Combined application of chemical fertilizers with organic amendments was recommended as a strategy for improving yield, soil carbon storage, and nutrient use efficiency.  However, how the long-term substitution of chemical fertilizer with organic manure affects rice yield, carbon sequestration rate (CSR), and nitrogen use efficiency (NUE) while ensuring environmental safety remains unclear.  This study assessed the long-term effect of substituting chemical fertilizer with organic manure on rice yield, CSR, and NUE.  It also determined the optimum substitution ratio in the acidic soil of southern China.  The treatments were: (i) NPK₀, unfertilized control; (ii) NPK₁, 100% chemical nitrogen, phosphorus, and potassium fertilizer; (iii) NPKM₁, 70% chemical NPK fertilizer and 30% organic manure; (iv) NPKM₂, 50% chemical NPK fertilizer and 50% organic manure; and (v) NPKM₃, 30% chemical NPK fertilizer and 70% organic manure.  Milk vetch and pig manure were sources of manure for early and late rice seasons, respectively.  The result showed that SOC content was higher in NPKM₁, NPKM₂, and NPKM₃ treatments than in NPK₀ and NPK₁ treatments.  The carbon sequestration rate increased by 140, 160, and 280% under NPKM₁, NPKM₂, and NPKM₃ treatments, respectively, compared to NPK₁ treatment.  Grain yield was 86.1, 93.1, 93.6, and 96.5% higher under NPK₁, NPKM₁, NPKM₂, and NPKM₃ treatments, respectively, compared to NPK₀ treatment.  The NUE in NPKM₁, NPKM₂, and NPKM₃ treatments was higher as compared to NPK₁ treatment for both rice seasons.  Redundancy analysis revealed close positive relationships of CSR with C input, total N, soil C:N ratio, catalase, and humic acids, whereas NUE was closely related to grain yield, grain N content, and phenol oxidase.  Furthermore, CSR and NUE negatively correlated with humin acid and soil C:P and N:P ratios.  The technique for order of preference by similarity to ideal solution (TOPSIS) showed that NPKM₃ treatment was the optimum strategy for improving CSR and NUE.  Therefore, substituting 70% of chemical fertilizer with organic manure could be the best management option for increasing CSR and NUE in the paddy fields of southern China

Understanding the composition and contents of carotenoids in various soybean seed accessions is important for their nutritional assessment.  This study investigated the variability in the concentrations of carotenoids and chlorophylls and revealed their associations with other nutritional quality traits in a genetically diverse set of Chinese soybean accessions comprised of cultivars and landraces.  Genotype, planting year, accession type, seed cotyledon color, and ecoregion of origin significantly influenced the accumulation of carotenoids and chlorophylls.  The mean total carotenoid content was in the range of 8.15–14.72 µg g^–1 across the ecoregions.  The total carotenoid content was 1.2-fold higher in the landraces than in the cultivars.  Soybeans with green cotyledons had higher contents of carotenoids and chlorophylls than those with yellow cotyledons.  Remarkably, lutein was the most abundant carotenoid in all the germplasms, ranging from 1.35–37.44 µg g^–1.  Carotenoids and chlorophylls showed significant correlations with other quality traits, which will help to set breeding strategies for enhancing soybean carotenoids without affecting the other components.  Collectively, our results demonstrate that carotenoids are adequately accumulated in soybean seeds, however, they are strongly influenced by genetic factors, accession type, and germplasm origin.  We identified novel germplasms with the highest total carotenoid contents across the various ecoregions of China that could serve as the genetic materials for soybean carotenoid breeding programs, and thereby as the raw materials for food sectors, pharmaceuticals, and the cosmetic industry.

The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown.  In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function.  This study investigated the role that CSRP3 plays in chicken skeletal muscle.  First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared.  Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed.  The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles.  A total of 650 genes with at least 1.5-fold differences (Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing.  Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly (P<0.05) enriched both in differentially expressed genes and all expressed genes.  The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation (Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction.  Meanwhile, two fast myosin heavy chain genes (MyH1B and MyH1E) were upregulated (Q<0.05) upon CSRP3 silencing.  These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.

In insects, ecdysteroids are synthesized by genes of the Halloween family and play important roles in several key developmental events, including molting and metamorphosis.  However, the roles of these genes in Agasicles hygrophila are still largely unknown.  In this study, the expression patterns of the two Halloween genes AhCYP307A2 and AhCYP314A1 were determined by quantitative PCR (qPCR) at different developmental stages.  Moreover, the functions of these two genes were explored using RNA interference (RNAi), and ovarian development was observed by dissecting the ovaries of A. hygrophila females.  The qPCR results showed that AhCYP307A2 and AhCYP314A1 were highly expressed in last instar larvae and in adult females.  In addition, AhCYP307A2 was also highly expressed in eggs and pupae but was markedly lower than in third-instar larvae and females.  The RNAi results showed that the injection of dsAhCYP307A2 or dsAhCYP314A1 markedly inhibited their expression and the transcription levels of three related AhVgs.  Knockdown of AhCYP307A2 or AhCYP314A1 significantly inhibited larval molting, impaired last instar larva–pupa–adult transition, delayed ovarian development, and stopped egg production (i.e., no eggs were laid).  These results indicate that AhCYP307A2 and AhCYP314A1 play important regulatory roles in last instar larva–pupa–adult transition and reproduction in A. hygrophila.

Fusarium head blight (FHB) caused by Fusarium graminearum is a devastating fungal disease on small grain cereal crops, because it reduces yield and quality and causes the mycotoxin contamination to the grain.  Dynamins and dynamin-related proteins (DRPs) are large GTPase superfamily members, which are typically involved in the budding and division of vesicles in eukaryotic cells, but their roles in Fusarium spp. remain unexplored.  Here, we found that FgDnm1, a DRP and homolog to Dnm1 in Saccharomyces cerevisiae, contributes to the normal fungal growth, sexual reproduction and sensitivity to fungicides.  In addition, we found FgDnm1 co-localizes with mitochondria and is involved in toxisome formation and deoxynivalenol (DON) production.  Several quinone outside inhibitors (QoIs) and succinate dehydrogenase inhibitors (SDHIs) cause fragmentated morphology of mitochondria.  Importantly, the deletion of FgDnm1 displays filamentous mitochondria and blocks the mitochondrial fragmentation induced by QoIs and SDHIs.  Taken together, our studies uncover the effect of mitochondrial dynamics in fungal normal growth and how such events link to fungicides sensitivity and toxisome formation.  Thus, we concluded that altered mitochondrial morphology induced by QoIs and SDHIs depends on FgDnm1.

Increasing prolificacy is an important aim in the pig industry.  Regions associated with litter size have been revealed, but detailed molecular mechanisms are unclear.  The Meishan pig is one of the most prolific breeds, with higher prolificacy than the Yorkshire pig, which exhibits high feeding efficiency and lean meat yield.  The ovary is the key organ determining reproductive traits during pregnancy by synthesizing and secreting reproductive hormones essential for conceptus maintenance.  In this comparative multi-omics study of the ovary transcriptome, proteome, and metabolome on day 49 of pregnancy, we aimed to identify genomic, proteomic, and metabolomic differences between the ovaries of Meishan and Yorkshire pigs to reveal potential molecular mechanisms conferring high prolificacy.  Meishan pigs demonstrated general downregulation of steroid biosynthesis and butanoate metabolism in the ovary during mid-pregnancy at both transcriptome and proteome levels but exhibited higher serum cholesterol, estradiol, and progesterone levels than Yorkshire pigs.  We also identified several single-nucleotide polymorphisms in the genes of the steroid hormone pathway associated with litter number, average birth weight, and total litter weight.  Lower biosynthesis rates but elevated serum levels of reproductive hormones during mid- and late pregnancy are essential for the greater prolificacy of Meishan pigs.

Chromatin accessibility plays a vital role in gene transcriptional regulation.  However, the regulatory mechanism of chromatin accessibility, as well as its role in regulating crucial gene expression and kernel development in maize (Zea mays) are poorly understood.  In this study, we isolated a maize kernel mutant designated as defective kernel219 (dek219), which displays opaque endosperm and embryo abortion.  Dek219 encodes the DICER-LIKE1 (DCL1) protein, an essential enzyme in miRNA biogenesis.  Loss of function of Dek219 results in significant reductions in the expression levels of most miRNAs and histone genes.  Further research showed that the Heat shock transcription factor17 (Hsf17)-Zm00001d016571 module may be one of the factors affecting the expression of histone genes.  Assay results for transposase-accessible chromatin sequencing (ATAC-seq) indicated that the chromatin accessibility of dek219 is altered compared with that of wild type (WT), which may regulate the expression of crucial genes in kernel development.  By analyzing differentially expressed genes (DEGs) and differentially accessible chromatin regions (ACRs) between WT and dek219, we identified 119 candidate genes that are regulated by chromatin accessibility, including some reported to be crucial genes for kernel development.  Taken together, these results suggest that Dek219 affects chromatin accessibility and the expression of crucial genes that are required for maize kernel development

Winter jujube (Ziziphus jujuba ‘Dongzao’) is an excellent late maturing variety of fresh-eating jujube in China.  Fruit texture is an important indicator of sensory quality.  To investigate the correlations among texture indices and establish an evaluation system for winter jujube texture, we used the TMS-Touch instrument to perform a texture profile analysis (TPA) on 1 150 winter jujubes from three major producing areas in China.  Eight indices and their best-fit distribution were obtained, including fracture (Pearson), hardness (InvGauss), adhesive force (Weibull), adhesiveness (LogLogistic), cohesiveness (LogLogistic), springiness (BetaGeneral), gumminess (InvGauss), and chewiness (InvGauss).  Based on the best-fit distribution curves, each index was divided into five grades (lower, low, medium, high and higher) by the 10th, 30th, 70th and 90th percentiles.  Among the texture indices, 82% of the correlation coefficients were highly significant (P<0.01); meanwhile, chewiness was significantly (P<0.01) and positively correlated with springiness and gumminess, of which the correlation coefficients were up to 0.8692 and 0.8096, respectively.  However, adhesiveness was significantly (P<0.01) and negatively related to adhesive force with a correlation coefficient of –0.7569.  Among hardness, cohesiveness, springiness, gumminess, and chewiness, each index could be well fitted by a multiple linear regression with the remaining four indices, with the coefficients above 0.94 and the mean fitting error and mean prediction error lower than 10%.  A comprehensive evaluation model was consequently established based on factor analysis to evaluate the texture quality of winter jujube.  The results demonstrated that winter jujube with higher comprehensive scores generally exhibited higher springiness and chewiness, but had lower adhesive force and adhesiveness.  We used factor analysis and clustering analysis to divide the eight studied texture into four groups (cohesive factor, adhesive-soft factor, tough-hard factor, and crispness factor), whose representative indices were springiness, adhesiveness, hardness, and fracture, respectively.  Overall, this study investigated the variation in each index of winter jujube texture, explored the association among these indices, screened the representative indices, and established a texture evaluation system.  The results provide a methodological basis and technical support for evaluating winter jujube texture.

Understanding the spatial-temporal dynamics of crop nitrogen (N) use efficiency (NUE) and the relationship with explanatory environmental variables can support land-use management and policymaking.  Nevertheless, the application of statistical models for evaluating the explanatory variables of space-time variation in crop NUE is still under-researched.  In this study, stepwise multiple linear regression (SMLR) and Random Forest (RF) were used to evaluate the spatial and temporal variation of NUE indicators (i.e., partial factor productivity of N (PFP_N); partial nutrient balance of N (PNB_N)) at county scale in Northeast China (Heilongjiang, Liaoning and Jilin provinces) from 1990 to 2015.  Explanatory variables included agricultural management practices, topography, climate, economy, soil and crop types.  Results revealed that the PFP_N was higher in the northern parts and lower in the center of the Northeast China and PNB_N increased from southern to northern parts during the 1990–2015 period.  The NUE indicators decreased with time in most counties during the study period.  The model efficiency coefficients of the SMLR and RF models were 0.44 and 0.84 for PFP_N, and 0.67 and 0.89 for PNB_N, respectively.  The RF model had higher relative importance of soil and climatic covariates and lower relative importance of crop covariates compared to the SMLR model.  The planting area index of vegetables and beans, soil clay content, saturated water content, enhanced vegetation index in November & December, soil bulk density, and annual minimum temperature were the main explanatory variables for both NUE indicators.  This is the first study to show the quantitative relative importance of explanatory variables for NUE at a county level in Northeast China using RF and SMLR.  This novel study gives reference measurements to improve crop NUE which is one of the most effective means of managing N for sustainable development, ensuring food security, alleviating environmental degradation and increasing farmer’s profitability.

β-Glucosidase belongs to the glycoside hydrolase I family, which is widely present in multiple species and responds to various biotic and abiotic stresses. In rice, whether β-glucosidase is involved in the interaction between plants and microorganisms is not clear. In this study, we found that the expression of several genes encoding β-glucosidases, including OsBGLU19 and OsBGLU23, were upregulated after inoculation with Xanthomonas oryzae pv. oryzicola (Xoc) and downregulated after inoculation with X. oryzae pv. oryzae (Xoo). The respective insertion mutants of OsBGLU19 and OsBGLU23, bglu19 and bglu23, were more susceptible to Xoc infection. The expression of OsAOS2, a key gene in the jasmonic acid signal pathway, was dramatically downregulated after inoculation with Xoc in the bglu19 and bglu23 mutants. Simultaneously, the expression of downstream disease resistance-related genes, such as OsPR1a, OsPR5 and a key transcription factors OsWRKY72 were obviously downregulated. The resistance mediated by OsBGLU19 and OsBGLU23 to bacterial leaf streak is related to disease resistance-related genes above mentioned.

Insects have developed a good adaptive mechanism in response to environmental stresses in the long-term evolution.
They have developed a helpful metabolism system to resist plant allelochemicals. Insects also harbor different kinds of
symbiotic bacteria, which provide them a competitive advantage. Here, using cotton aphid as an example, we investigated
the effects of four plant allelochemicals on the differential expression of symbiotic bacteria based on transcriptome data.
We also studied the composition of symbiotic bacteria and function on pathway level in three kinds of aphids. We found that
the bacteria have a significant role in resisting the plant allelochemicals stress and host plant selection by aphids. These
results should be useful to investigate the environmental adaption mechanism of aphids in the view of symbiotic bacteria.
These results would offer a new insight for improving strategy of aphids and developing new pest control systems.

The root-knot nematode Meloidogyne graminicola, which is distributed worldwide, is considered a major constraint on rice production in Asia.  The present study used the root gall index and number of nematodes inside the roots to evaluate resistance/susceptibility to M. graminicola in different subpopulations of Oryza sativa (aus, hybrid aus, indica, hybrid indica, temperate japonica, tropical japonica).  Nematode development in highly resistant varieties was also evaluated.  Analyses of randomly selected 35 varieties showed the number of M. graminicola nematodes inside the roots correlated very strongly (r=0.87, P≤0.05) with the nematode gall index, and the results from pot and field experiments revealed similar rankings of the varieties for resistance/susceptibility.  Among the 136 tested varieties, temperate japonica displayed the highest gall index, followed by tropical japonica, indica, hybrid indica, aus, and hybrid aus. Zhonghua 11 (aus), Shenliangyou 1 (hybrid aus) and Cliangyou 4418 (hybrid indica) were highly resistant to M. graminicola under both pot and field conditions.  Further examination of nematode development suggested that compared to susceptible rice, M. graminicola penetrated less often into highly resistant varieties and more frequently failed to develop into females.  The promising varieties found in the present research might be useful for the breeding of hybrid rice in China and for the further development of practical nematode management measures.   

Effects of four different drying methods on the colour, texture, sensory quality, microstructure, bacterial viability and storage stability of probiotic-enriched apple snacks were assessed.  The drying methods were air drying (AD), freeze drying (FD), freeze drying followed by microwave vacuum drying (FD+MVD) and air drying followed by explosion puffing drying (AD+EPD).  Overall, FD+MVD can be used as a suitable drying method for the development of probiotic enriched apple snacks in consideration of colour, texture, sensory quality, bacterial viability and storage stability.  Probiotic bacteria in FD+MVD-dried samples remained above 1×10⁶ CFU g^–1 for 120 days at 25°C.  Interestingly, bacterial viability in FD+MVD-dried samples turned out to be significantly higher than FD-dried samples during storage for 120 days.  

Plant structures and chemicals, which are developed from the shoot apical meristem (SAM), form the main barriers to insect feeding.  A plant chimera containing cells of different genetic origins in the SAM will be morphologically and chemically different compared with the parents and thus may result in differential resistance to herbivores.  In this study, we explore if particular elements of plant resistance are localized in one of the layers of SAM; the replacement of one cell layer in a chimera may be linked to change of a single resistance trait to herbivores.  The morphology and glucosinolate profiles of two periclinal chimeras (labeled as TTC and TCC, respectively) and grafted parents tuber mustard (labeled as TTT) and red cabbage (labeled as CCC) were compared and the performance of whitefly (Bemisia tabaci) in host selection, oviposition preference and development were assessed under controlled conditions.  Both chimeras possessed leaf trichomes as parent tuber mustard TTT, however, TTC had significantly more trichomes than TCC and parent TTT.  Leaf wax content of both chimeras was intermediate between the two parents.  Five aliphatic and two indole glucosinolates were detected in both chimeras, whereas three aliphatic glucosinolates (3-methyl-sulfinylpropyl, 4-methyl-sulfinylbutyl and 2-hydroxy-3-butenyl) were not detected in tuber mustard, and one aliphatic glucosinolate (3-butenyl) was not detected in red cabbage.  Unexpectedly for a chimera, the quantities of two aliphatic glucosinolates (3-methyl-sulfinylpropyl and 4-methyl-sulfinylbutyl) in both TTC and TCC were 3- to 5-fold higher than parents.  In olfactory preference assays, B. tabaci showed preference to CCC, followed by TCC, TTC and TTT, and number of eggs laid showed the same pattern: CCC>TCC>TTC>TTT.  Interestingly, more whiteflies landed on TTT plants than the other three types in a free choice experiment and the developmental duration from egg to adult was the shortest on TTT and increased in the order TTT<TTC<TCC<CCC.  Our results indicate plant defenses traits of leaf waxes, trichomes and glucosinolates are not controlled by one cell layer of SAM, but are influenced by interactions amongst cell layers.  The overall findings suggest that periclinal chimera systems can be a valuable approach for the study of plant-insect interactions and may also be useful for future resistance breeding. 

    Porcine reproductive traits are characterized by low heritability, making improvement by traditional selective breeding rather difficult. Molecular breeding offers powerful approaches to overcome previous limitations and is expected to generate economic benefits via progress in pig breeding. Cytochrome P450 family 19 subfamily A polypeptide 1 (CYP19A1) gene is a key enzyme of estradiol biosynthesis that plays an important role in the establishment of gestation and maintenance of pregnancy. In this study, the sequence and structure characteristics of the porcine CYP19A1 gene was analyzed and expression patterns of CYP19A1 in different tissues of adult female pigs were detected. Fourteen single-nucleotide polymorphisms (SNPs) in the exons and introns of porcine CYP19A1 were identified and genotyped using the Sequenom MassARRAY platform, after which the allele frequency of each SNP was analyzed. The association between CYP19A1 SNPs and litter size and piglet birth weight was assessed in a crossbred pig population (n=375). The expression pattern of CYP19A1 revealed that it was highly expressed in the ovary, spleen, and uterus and lowly expressed in the other tissues. Moreover, one SNP, rs341891833, was significantly associated with piglet birth weight during the multiparity period (P<0.01). We concluded that CYP19A1 could be used as a candidate molecular marker in breeding aimed at rapid improvement of the reproductive characteristics of pigs.  

Sucrose is known to play an important role in the cryopreservation of sperm and female gonads; however, its effect on the cryopreservation of pig spermatogonial stem cells (pSSCs) has not been tested.  The aim of this work was to study the effect of sucrose during pSSC cryopreservation and to find the most effective concentration in freezing medium.  pSSCs were cryopreserved with freezing media containing different concentrations of sucrose (70, 140, 210, and 280 mmol L^–1) and a control group without sucrose.  The survival rates, plasma membrane integrity, and mitochondrial membrane potential of thawed cells were detected by trypan blue (TB) staining, SYBR-14/propidium iodide (PI) dual staining, and JC-1 staining, respectively.  All the staining results showed an obvious increase in cell survival in the sucrose-treated groups as compared to that in the control group, with the exception of 280 mmol L^–1 sucrose.  Moreover, the 210 mmol L^–1 sucrose group yielded the highest survival rate among all the groups (P<0.05).  The results of SYBR-14/PI dual staining and JC-1 staining were consistent with those of TB staining as above described.  Quantitative real-time PCR (qRT-PCR) indicated that the mRNA levels of three apoptosis-promoting genes (BAX, APAF1 and CASPASE9) were significantly higher in thawed cells than in cells before freezing (P<0.05).  Moreover, the mRNA level of one anti-apoptotic gene (XIAP) was significantly lower in thawed cells than in cells before freezing (P<0.05).  When comparing the mRNA expression of apoptosis-related genes in thawed cells, the mRNA level of the anti-apoptotic genes in the control group was significantly lower than that in the sucrose-treated
groups (P<0.05).  Western blot analyses showed that the expression levels of cleaved CASPASE9, CASPASE3 and PARP-1 in the sucrose-treated groups were lower than those in the control group and were the lowest in the 210 mmol L^–1 sucrose group.  Both qRT-PCR and Western blot analyses suggested that sucrose inhibited cell apoptosis during freezing and thawing.  Briefly, sucrose promoted pSSCs survival after freezing and thawing, especially at a concentration of 210 mmol L^–1, which possibly assisted pSSC dehydration and inhibited cell apoptosis.  These findings hold great promise for further studies of the regulatory mechanism of proliferation and differentiation of pSSCs. 

   Agro-ecological conditions associated with the spread and persistence of highly pathogenic avian influenza (HPAI) are not well understood, but the trade of live poultry is suspected to be a major pathway. Although market chains of live bird trade have been studied through indirect means including interviews and questionnaires, direct methods have not been used to identify movements of individual poultry. To bridge the knowledge gap on quantitative movement and transportation of poultry, we introduced a novel approach for applying telemetry to document domestic duck movements from source farms at Poyang Lake, China. We deployed recently developed transmitters that record Global Positioning System (GPS) locations and send them through the Groupe Spécial Mobile (GSM) cellular telephone system. For the first time, we were able to track individually marked ducks from 3 to 396 km from their origin to other farms, distribution facilities, or live bird markets. Our proof of concept test showed that the use of GPS-GSM transmitters may provide direct, quantitative information to document the movement of poultry and reveal their market chains. Our findings provide an initial indication of the complexity of source-market network connectivity and highlight the great potential for future telemetry studies in poultry network analyses.

A hydroponic study was conducted to determine the effects of selenium (Se: 0, 3, 6 μmol L−1) on senescence-related oxidative stress in garlic plants grown under two sulfur (S) levels. We evaluated the yields of plants harvested at 160 and 200 days after sowing. Plants grown under a low Se dose (0.3 μmol L−1) at low S level showed higher yields (12.0% increase in fresh weight yield, 13.7% increase in dry weight yield) than the controls, despite a decrease in chlorophyll concentration. Compared with control plants, the Se-treated plants showed lower levels of lipid peroxidation. The Se-treated plants also showed higher activities of glutathione peroxidase and catalase, but lower superoxide dismutase activities. Changes in Fv/Fm values and proline contents were affected more strongly by S than by Se. On the basis of our results, we can conclude that Se plays a key role in the antioxidant systems in garlic seedlings. It delays senescence by alleviating the peroxide stress, but it can be toxic at high levels. A high S level may increase tolerance to high Se concentrations through reducing Se accumulation in plants.