ear (r=0.9369, P<0.01).  These parameters can be used for breeders and farmers to select hybrids suitable for mechanized grain harvest.  

MicroRNAs (miRNAs) are small (ca. 20–24 nucleotides) non-coding RNAs that have recently been recognized as key post-transcriptional modulators of gene expression; and they are involved in many biological processes in plants, such as root growth and development.  The miRNAs regulate root elongation, lateral root (LR) formation and adventitious root (AR) development in response to hormone signaling, nutrient uptake and biotic/abiotic stress.  This review provides multiple perspectives on the involvement of miRNAs in regulating root growth and development in plants.  We also discuss several crucial mechanisms of miRNAs, their relationships with transcription factors and the target gene-mediated hormone signaling interactions in the regulation of root growth and development.

Nitrate reductase (NR) is a key enzyme for nitrogen assimilation in plants, and its activity is regulated by posttranslational phosphorylation.  To investigate the effects of dephosphorylation of the NIA1 protein on the growth and the physiological and biochemical characteristics of rice under different forms of nitrogen supplies, the phenotypes, nitrogen metabolism and reactive oxygen metabolism were measured in NIA1 phosphorylation site-directed mutant lines (S532D and S532A), an OsNia1 over-expression line (OE) and Kitaake (wild type, WT).  Compared with WT and OE, S532D and S532A have stronger nitrogen assimilation capacities.  When ammonium nitrate served as the nitrogen source, the plant heights, dry weights of shoots and chlorophyll (Chl) contents of S532D and S532A were lower than those of the WT and OE, whereas hydrogen peroxide (H₂O₂), malondialdehyde (MDA) and nitrite contents were higher.  When potassium nitrate served as the nitrogen source, the plant heights, dry weights of shoots and Chl contents of S532D and S532A were higher than those of the WT and OE, there were no significant differences in the contents of H₂O₂ and MDA in the leaves of the test materials, and the difference in nitrite contents among different lines decreased.  When ammonium sulfate served as the nitrogen source, there were no significant differences in the physiological indexes of the test materials, except NR activity.  Compared with ammonium nitrate and ammonium sulfate, the content of NH₄⁺-N in the leaves of each plant was lower when potassium nitrate was used as the nitrogen source.  The qPCR results showed that OsGS and OsNGS1 were negatively regulated by downstream metabolites, and OsNrt2.2 was induced by nitrate.  In summary, when ammonium nitrate served as the nitrogen source, the weak growth of NIA1 phosphorylation site-directed mutant lines was due to the toxicity caused by the excessive accumulation of nitrite.  When potassium nitrate served as the nitrogen source, the assimilation rates of nitrate, nitrite and ammonium salt were accelerated in NIA1 phosphorylation site-directed mutant lines, which could provide more nitrogen nutrition and improve the tolerance of rice to ammonium nitrogen deficiency.  These results could provide a possible method to improve the efficiency of nitrogen utilization in rice under low-nitrogen conditions.  

In China, the traditional early and late season double rice (DR) system is declining accompanied by the fast increase of two newly developed cropping systems: ratoon rice (RR) and rice–crawfish (RC).  Three methodologies: economic analysis, emergy evaluation and life cycle assessment (LCA) were employed to evaluate the economics and sustainability of this paddy cropping system change.  Economic analysis indicated that the income and profit of the RC system were far larger than those of RR and DR.  The income to costs ratio of RR and RC increased by 25.5 and 122.7% compared with that of DR, respectively.  RC had the highest emergy input thanks to increasing irrigation water, electricity, juvenile crawfish and forage input while RR showed a lower total emergy and nonrenewable emergy input, such as irrigation water, electricity, fertilizers and pesticides than DR.  The environmental loading ratios decreased by 16.7–50.4% when cropping system changed from DR to RR or from DR to RC while the emergy sustainability indexes increased by 22.6–112.9%.  The life cycle assessment indicated lower potential environmental impacts of RR and RC, whose total environmental impact indexes were 35.0–61.0% lower than that of DR.  Grain yield of RR was comparable with that of DR in spite of less financial and emergy input of RR, but RC had a much lower grain yield (a 53.6% reduction compared to DR).  These results suggested that RR is a suitable cropping system to achieve the food security, economic and environmental goals.

Understanding the characteristics and influences of various factors on phosphorus (P) fractions is of significance for promoting the efficiency of soil P.  Based on long-term experiments on black soil, fluvo-aquic soil, and loess soil, which belong to Phaeozems, Cambisols, and Anthrosols in the World Reference Base for Soil Resources (WRB), respectively, five fertilization practices were selected and divided into three groups: no P fertilizer (CK/NK), balanced fertilizer (NPK/NPKS), and manure plus mineral fertilizer (NPKM).  Soil inorganic P (Pi) fractions and soil properties were analyzed to investigate the characteristics of the Pi fractions and the relationships between Pi fractions and various soil properties.  The results showed that the proportion of Ca₁₀-P in the sum of total Pi fractions was the highest in the three soils, accounting for 33.5% in black soil, 48.8% in fluvo-aquic soil, and 44.8% in loess soil.  Long-term fertilization practices resulted in periodic changes in soil Pi accumulation or depletion.  For black soil and fluvo-aquic soil, the Pi accumulation was higher in the late period (10–20 years) of fertilization than in the early period (0–10 years) under NPK/NPKS and NPKM, whereas the opposite result was found in loess soil.  The Pi accumulation occurred in all Pi fractions in black soil; mainly in Ca₈-P, Fe-P, and Ca₁₀-P in fluvo-aquic soil; and in Ca₂-P, Ca₈-P, and O-P in loess soil.  Under CK/NK, the soil Pi was depleted mainly in the early period in each of the three soils.  In addition to the labile Pi (Ca₂-P) and moderately labile Pi (Ca₈-P, Fe-P, Al-P), the Ca₁₀-P in black soil and fluvo-aquic soil and O-P in loess soil could also be used by crops.  Redundancy analysis showed that soil properties explained more than 90% of the variation in the Pi fractions in each soil, and the explanatory percentages of soil organic matter (SOM) were 43.6% in black soil, 74.6% in fluvo-aquic, and 38.2% in loess soil.  Consequently, decisions regarding the application of P fertilizer should consider the accumulation rate and the variations in Pi fractions driven by soil properties in non-acidic soils.

YABBY genes are plant-specific transcription factors (TF) that function in plant growth and development.  To investigate the functions of the YABBY genes in plants’ stress tolerance, we analyzed the YABBY genes in foxtail millet (Setaria italica) and investigated their functions on plant growth and responses to different stresses.  Eight YABBY genes were identified on five chromosomes. These genes showed strong relationships with YABBY genes in other monocot species.  Phylogenetical SiYABs were classified into four clades: FIL/YAB3, YAB2, INO, and CRC.  No monocot YABBY member was classified into the YAB5 clade.  Four conserved motifs were identified and motif 1 constituted the YABBY domain, whereas motifs 2 and 3 formed the C2-C2 region. SiYAB genes were highly expressed in reproductive tissues.  Among all the SiYABs, SiDL was selected to be overexpressed in Arabidopsis thaliana to check the functions of the YABBY genes.  Overexpression of SiDL in Arabidopsis thaliana caused delayed flowering, leaf curling, and reduced seed size.  In addition, SiDL acted as a negative regulator in plant response to salt stress. Our study provides information to assist the study of YABBY gene function in S. italica.

Plant photosynthesis assimilates CO₂ from the atmosphere, and CO₂ diffusion efficiency is mainly constrained by stomatal and mesophyll resistance.  The stomatal and mesophyll conductance of plants are sensitive to abiotic stress factors, which affect the CO₂ concentrations at carboxylation sites to control photosynthetic rates.  Early studies conducted relevant reviews on the responses of stomatal conductance to the environment and the limitations of mesophyll conductance by internal structure and biochemical factors.  However, reviews on the abiotic stress factors that systematically regulate plant CO₂ diffusion are rare.  Therefore, in this review, the rapid and long-term responses of stomatal and mesophyll conductance to abiotic stress factors (such as light intensity, drought, CO₂ concentration and temperature) and their physiological mechanisms are summarized.  Finally, future research trends are also investigated.

The wheat aphid, Sitobion miscanthi, is one of the most destructive pests of wheat plants in the temperate regions of China.  Little is known about the genetic structure evolution of  the different geographic populations of S. miscanthi with its migration.  In this study, we investigated the population genetic structure and demographic history of S. miscanthi by analysing 18 geographical populations across China using one mitochondrial gene, COI; one nuclear gene, EF-1α; and two endosymbiont Buchnera genes, gnd and trpA.  Analysis of data from the various groups showed high haplotype diversity and low nucleotide variation.  SAMOVA analysis did not find a correlation between genetic distance and geographic distance.  However, areas with high population diversity exhibited high haplotype diversity.  Therefore, we speculate that there are two main natural migration pathways of S. miscanthi in China.  One is from Yunnan to the Sichuan Basin, and the other is from Wuhan, Xinyang and Jiaodong Peninsula areas to the northwest.  Based on this hypothesis, we inferred that these aphid populations appear first in the southwestern and southern regions and spread to the north with the help of the southeastern and southwestern monsoons, which occur in spring and summer.  In autumn, the aphids spread southward with the northeastern and northwestern monsoons.

Genetic linkage maps are important for quantitative trait locus (QTL) and marker-assisted selection breeding.  The wolfberry (Lycium spp.) is an important food and traditional medicine in China.  However, few construction genetic linkage maps have been reported because of the lack of genomic and genetic resources.  In this study, a population of 89 F₁ seedings was derived from a cross between two heterozygous parents, L. chinense var. potaninii ‘BF-01’ (female) and L. barbarum var. auranticarpum ‘NH-01’ (male), in order to construct a genetic linkage map using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers based on the double pseudo-test cross mapping strategy.  The resulting genetic map consisted of 165 markers (74 AFLPs and 91 SSRs) distributed across 12 linkage groups and spanned a total length of 557.6 cM with an average distance of 3.38 cM between adjacent markers.  The 12 linkage groups contained 3 to 21 markers and ranged in length from 8.6 to 58.3 cM.  Twenty-nine segregated markers distributed in the map were mainly located on LG4 and LG9 linkage groups at P<0.05.  This is the first linkage map of Lycium species using SSR and AFLP markers, which can serve as basis for improving genes and selective breeding of the genome assembly.

Nitrate reductase (NR) is an important enzyme for nitrate assimilation in plants, and post-translational phosphorylation regulates NR activity.  To evaluate the impact of the dephosphorylation of nitrate reductase 1 (NIA1) protein on NR activity, nitrogen metabolism and plant growth, NIA1 phosphorylation site directed mutant lines (S532D and S532A) and an OsNia1 over-expression line (OE) were constructed, and the phenotype, NIA1 protein and its phosphorylation level, NR activity, nitrate metabolism and reactive oxygen metabolism of the transgenic lines were analysed.  Exogenous NIA1 protein was not phosphorylated in S532D and S532A mutant lines, and their NR activities, activity states of NR and assimilation efficiencies of NO3–-N were higher than those in Kitaake (WT) and OE.  The changes in these physiological and biochemical indexes in the OE line were less than in S532D and S532A compared to WT.  These results suggest that the removal of transcriptional level control had little effect on nitrogen metabolism, but the removal of post-translational modification had a profound effect on it.  With the removal of NIA1 phosphorylation and the improvement in the nitrate assimilation efficiency, the plant height and chlorophyll content of S532D and S532A decreased and the hydrogen peroxide and malondialdehyde contents of rice seedlings increased, which may be related to the excessive accumulation of nitrite as an intermediate metabolite.  These results indicated that the phosphorylation of NR may be a self-protection mechanism of rice.  The reduced phosphorylation level of nitrate reductase improved the assimilation of nitrate, and the increased phosphorylation level reduced the accumulation of nitrite and prevented the toxic effects of reactive oxygen species in rice. 

The panicle architecture and grain size of rice affect not only grain yield but also grain quality, especially grain appearance. The erect-panicle (EP) trait controlled by the qpe9-1/dep1 allele has been widely used in high-yielding japonica rice breeding, but usually accompanied with moderate appearance of milled rice. The null gs9 allele shows a good potential for improving grain shape and appearance. However, GS9 and qPE9-1/DEP1 loci are tightly linked, and their interaction is unclear, which obviously restricts their utilization in modern rice breeding. In the present study, comparative analyses of protein and mRNA levels revealed that GS9 and qPE9-1 function independently. Three near-isogenic lines (NILs) carrying various allelic combinations of these two loci, NIL (gs9/qpe9-1), NIL (GS9/qPE9-1) and NIL (gs9/qPE9-1), in the EP japonica cultivar 2661 (GS9/qpe9-1) background were developed for genetic interaction analysis. GS9 and qPE9-1 had additive effects on determining grain size, and the null gs9 allele could decrease grain chalkiness and improve grain appearance without affecting plant and panicle architecture in EP japonica cultivars. Additionally, introgression lines (ILs) developed in another released EP japonica cultivar Wuyujing 27 (WYJ27) background showed the same additive effect and the feasibility of utilizing the gs9 allele to improve grain appearance quality in high-yielding EP cultivars. This study provides an effective strategy for rice breeders to improve rice grain appearance in EP japonica and related cultivars.