Type I interferon (IFN-I) provides an important first line to protect avian species against pathogens invasion. IFN regulatory factor 7 (IRF7) has been identified as the most important regulator for both DNA and RNA virus-induced IFN-I production in chickens. Although four splicing variants of IRF7 have been identified in mammals, it is still unclear whether alternative splicing patterns and the function of IRF7 isoform(s) exist in chickens. In this study, we reported a novel short transcript isoform of chicken IRF7 (chIRF7), termed chIRF7-iso, which contained an intact N-terminal DNAbinding domain (DBD) and 14 amino acids different from chIRF7 in the C-terminal. Overexpression of chIRF7 in chicken leghorn male hepatocellular (LMH) cells activated the IFN-β promoter and significantly inhibited Newcastle disease virus (NDV) and fowl adenovirus serotype 4 (FAdV-4) replication. Conversely, overexpression of chIRF7-iso blocked the IFN-β promoter activity and was favorable for NDV and FAdV-4 replication in vitro. Collectively, our results confirm that a novel chIRF7 isoform-mediated negative regulates IFN-β production, which will contribute to understanding the role of chIRF7 in innate antiviral response in chicken.

Skeletal muscle regeneration is a complex process where various cell types and cytokines are involved.  Single-cell RNA-sequencing (scRNA-seq) provides the opportunity to deconvolute heterogeneous tissue into individual cells based on their transcriptomic profiles.  Recent scRNA-seq studies on mouse muscle regeneration have provided insights to understand the transcriptional dynamics that underpin muscle regeneration.  However, a database to investigate gene expression profiling during skeletal muscle regeneration at the single-cell level is lacking.  Here, we collected over 105 000 cells at 7 key regenerative time-points and non-injured muscles and developed a database, the Single-cell Skeletal Muscle Regeneration Database (SCSMRD).  SCSMRD allows users to search the dynamic expression profiles of genes of interest across different cell types during the skeletal muscle regeneration process.  It also provides a network to show the activity of regulons in different cell types at different time points.  Pesudotime analysis showed the state changes trajectory of muscle stem cells (MuSCs) during skeletal muscle regeneration.  This database is freely available at https://scsmrd.fengs-lab.com.

Grain filling is the physiological process for determining the obtainment of yield in cereal crops.  The grain-filling characteristics of 50 maize brand hybrids released from 1964 to 2014 in China were assayed across multiple environments.  We found that the grain-filling duration (54.46%) and rate (43.40%) at the effective grain-filling phase greatly contributed to the final performance parameter of 100-kernel weight (HKW).  Meanwhile, along with the significant increase in HKW, the accumulated growing degree days (GDDs) for the actual grain-filling period duration (AFPD) among the selected brand hybrids released from the 1960s to the 2010s in China had a decadal increase of 23.41°C d.  However, there was a decadal increase of only 19.76°C d for GDDs of the days from sowing to physiological maturity (DPM), which was also demonstrated by a continuous decrease in the ratio between the days from sowing to silking (DS) and DPM (i.e., from 53.24% in the 1960s to 49.78% in the 2010s).  In contrast, there were no significant changes in grain-filling rate along with the release years of the selected hybrids.  Moreover, the stability of grain-filling characteristics across environments also significantly increased along with the hybrid release years.  We also found that the exotic hybrids showed a longer grain-filling duration at the effective grain-filling phase and more stability of the grain-filling characteristics than those of the Chinese local hybrids.  According to the results of this study, it is expected that the relatively longer grain-filling duration, shorter DS, higher grain-filling rate, and steady grain-filling characteristics would contribute to the yield improvement of maize hybrids in the future.  

The crown root system is the most important root component in maize at both the vegetative and reproductive stages.  However, the genetic basis of maize crown root traits (CRT) is still unclear, and the relationship between CRT and aboveground agronomic traits in maize is poorly understood.  In this study, an association panel including 531 elite maize inbred lines was planted to phenotype the CRT and aboveground agronomic traits in different field environments.  We found that root traits were significantly and positively correlated with most aboveground agronomic traits, including flowering time, plant architecture and grain yield.  Using a genome-wide association study (GWAS) coupled with resequencing, a total of 115 associated loci and 22 high-confidence candidate genes were identified for CRT.  Approximately one-third of the genetic variation in crown root was co-located with 46 QTLs derived from flowering and plant architecture.  Furthermore, 103 (89.6%) of 115 crown root loci were located within known domestication- and/or improvement-selective sweeps, suggesting that crown roots might experience indirect selection in maize during domestication and improvement.  Furthermore, the expression of Zm00001d036901, a high-confidence candidate gene, may contribute to the phenotypic variation in maize crown roots, and Zm00001d036901 was selected during the domestication and improvement of maize.  This study promotes our understanding of the genetic basis of root architecture and provides resources for genomics-enabled improvements in maize root architecture.

High yields of wheat are mainly obtained through a high level of nitrogen and irrigation supplementation.  However, excessive nitrogen and irrigation supplication increase the risk of lodging.  The main objectives of this work were to clarify the capacity of lodging resistance of wheat in response to nitrogen and irrigation, as well as to explore the effective ways of improving lodging resistance in a high-yield wheat cultivar. In this study, field experiments were conducted in the 2015–2016 and 2016–2017 growing seasons.  A wheat cultivar Jimai 22 (JM22), which is widely planted in the northern of Huang-Huai winter wheat region, was grown at Tai’an, Shandong Province, under three nitrogen rates and four irrigation treatments.  The lodging risk was increased with increased nitrogen rate, as indicated by increasing lodging index (LI) and lodging rate across both growing seasons.  With nitrogen increasing, the plant height, the basal internode length and the center of gravity height, which were positively correlated with LI, increased significantly.  While the density of the basal 2nd internode (for culm and leaf sheath) and cell wall component contents, which were negatively correlated with LI, decreased conspicuous along with nitrogen increased.  Increasing irrigation supplementation increased the 2nd internode culm wall thickness, breaking strength and leaf sheath density within limits which increased stem strength.  Among the treatments, nitrogen application at a rate of 240 kg ha^–1 and irrigation application at 600 m3 ha^–1 at both the jointing and anthesis stages resulted in the highest yield and strongest stem.  A suitable plant height ensures sufficient biomass for high yield, and higher stem stiffness, which was primarily attributed to thicker culm wall, greater density of the culm and leaf sheaths and higher cell wall component contents are the characteristics that should be taken into account to improving wheat lodging resistance.

   Straw return is an important management tool for tackling and promoting soil nutrient conservation and improving crop yield in Huang-Huai-Hai Plain, China. Although the incorporation of maize straw with deep plowing and rotary tillage practices are widespread in the region, only few studies have focused on rotation tillage. To determine the effects of maize straw return on the nitrogen (N) efficiency and grain yield of winter wheat (Triticum aestivum L.), we conducted experiments in this region for 3 years. Five treatments were tested: (i) rotary tillage without straw return (RT); (ii) deep plowing tillage without straw return (DT); (iii) rotary tillage with total straw return (RS); (iv) deep plowing tillage with total straw return (DS); (v) rotary tillage of 2 years and deep plowing tillage in the 3rd year with total straw return (TS). Treatments with straw return increased kernels no. ear^–1, thousand-kernel weight (TKW), grain yields, ratio of dry matter accumulation post-anthesis, and nitrogen (N) efficiency whereas reduced the ears no. ha^–1 in the 2011–2012 and 2012–2013 growing seasons. Compared with the rotary tillage, deep plowing tillage significantly increased the grain yield, yield components, total dry matter accumulation, and N efficiency in 2013–2014. RS had significantly higher straw N distribution, soil inorganic nitrogen content, and soil enzymes activities in the 0–10 cm soil layer compared with the DS and TS. However, significantly lower values were observed in the 10–20 and 20–30 cm soil layers. TS obtained approximately equal grain yield as DS, and it also reduced the resource costs. Therefore, we conclude that TS is the most economical method for increasing grain yield and N efficiency of winter wheat in Huang-Huai-Hai Plain.

    Increasing leaf photosynthesis per area (A) is of great importance to achieve yield further improvement. The aim of this study was to exploit varietal difference in A and its correlation with specific leaf weight (SLW). Twelve rice cultivars, including 6 indica and 6 japonica varieties, were pot-grown under two N treatments, low N (LN) and sufficient N (SN). Leaf photosynthesis and related parameters were measured at tillering stage. Compared with LN treatment, A, stomatal conductance (g_s), mesophyll conductance (g_m), leaf N content (Narea), and chlorophyll content were significantly improved under SN treatment, while SLW and photosynthetic N use efficiency (PNUE) were generally decreased. Varietal difference in A was positively related to both gs and gm, but not related to Narea. This resulted in a low PNUE in high Narea leaves. Varietal difference in PNUE was generally negatively related to SLW. Response of PNUE to N supply varied among different rice cultivars, and interestingly, the decrease in PNUE under SN was negatively related to the decrease in SLW. With a higher N_area, japonica rice cultivars did not show a higher A than indica rice cultivars because of possession of high-SLW leaves. Therefore, varietal difference in A was not related to N_area, and SLW can substantially interfere with the correlation between A and N_area. These findings may provide useful information for rice breeders to maximize A and PNUE, rather than over reliance on N_area as an indicator of photosynthetic performance.

    Soil loss due to crop harvesting (SLCH) is a soil erosion process that significantly contributes to soil degradation in croplands. However, little is known about soil nutrient losses caused by SLCH and its environmental impacts. In the North China Plain area, we measured the losses of soil organic carbon (SOC) and nitrogen as well as phosphorus due to SLCH and assessed their relationship with soil particle size composition, agronomic practices and soil moisture content. Our results show that the losses by harvesting potato of SOC, total nitrogen (TN), available nitrogen (AN), available phosphorus (AP) and total phosphorus (TP) were 1.7, 1.8, 1.8, 15.9 and 14.1 times compared by harvesting sweet potato, respectively. The variation of SOC, N and P loss by SLCH are mainly explained by the variation of plant density (PD) (17–50%), net mass of an individual tuber (M_crop/p) (16–74%), soil clay content (34–70%) and water content (19–46%). Taking into account the current sewage treatment system and the ratio of the nutrients adhering to the tubers during transportation from the field (NTR_P/SP), the loss of TN and TP by harvesting of potato and sweet potato in the North China Plain area amounts to 3% N and 20% P loads in the water bodies of this region. The fate of the exported N and P in the sewage treatment system ultimately controls the contribution of N and P to the pollution of lakes and rivers. Our results suggest that a large amount of SLCH-induced soil nutrient export during transportation from the field is a potential pollutant source for agricultural water for vast planting areas of tuber crops in China, and should not be overlooked.

   Winter chill is essential for the growth and development of deciduous species. To understand the relationship between accumulated chilling hours during endodormancy and blooming and fruit shape development, we controlled chilling hours and investigated their effects on blooming date and fruit shape of peaches. The results showed that the number of days to full bloom date and the heat requirement for blooming were negatively correlated with accumulated chilling hours. Accumulated chilling hours were significantly negatively correlated with fruit shape index and fruit tip lengths, suggesting that the number of chilling hours affect the fruit shape development. Fewer accumulated chilling hours may be the major reason for longer fruit shape and protruding fruit tips. In conclusion, our results indicate specifically that decreased winter chilling hours can delay the bloom date and may lead to aberrant fruit shape development in peaches. Our study provides preliminary insights into the response of temperate fruit species to global climate change.

Study on soil phosphorus (P) fraction is an important aspect in probing the mechanisms of soil P accumulation in farmland and mitigating its losing risk to the environment. We used a sequential extraction method to evaluate the impacts of long-term fertilization and straw incorporation on inorganic, organic, and residual P (Pi, Po, and Pre) fractions in the plow layer (0–20 cm) of acidic paddy soil in southern China. The experiment comprised of six treatments: (i) no fertilizer control (CK); (ii) straw incorporation and green manure (SG); (iii) nitrogen and P fertilizer (NP); (iv) NP+SG; (v) NP+K fertilizer (NPK); and (vi) NPK+SG. The results showed that, compared to the initial total soil P content (TSP, 600 mg kg–1 in 1990), long-term (20 years) combined continuous P fertilizer and SG significantly increased P accumulation (by 13–20%) while single fertilization (39.3 kg P ha–1 yr–1) could maintain soil P status at the most. The average soil P fractions comprised of extractable Pi, Po, and Pre by 51.7, 33.4, and 14.9% in total soil P, respectively. With comparison of no fertilizer addition (CK), long-term single fertilization significantly (P<0.05) increased the accumulation of NaHCO3 –, NaOH–, and HCl– extractable Pi fractions accounting for two- to three-fold, while SG increased the accumulation of NaHCO3 – and NaOH– extractable Pi and Po accounting for 12–60%. Though the mobilization of Pre fractions was not significant (P>0.05), our data indicate that SG may partially substitute for fertilizer P input and minimizing soil P accumulation and subsequent environmental risk in the subtropical paddy soil.

Based on climate data from 254 meteorological stations, this study estimated the effects of climate change on rice planting boundaries and potential yields in the southern China during 1951-2010. The results indicated a significant northward shift and westward expansion of northern boundaries for rice planting in the southern China. Compared with the period of 1951-1980, the average temperature during rice growing season in the period of 1981-2010 increased by 0.4°C, and the northern planting boundaries for single rice cropping system (SRCS), early triple cropping rice system (ETCRS), medium triple cropping rice system (MTCRS), and late triple cropping rice system (LTCRS) moved northward by 10, 30, 52 and 66 km, respectively. In addition, compared with the period of 1951-1980, the suitable planting area for SRCS was reduced by 11% during the period of 1981-2010. However, the suitable planting areas for other rice cropping systems increased, with the increasing amplitude of 3, 8, and 10% for ETCRS, MTCRS and LTCRS, respectively. In general, the light and temperature potential productivity of rice decreased by 2.5%. Without considering the change of rice cultivars, the northern planting boundaries for different rice cropping systems showed a northward shift tendency. Climate change resulted in decrease of per unit area yield for SRCS and the annual average yields of ETCRS and LTCRS. Nevertheless, the overall rice production in the entire research area showed a decreasing trend even with the increasing trend of annual average yield for MTCRS.

Effects of different polarity solvents on the ultrastructure and chemical composition of cuticular wax in Pingguoli pear as well as their bioactive role against Alternaria alternate were studied and the results showed that the highest wax content was extracted with chloroform, and its wax content was up to 322.2 μg cm-2. Long-chain fatty acids predominated in menthol extracts and n-alkanes were predominant in wax extracted with ether, chloroform and n-hexane. Pingguoli pear fruit surface was covered by a smooth and amorphous wax layer with small, scattered crystal. The morphology of recrystallized wax in vitro after removal with different solvents was not similar to that of the intact fruit surface. Removal of cuticular wax with various solvents significantly enhanced A. alternata infection, except for wax removed by methanol. The solvent extracts of methanol and chloroform stimulated the spore germination and mycelium growth of A. alternata, but the ether and n-hexane extracts showed antifungal activity.

Two wheat cultivars (Triticum aestivum L.) were used to evaluate the effects of post-anthesis severe water deficit (SD) on starch content and granule size distribution and their relations with ethylene and spermidine (Spd). Comparison to the well-watered (WW) treatment, SD led to lower Spd and higher 1-aminocylopropane-1-carboxylic acid (ACC) concentrations and ethylene evolution rate (EER) in grains at the critical stage of forming starch granules. Application of Spd or aminoethoxyvinylglycine (AVG) significantly reduced ACC concentration and EER and increased Spd concentration, while ethephon or methylglyoxal-bis (MGBG) had an opposite impact. The volume and surface area distribution of starch granules showed a bimodal curve, while the number distribution exhibited a unimodal curve. SD caused a marked drop in grain weight, grain number and starch content, also led to a significant reduction in the proportion (both by volume and by surface area) of B-type starch granules (<10 μm), with an increase in those of A-type starch granules (>10 μm). Application of Spd or AVG increased the proportion (both by volume and by surface area) of B-type starch granules under SD. Correlation analysis suggested that ethylene and Spd showed an antagonism relation in the formation of B-type granules. These results suggested that it would be good for the formation of B-type starch granules to have the physiological traits of higher Spd and lower ACC concentrations and ethylene emission under SD.

The importance of microRNA (miRNA) at the post-transcriptional regulation level has recently been recognized in both animals and plants. In recent years, many studies focused on miRNA target identification and functional analysis. However, little is known about the transcription and regulation of miRNAs themselves. In this study, the transcription start sites (TSSs) for 11 miRNA primary transcripts of soybean from 11 miRNA loci (of 50 loci tested) were cloned by a 5´ rapid amplification of cDNA ends (5´ RACE) procedure using total RNA from 30-d-old seedlings. The features consistent with a RNA polymerase II mechanism of transcription were found among these miRNA loci. A position weight matrix algorithm was used to identify conserved motifs in miRNA core promoter regions. A canonical TATA box motif was identified upstream of the major start site at 8 (76%) of the mapped miRNA loci. Several cis-acting elements were predicted in the 2 kb 5´ to the TSSs. Potential spatial and temporal expression patterns of the miRNAs were found. The target genes for these miRNAs were also predicted and further elucidated for the potential function of the miRNAs. This research provides a molecular basis to explore regulatory mechanisms of miRNA expression, and a way to understand miRNAmediated regulatory pathways and networks in soybean.

The reverse genetics for classical swine fever virus (CSFV) is currently based on the transfection of in vitro transcribed RNA from a viral genomic cDNA clone, which is inefficient and time-consuming. This study was aimed to develop an improved method for rapid recovery of CSFV directly from cloned cDNA. Full-length genomic cDNA from the CSFV Shimen strain, which was flanked by a T7 promoter, the hepatitis delta virus ribozyme and T7 terminator sequences, was cloned into the lowcopy vector pOK12, producing pOKShimen-RzT . Direct transfection of pOKShimen-RzT into PK/T7 cells, a PK-15- derived cell line stably expressing bacteriophage T7 RNA polymerase, allowed CSFV to be rescued rapidly and efficiently, i.e., at least 12 h faster and 31.6-fold greater viral titer when compared with the in vitro transcription-based rescue system. Furthermore, the progeny virus rescued from PK/T7 cells was indistinguishable, both in vitro and in vivo, from its parent virus and the virus rescued from classical reverse genetics. The reverse genetics based on intracellular transcription is efficient, convenient and cost-effective. The PK/T7 cell line can be used to rescue CSFV directly from cloned cDNA and it can also be used as an intracellular transcription and expression system for studying the structure and function of viral genes.

Nitric oxide (NO) is a key signaling molecule in different physiological processes of plants, including programmed cell death (PCD). PCD of tillers plays an important role in surviving which are major components of grain yield. PCD was triggered in wheat leaves of main stem and tillers by NO content under different nitrogen treatments. In wheat, NO could be synthesized endogenously by nitrate reductase (NR). As an inducible enzyme, NR activity was closely related to substrate concentration. Therefore, different nitrogen levels would change NR activity and NO production. The objective of this study was to determine the effects of NR activity, NO production, and the correlation between them on different tillers growth, development, senescence, and kernel protein content under different nitrogen levels. Field-experiments were conducted in 2009-2011 growing seasons, using two wheat cultivars with different spike-types. Results showed that for main stem and primary tillers, NR activity and NO content reached high level at heading stage, while for secondary tiller, the level of NR activity was low, but NO content was high in the present research. The NO synthesis depending on NR activity in wheat leaves was significant in the early growing stage, but the NO synthesis weakened with the progress of growing period. NO was related to the senescence of wheat leaves, but PCD was more sensitive to marked changes of NO content than NO content itself. N application had marked influence on the aging process of primary tiller, while had little influence on that of main stem and secondary tiller. Moreover, N fertilizer application could increase spike rate and protein content of primary tiller by N fertilizer application.

The spatiotemporal characteristics of hydrothermal resources in southern rice production area of China have changed under the background of climate change, and this change would affect the effectiveness of hydrothermal resources during local rice growing period. According to the cropping system subdivision in southern rice production area of China during 1980s, this study used climate data from 254 meteorological stations and phonological data from 168 agricultural observation stations in the south of China, and adopted 6 international evaluation indices about the effectiveness of hydrothermal resources to analyze the temporal and spatial characteristics of hydrothermal resources during the growing period of single cropping rice system and double cropping rice system for 16 planting zones in the whole study area. The results showed that: in southern rice production area of China, the effectiveness of thermal resources of single cropping rice area (SCRA) was less than that of double cropping rice area (DCRA), whereas the effectiveness of thermal resources of both SARA and DCRA showed a decreasing trend. The index value of effective precipitation satisfaction of SCRA was higher than that of DCRA, nevertheless the index value of effective precipitation satisfaction of both SCRA and DCRA showed a decreasing trend. There was a significant linear relationship between effective thermal resource and water demand, likely water demand increased by 18 mm with every 100°C d increase of effective heat. Effective precipitation satisfaction index (EPSI) showed a negative correlation with effective heat, yet showed a positive correlation with effective precipitation. EPSI reduced by 1% when effective heat resource increased by 125°C d. This study could provide insights for policy makers, land managers or farmers to improve water and heat resource uses and rationally arrange rice production activities under global climate change condition.

The erythropoietin receptor (EPOR) has shown to play an important role in fetal survival by promoting the maturation of red blood cells in many studies of uterine capacity and litter size in swine. In this study, we screened the porcine EPOR gene for mutations and identified five single nucleotide polymorphisms (SNPs): g.705G>T in intron 1, g.2 373C>T in intron 4, and g.2 882C>T, g.3 035A>G, and g.3 132A>T in intron 6. We then genotyped 247 Beijing Black (BB) sows and compared the polymorphism data with the litter sizes of 1 375 parities among the sows. At first parity, there was no association of g.2 882C>T and g.3 132A>T with litter sizes. However, the CT sows in g.2 882C>T had 2.13 higher total number born (TNB) (P<0.01) and 1.81 higher number born alive (NBA) (P<0.01) than the CC sows and the heterozygous sows in g.3 132A>T had the highest litter size when compared to the two homozygotes for the later parities (P<0.05). In the g.3 035A>G SNP, for the later parities, the TNB of the sows with the GG genotype was 3.81 higher (P<0.01) and the NBA was 2.75 higher (P<0.01) than that with the AA genotype but no difference at first parity. The G allele of the EPOR g.705G>T SNP was associated with a greater litter size at both the first parity (P<0.05) and later parities (P<0.01). Furthermore, we determined the allele frequencies for this SNP among five Chinese indigenous pig breeds (Erhualian, Laiwu Black, Meishan, Min, and Rongchang) and three western commercial pig breeds (Duroc, Landrace, and Large White). The G allele of the EPOR g.705G>T SNP was significantly more common in the more prolific Chinese breeds. These results indicated that the EPOR could be an important candidate gene for litter size and g.705G>T can serve as a useful genetic marker for improving litter size in both first and later parities in swine.

Soybean root and stem rot caused by Phytophthora sojae is a destructive disease worldwide. Using genetic resistance is an important and major component in the integrated pest management of this disease. To understand molecular mechanisms of root and stem rot resistance in soybeans, the gene and protein expression in hypocotyls and stems of variety Suinong 10 carrying resistance genes Rps1a and Rps2 was investigated by using mRNA differential display reverse transcription PCR and two-dimensional electrophoresis at 0, 0.5, 1, 2, and 4 h after inoculation with P. sojae race 1. The results of the comparison of gene and protein expression showed that at least eight differential fragments at the transcriptional level were related to metabolic pathway, phytoalexin, and signal transduction in defense responses.Sequence analyses indicated that these fragments represented cinnamic acid 4-hydroxylase gene, ATP β gene coding ATP synthase β subunit and ubiquitin-conjugating enzyme gene which upregulated at 0.5 h post inoculation, blue copper protein gene and UDP-N-acetyl-α-D-galactosamine gene which upregulated at 2 h post inoculation, TGA-type basic leucine zipper protein TGA1.1 gene, cyclophilin gene, and 14-3-3 protein gene which upregulated at 4 h post inoculation.Three resistance-related proteins, α-subunit and β-subunit of ATP synthase, and cytochrome P450-like protein, were upregulated at 2 h post inoculation. The results suggested that resistance-related multiple proteins and genes were expressed in the recognition between soybean and P. sojae during zoospore germination, penetration and mycelium growth of P. sojae in soybean.