The soybean rhizosphere has a specific microbial community, but the differences in microbial community structure between different soybean genotypes have not been explained.  The present study analyzed the structure of the rhizosphere microbial community in three soybean genotypes.  Differences in rhizosphere microbial communities between different soybean genotypes were verified using diversity testing and community composition, and each genotype had a specific rhizosphere microbial community composition.  Co-occurrence network analysis found that different genotype plant hosts had different rhizosphere microbial networks.  The relationship between rhizobia and rhizosphere microorganisms in the network also exhibited significant differences between different genotype plant hosts.  The ecological function prediction found that different genotypes of soybean recruited the specific rhizosphere microbial community.  These results demonstrated that soybean genotype regulated rhizosphere microbial community structure differences.  The study provides a reference and theoretical support for developing soybean microbial inoculum in the future.

Root-knot nematodes (RKNs) cause huge yield losses to agricultural crops worldwide.  Meanwhile, livestock manure is often improperly managed by farmers, which leads to serious environmental pollution.  To resolve these two problems, this study developed a procedure for the conversion of chicken manure to organic fertilizer by larvae of Hermetia illucens L. and Bacillus subtilis BSF-CL.  Chicken manure organic fertilizer was then mixed thoroughly with Paenibacillus polymyxa KM2501-1 to a final concentration of 1.5×10⁸ CFU g^–1.  The efficacy of KM2501-1 microbial organic fertilizer in controlling root-knot nematodes was evaluated in pot and field experiments.  In pot experiments, applying KM2501-1 microbial organic fertilizer either as a base fertilizer or as a fumigant at the dose of 40 g/pot suppressed root-knot disease by 61.76 and 69.05% compared to the corresponding control treatments, respectively.  When applied as a fumigant at the dose of 1 kg m^–2 in field experiments, KM2501-1 microbial organic fertilizer enhanced the growth of tomato plants, suppressed root-knot disease by 49.97%, and reduced second stage juveniles of RKN in soil by 88.68%.  KM2501-1 microbial organic fertilizer controlled RKNs better than commercial bio-organic fertilizer in both pot and field experiments.  These results demonstrate that this co-conversion process efficiently transforms chicken manure into high value-added larvae biomass and KM2501-1 microbial organic fertilizer with potential application as a novel nematode control agent.

In agricultural production, temperature and moisture are important factors affecting grain yield and quality.  Although moderate drought at the grain-filling stage can effectively alleviate the damage caused by high temperature, the specific regulatory mechanism driving the effect of moderate drought at the high temperature on starch synthesis is still unclear.  To explore the effects and mechanisms of high temperature and moderate drought on rice starch synthesis at the grain-filling stage, the activities of enzymes and expression levels of the genes involved in starch synthesis under four different treatments involving high temperature and/or water stress (CK, HT, WS, and HT+WS) were investigated in this study.  The starch synthesis of a japonica inbred rice was measured under the four treatments during the grain filling.  The results show that the effects of high temperature and moderate drought on grain filling mainly occur in the inferior grains of rice.  Through the regulation of enzymes involved in starch synthesis and the expression levels of their main genes, the synthesis of rice starch can be affected.  Therefore, the high temperature and moderate drought were antagonistic, and moderate drought can alleviate the damage to grain quality at a high temperature by improving the starch synthesis of inferior grains in japonica rice.  This study provides a basis for stress-resistance cultivation and breeding strategies of rice with high temperature tolerance.

The additions of straw and biochar have been suggested to increase soil fertility, carbon sequestration, and crop productivity of agricultural lands.  To our knowledge, there is little information on the effects of straw and biochar addition on soil nitrogen form, carbon storage, and super rice yield in cold waterlogged paddy soils.  We performed field trials with four treatments including conventional fertilization system (CK), straw amendment 6 t ha^–1 (S), biochar amendment 2 t ha^–1 (C1), and biochar amendment 40 t ha^–1 (C2).  The super japonica rice variety, Shennong 265, was selected as the test crop.  The results showed that the straw and biochar amendments improved total nitrogen and organic carbon content of the soil, reduced N₂O emissions, and had little influence on nitrogen retention, nitrogen density, and CO₂ emissions.  The S and C1 increased NH₄⁺-N content, and C2 increased NO₃^–-N content.  Both S and C1 had little influence on soil organic carbon density (SOCD) and C/N ratio.  However, C2 greatly increased SOCD and C/N ratio.  C1 and C2 significantly improved the soil carbon sequestration (SCS) by 62.9 and 214.0% (P<0.05), respectively, while S had no influence on SCS.  C1 and C2 maintained the stability of super rice yield, and significantly reduced CH₄ emissions, global warming potential (GWP), and greenhouse gas intensity (GHGI), whereas S had the opposite and negative effects.  In summary, the biochar amendments in cold waterlogged paddy soils of North China increased soil nitrogen and carbon content, improved soil carbon sequestration, and reduced GHG emission without affecting the yield of super rice.

Super rice breeding in China has been very successful over the past 3 decades, and the Chinese government has made great efforts to support breeding and cultivation of both conventional and hybrid super rice.  In this review, we focus on the progress in and potential of super rice breeding.  After the establishment of the breeding theory and strategy of “generating an ideotype with strong heterosis through inter-subspecies hybridization, by using gene pyramiding to combine elite traits through composite-crossing to breed super rice varieties with both ideotype and strong hybrid vigor”, a series of major breakthroughs have been achieved in both conventional and super hybrid rice breeding.  A number of new genetic materials with ideotype have been created successfully, and the Ministry of Agriculture of China has approved 156 novel super rice varieties and combinations for commercialization.  During the Developing the Super Rice Varieties Program, great attention has also been paid to the integration and demonstration of the rice production technology.  Collaboration between industry and university researchers has led to technological innovations and initiation of a demonstration system for super hybrid rice.  With widespread cultivation of super rice with higher quality and yield, as well as resistance or tolerance to abiotic or biotic stresses, the yield of rice production per unit has reached a new level.  In addition to increased quality and yield, hybrid rice breeding has also led to improvements in many other agronomic traits, such as resistance to pests and diseases, resistance to lodging, and optimized light distribution in population.  Achievements in super rice breeding and innovation in rice production have made major contributions to the progress in rice sciences and worldwide food security.

Biochar has been shown to influence soil microbial communities in terms of their abundance and diversity.  However, the relationship among microbial abundance, structure and C metabolic traits is not well studied under biochar application.  Here it was hypothesized that the addition of biochar with intrinsic properties (i.e., porous structure) could affect the proliferation of culturable microbes and the genetic structure of soil bacterial communities.  In the meantime, the presence of available organic carbon in biochar may influence the C utilization capacities of microbial community in Biolog Eco-plates.  A pot experiment was conducted with differenct biochar application (BC) rates: control (0 t ha^–1), BC1 (20 t ha^–1) and BC2 (40 t ha^–1).  Culturable microorganisms were enumerated via the plate counting method.  Bacterial diversity was examined using denaturing gradient gel electrophoresis (DGGE).  Microbial capacity in using C sources was assessed using Biolog Eco-plates.  The addition of biochar stimulated the growth of actinomyces and bacteria, especially the ammonifying bacteria and azotobacteria, but had no significant effect on fungi proliferation.  The phylogenetic distribution of the operational taxonomic units could be divided into the following groups with the biochar addition: Firmicutes, Acidobacteria, Gemmatimonadetes, Actinobacteria, Cyanobacteria and α-, β-, γ- and δ-Proteobacteria (average similarity >95%).  Biochar application had a higher capacity utilization for L-asparagine, Tween 80, D-mannitol, L-serine, γ-hydroxybutyric acid, N-acetyl-D-glucosamine, glycogen, itaconic acid, glycyl-L-glutamic acid, α-ketobutyricacid and putrescine, whereas it had received decreased capacities in using the other 20 carbon sources in Biolog Eco-plates.  Redundancy analysis (RDA) revealed that the physico-chemical properties, indices of bacterial diversity, and C metabolic traits were positively correlated with the appearance of novel sequences under BC2 treatment.  Our study indicates that the addition of biochar can increase culturable microbial abundance and shift bacterial genetic structure without enhancing their capacities in utilizing C sources in Biolog Eco-plates, which could be associated with the porous structure and nutrients from biochar.

   Cucumber mosaic virus (CMV) can infect a wide range of host species. For the lacking of CMV resistant varieties of tomato, RNA interference (RNAi) can be used as a fast and effective method for the generation of transgenic resistant varieties. In this current study, five intron-spliced hairpin RNA (ihpRNA) plant expression vectors aimed at five genes of CMV have been constructed. Transgenic tomatoes were obtained by Agrobacterium tumefaciens-mediated transformation with expression vectors. Highly resistant generations of transgenic plants were employed as rootstocks and grafted onto non-transgenic tomatoes that resulted in the successful transfer of resistance to the scions. Using a novel method of plant cuttings for rootstock propagation, we obtained large quantities of disease-resistant material. Further, this method produces scions that can remain undetectable for transgenic resistance marker genes that may provide novel approaches to evade collective concerns about genetically-modified organism (GMO) biosafety.

   Virus-tolerant plant, which allows the accumulation of virus and then generates virus-derived small RNAs (vsRNAs), is a valuable material to reveal the antiviral efficiency of vsRNAs. Here, a comparison of vsRNAs in Tomato yellow leaf curl virus tolerant and in susceptible tomato varieties showed the consistent trend of vsRNAs’ distribution on virus genome, which is presented as an obvious characteristic. However, the expression level of vsRNA in tolerant variety is less than that in susceptible variety. Slicing targets of vsRNA-mediated viral transcripts were investigated using parallel analysis of RNA ends, and geminivirus DNA methylation was determined by bisulfite sequencing, which uncovered that not all vsRNAs participated in viral mRNA degradation and DNA methylation. Additionally, by comparing with the expression pattern of vsRNAs, viral DNA and mRNA, we proposed the quantity of vsRNAs is corresponding to the expression level of viral mRNA, while the virus-suppression of vsRNAs is not high-efficient.

    Grassland is the important component of the terrestrial ecosystems. Estimating net primary productivity (NPP) of grassland ecosystem has been a central focus in global climate change researches. To simulate the grassland NPP in southern China, we built a new climate productivity model, and validated the model with the measured data from different years in the past. The results showed that there was a logarithmic correlation between the grassland NPP and the mean annual temperature, and there was a linear positive correlation between the grassland NPP and the annual precipitation in southern China. All these results reached a very significant level (P<0.01). There was a good correlation between the simulated and the measured NPP, with R² of 0.8027, reaching the very significant level. Meanwhile, both root mean square errors (RMSE) and relative root-mean-square errors (RRMSE) stayed at a relatively low level, showing that the simulation results of the model were reliable. The NPP values in the study area had a decreasing trend from east to west and from south to north, and the mean NPP was 471.62 g C m⁻² from 2000 to 2011. Additionally, there was a rising trend year by year for the mean annual NPP of southern grassland and the tilt rate of the mean annual NPP was 3.49 g C m⁻² yr⁻¹ in recent 12 years. The above results provided a new method for grassland NPP estimation in southern China.

Little is known about the muscle developmental patterns during embryonic to neonatal development in ducks. We investigated the developmental patterns in the lateral gastrocnemius muscles of Gaoyou and Jinding ducks differing in their muscle growth rates during the final stages of egg incubation and the first week after hatching. Expression of the MyoD gene was quantified by quantitative real-time PCR (qRT-PCR). The average cross-sectional area and diameter of the fibers increased from embryonic day 21 (E21), peaking at E27, and then declining slightly 7 d after hatching. The density of the fibers decreased initially but increased after hatching in both breeds and sexes. The within-breed variation in muscle fiber-type composition was greater than the average variation between the breeds. Overall, the percentage of type I fibers increased and that of type IIb fibers decreased consistently. However, the percentage of type IIa fibers was almost constant as development proceeded in both duck breeds. The profiles of MyoD mRNA expression were similar in both breeds, and a significantly positive relationship was observed between the expression of MyoD and the percentage of type IIb fibers. This study firstly revealed the characteristics of duck muscle development and differences between the two breeds differing in growth rates. Moreover, type IIb fibers might convert to type I fibers in the lateral gastrocnemius, while MyoD may potentially function in controlling the muscle fiber phenotype during the secondary myogenesis of muscle development.

    Cytoplasmic effects are important agronomical phenomena that have generated widespread interest in both theory and application. In the present study, five high yield rice cultivars (Oryza sativa L. ssp. japonica) in large-scale cultivation in northeast China were determined to possess Oryza sativa L. ssp. indica-type cytoplasm using cytoplasmic subspecies-specific molecular markers. This was confirmed by cytoplasmic genome-wide single nucleotide polymorphisms (SNPs) and functional gene sequencing. Two of these five japonica cultivars were core breeding parents with high yield and the other three were super-high-yield varieties registered by the Ministry of Agriculture of China. We constructed nuclear substitution lines to further demonstrate whether and how this indica-type cytoplasm contributed to yield improvement by comparing yield components. The results showed that under the same japonica nuclear background, the lines with indica-type cytoplasm had a significant decrease in tillers in exchange for increased grain number per panicle compared with their recurrent parents. Our results implied that botanical basis of this cytoplasmic effect was to reduce the plant’s branching differentiation to produce more floral organs under the constant nutrition. Our findings open another door for the utilization of inter-subspecific hybridization for the improvement of rice cultivar.

Abundant genetic diversity and rational population structure of germplasm benefit crop breeding greatly. To investigate genetic variation among geographically diverse set of japonica germplasm, we analyzed 233 japonica rice cultivars collected from Liaoning, Jilin and Heilongjiang provinces of China, which were released from 1970 to 2011 by using 62 simple sequence repeat (SSR) markers and 8 functional gene tags related to yield. A total of 195 alleles (Na) were detected with an average of 3.61 per locus, indicating a low level of genetic diversity level among all individuals. The genetic diversity of the cultivars from Jilin Province was the highest among the three geographic distribution zones. Moreover, the genetic diversity was increased slightly with the released period of cultivars from 1970 to 2011. The analysis of molecular variance (AMOVA) revealed that genetic differentiation was more diverse within the populations than that among the populations. The neighbor-joining (NJ) tree indicated that cultivar clusters based on geographic distribution represented three independent groups, among which the cluster of cultivars from Heilongjiang is distinctly different to the cluster of cultivars from Liaoning. For the examined functional genes, two or three allelic variations for each were detected, except for IPA1 and GW2, and most of elite genes had been introgressed in modern japonica rice varieties. These results provide a valuable evaluation for genetic backgrounds of current japonica rice and will be used directly for japonica rice breeding in future.

It is of great importance to solve the threats induced by cadmium pollution on crops. This paper examined the effect of biochar on cadmium accumulation in japonica rice and revealed the mechanism underlying the response of protective enzyme system to cadmium stress. Biochar derived from rice straw was applied at two application rates under three cadmium concentrations. Shennong 265, super japonica rice variety, was selected as the test crop. The results indicated that cadmium content in above-ground biomass of rice increased with increasing soil cadmium concentrations, but the biochar application could suppress the accumulation of cadmium to some extent. Under high concentrations of cadmium, content of free proline and MDA (malondialdehyde) were high, so did the SOD (superoxide dismutase), POD (peroxidase) and CAT (catalase) activity in the flag leaf of rice. However, the protective enzyme activities remained at low level when biochar was added.

indica and japonica are the two most important subspecies of Asian cultivated rice. Identifying mechanisms responsible for population differentiation in these subspecies is important for indica-japonica hybridization breeding. In this study, subspecies and economic trait differentiation patterns were analyzed using morphological and molecular (InDel and Intron Length Polymorphism) data in F2 and F3 populations derived from indica-japonica hybridization. Populations were grown in Liaoning and Guangdong provinces, China, with F3 populations generated from F2 populations using bulk harvesting (BM) and single-seed descent methods (SSD). Segregation distortion was detected in F3-BM populations, but not in F3- SSD or in F2 populations. Superior performance was observed with respect to economic traits in Liaoning compared with that in Guangdong and 1 000-grain weight (KW), seed setting rate (SSR) and grain yield per plant (GYP) were significantly correlated with indica and japonica subspecies types. Analysis of molecular and morphological data demonstrated that the environment is the main factor giving rise to population differentiation in indica-japonica hybridization. In addition, we also found that KW, SSR and GYP are related to subspecies characteristics and kinship, which is possibly a significant factor resulting in economic trait differentiation and determining environmental adaptability. Our study has provided new insights into the process of population differentiation in these subspecies to inform indica-japonica hybridization breeding.

Erythropoietin-producing hepatocellular receptor and its membrane-bound ligands (Eph-Ephrin) system could regulatesome mammalian blastocyst attachment and spreading. In order to investigate the involvement of the Eph-Ephrin systemin swine embryo attachment, mRNA expression of Eph-Ephrin molecules in endometrium was examined by real-time RTPCRduring embryo implantation in pigs. The results indicated that mRNA expressions of Eph A5, A7 and Ephrin A5 allcontinually increased from pregnancy day 13 to 24. Ephrin A3 mRNA expression significantly increased from day 13 to 18and decreased from day 18 to 24, and the expression was the lowest on pregnancy day 13 and the highest on day 18.However, Ephrin A4 mRNA expression was the lowest on pregnancy day 18 and the highest on day 24, and the expressiondecreased from day 13 to 18 and increased from day 18 to 24. Furthermore, mRNA expressions of Eph A5 and A7 were bothfound in other tissues, such as brain, muscle, intestine, stomach, etc. These findings suggest that the Eph-Ephrin systemmay play an important role in regulating the contact between blastocysts and endometrium during swine embryoimplantation.

Spermatogonial stem cells (SSCs) are the key to maintaining production of the sperms and healthy offsprings, and also treating breeding livestock’s reproductive damage and infertility. MicroRNAs act a decisive role in regulating gene expression in many cells and tissues, including in processes such as proliferation, self-renewal, differentiation, and apoptosis of stem cells. However, the miRNA mechanism in regulation of SSCs is still unclear. Here, high-throughput sequencing was used to identify specific miRNAs. We confirmed that miR-21-5p was concentrated in both goat and mouse SSCs, and enhanced the proliferation and antiapoptotic ability of SSCs. In vivo experiments have shown that miR-21-5p resisted the damage of the chemotherapy drug Busulfan to germ cells, ameliorated Busulfan-induced testicular dysfunction, and maintained spermatogenesis. Further RNA-seq and target gene prediction revealed that SPRY1 and FASLG are targets of miR-21-5p, thereby activating downstream signaling pathways such as MAPK/ERK, PI3K-AKT, and apoptosis. In summary, miR-21-5p is crucial for the self-renewal and maintenance of SSCs. This study provides new avenues for treating breeding livestock’s reproductive damages, infertility, oligospermia, and other conditions.