2019 Vol. 18 No. 7 Previous Issue    Next Issue

    Special Focus: Animal influenza virus
    Special Focus: Ecological functions of biochar
    Crop Science
    Plant Protection
    Food Science

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    Special Focus: Animal influenza virus
    Editorial – Animal influenza virus
    CHEN Hua-lan
    2019, 18(7): 1419-1420.  DOI: 10.1016/S2095-3119(19)62727-9
    Abstract ( )   PDF in ScienceDirect  

    Animal influenza viruses continuously circulate in their reservoirs in nature and pose severe threat to human and animal; therefore, understanding and control of animal influenza viruses will have important implication to public health and social economy.  In this special focus of “Animal influenza virus”, we have one review and five research articles that cover the development of new diagnostic method, surveillance, pathogenicity, and host response to influenza viruses.  

    The article by Zou et?al. (2019) reviewed the role and significance of microRNAs (miRNAs) in the pathogenesis influenza virus infection and discussed the potential application of miRNAs.  The article by Shi et?al. (2019) reported the development of a novel loop-mediated isothermal amplification (RT-LAMP) method to detect and identify different subtype influenza viruses.  The article by Sun et?al. (2019) reported the surveillance of swine influenza virus in Shandong Province of China and identification of a novel H1N1 swine influenza reassortant.  The article by Tan et?al. (2019) analyzed the variation of HA proteins of naturally isolated H9N2 viruses and evaluated the function of the potential N-linked glycosylation sites on viral pathogenicity in mice.  The study by Wang et?al. (2019) explored the possible molecular mechanism of duck 2´-5´-oligoadenylate synthetase like protein (dOASL) in response to H5N1 virus infection.  The last article by Huang et?al. (2019) performed transcriptomic analysis of the brain and spleen of ducks that infected with different H5N1 viruses and suggested that H5N1 viruses may escape or subvert host immune response by affecting translation of different immune genes.

    The findings reported in these papers will enrich our knowledge on influenza virus infection and provide important information in the prevention and control of influenza.

    Regulation of influenza virus infection by microRNAs
    ZOU Zhong, GONG Wen-xiao, HUANG Kun, SUN Xiao-mei, JIN Mei-lin
    2019, 18(7): 1421-1427.  DOI: 10.1016/S2095-3119(18)62134-3
    Abstract ( )   PDF in ScienceDirect  
    MicroRNAs (miRNAs) are small noncoding RNAs of 18–25 nucleotides (nt) in length that represent key regulators of many normal cellular functions through the inhibition of mRNA translation and mRNA degradation.  To date, over 2 500 mature miRNAs have been identified in plants, animals and several types of viruses.  Influenza A virus (IAV), which is a negative-sense, single-stranded RNA virus, does not encode viral miRNA.  However, IAV infection can alter the expression of host miRNAs, either in cell culture or in host.  In turn, host miRNAs regulate IAV life cycle through directly binding to IAV genome or indirectly targeting host factors associated with viral replication.  In this review, we briefly summarized the role and significance of miRNA in relation to IAV pathogenesis.  Understanding the role of cellular miRNAs during viral infection may be beneficial to the identification of novel therapeutic strategies to block IAV replication.
    Development of a reverse-transcription loop-mediated isothermal amplification assay to detect avian influenza viruses in clinical specimens
    SHI Lin, YU Xue-wu, YAO Wei, YU Ben-liang, HE Li-kun, GAO Yuan, ZHANG Yun-xian, TIAN Guo-bin, PING Ji-hui, WANG Xiu-rong
    2019, 18(7): 1428-1435.  DOI: 10.1016/S2095-3119(19)62700-0
    Abstract ( )   PDF in ScienceDirect  
    In recent years, the avian influenza has brought not only serious economic loss to the poultry industry in China but also a serious threat to human health because of the avian influenza virus (AIV) gene recombination and reassortment.  Until now, traditional RT-PCR, fluorescence RT-PCR and virus isolation identification have been developed and utilized to detect AIV, but these methods require high-level instruments and experimental conditions, not suitable for the rapid detection in field and farms.  In order to develop a rapid, sensitive and practical method to detect and identify AIV subtypes, 4 specific primers to the conserved region of AIV M gene were designed and a loop-mediated isothermal amplification (RT-LAMP) method was established.  Using this method, the M gene of H1–H16 subtypes of AIV were amplified in 30 min with a water bath and all 16 H subtypes of AIV were able to be visually identified in presence of fluorescein, without cross reaction with other susceptible avian viruses.  In addition, the detection limit of the common H1, H5, H7, and H9 AIV subtypes with the RT-LAMP method was 0.1 PFU (plaque-forming unit), which was 10 times more sensitive than that using the routine RT-PCR.  Further comparative tests found that the positivity rate of RT-LAMP on detecting clinical samples was 4.18% (14/335) comparing with 3.58% (12/335) from real-time RT-PCR.  All these results suggested that the RT-LAMP method can specifically detect and identify AIV with high sensitivity and can be considered as a fast, convenient and practical method for the clinic test and epidemiological investigation of AIV.
    Identification of an H1N1 subtype of swine influenza virus and serological analysis
    SUN Fa-chao, TAN Min, ZHANG Yuan-chao, WANG Yu-chao, CAO Sheng-liang, DING Guo-fei, CONG Fang-yuan, GUO Li-hong, LIU Si-dang, XIAO Yi-hong
    2019, 18(7): 1436-1442.  DOI: 10.1016/S2095-3119(19)62579-7
    Abstract ( )   PDF in ScienceDirect  
    To investigate the epizootic of swine influenza virus (SIV), 60 nasal swabs were collected from a clinical cases of pig farm in Tai’an City, Shandong Province of China in April 2017.  SIV was isolated by inoculating into 10-day-old Special Pathogen Free embryonated eggs and the whole genome was sequenced.  An H1N1 subtype SIV was isolated and designated as A/swine/Shandong/TA04/2017(H1N1).  Phylogenetic analysis showed that apart from the polymerase A (PA) fragment belonging to the 2009 pandemic H1N1 branch, seven genome segments belonged to avian-like H1N1 influenza virus lineage.  The cleavage site sequence of the hemagglutinin (HA) protein was PSIQSR↓G, which is a typical molecular biological characteristic.  Five potential N-glycosylation sites (N14, N26, N277, N484 and N543) were found in the HA gene.  To further investigate the epidemiology of SIV in this farm, the 995 serum samples were assessed with EAH1N1 2009 pandemic H1N1 and H3N2 antigens.  The results showed that the total positive rate was 65.43%.  The positive rates of single virus infection detected by EAH1N1, 2009pdmH1N1 and H3N2 for serum HI (Hemagglutination inhibition) were 48.35, 30.85 and 7.47%, respectively.  The results showed that SIV in Shandong Province has been reassorted in some segments and the SIV-positive rate was high on the SIV outbreak farm.  These data provide evidence of an epizootic of SIV.
    Glycosylation of the hemagglutinin protein of H9N2 subtype avian influenza virus influences its replication and virulence in mice
    TAN Liu-gang, CHEN Zhao-kun, MA Xin-xin, HUANG Qing-hua, SUN Hai-ji, ZHANG Fan, YANG Shao-hua, XU Chuan-tian, CUI Ning
    2019, 18(7): 1443-1450.  DOI: 10.1016/S2095-3119(19)62669-9
    Abstract ( )   PDF in ScienceDirect  
    N-Linked glycosylation of hemagglutinin (HA) has been demonstrated to regulate the virulence and receptor-binding specificity of avian influenza virus (AIV).  In this study, we characterized the variation trend of naturally isolated H9N2 viruses for the potential N-linked glycosylation sites in HA proteins, and explored any important role of some glycosylation sites.  HA genes of 19 H9N2 subtype AIV strains since 2001 were sequenced and analyzed for the potential glycosylation sites.  The results showed that the viruses varied by losing one potential glycosylation site at residues 200 to 202, and having an additional one at residues 295 to 297 over the past few years.  Further molecular and single mutation analysis revealed that the N200Q mutation lost an N-linked glycosylation at positions 200 to 202 of the HA protein and affected the human-derived receptor affinity.  We further found that this N-linked glycosylation increased viral productivity in the lung of the infected mice.  These findings provide a novel insight on understanding the determinants of host adaption and virulence of H9N2 viruses in mammals.
    Identification of novel genes associated with duck OASL in response to influenza A virus
    WANG Xiao-xue, LU Chang, RONG En-guang, HU Jia-xiang, XING Yan-ling, LIU Zheng-yu, GAO Chu-ze, LIU Jin-hua, HUANG Yin-hua
    2019, 18(7): 1451-1459.  DOI: 10.1016/S2095-3119(19)62685-7
    Abstract ( )   PDF in ScienceDirect  
    2´-5´-Oligoadenylate synthetase like protein (OASL) plays a key role in response to viral infections through selectively activating the OAS/RNase L or OASL/RIG-I signaling pathway.  Although classic pathway of OASL is well-known, its regulated genes or co-actors are largely unknown.  To study the possible molecular mechanism of duck OASL (dOASL), we performed RNA-sequencing (RNA-seq) and immunoprecipitation and mass spectrometry (IP-MS) at the level of mRNA and protein, respectively.  For RNA-seq, we used DF1 cell lines (DF1dOASL+/+, DF1cOASL–/–, and DF1) with or without the CK/0513 H5N1 virus (A/chicken/huabei/0513/2007) infection.  1 737 differentially expressed genes (DEGs) were identified as candidate target genes regulated by dOASL.  Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Weighted Correlation Network Analysis (WGCNA) were performed.  We identified one important yellow co-expression module correlated with antiviral immune response.  In this module, Ankyrin repeat and FYVE domain containing 1 (ANKFY1), harboring a BTB domain similar to the methyl CpG-binding protein 1 (MBD1) which bound to OASL in human, was regulated by dOASL.  At protein level, 133 host proteins were detected.  Interestingly, ANKFY1 was one of them binding to dOASL protein.  Further phylogenomic and chromosomal syntenic analysis demonstrated MBD1 was absent in birds, while mammals retained.  It is suggested that OASL-ANKFY1 interaction might act as a compensatory mechanism to regulate gene expression in birds.  Our findings will provide a useful resource for the molecular mechanism research of dOASL.
    Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (Anas platyrhynchos)
    HUANG Yin-hua, FENG Hua-peng, HUANG Li-ren, YI Kang, RONG En-guang, CHEN Xiao-yun, LI Jian-wen, WANG Zeng, ZHU Peng-yang, LIU Xiao-juan, WANG Xiao-xue, HU Jia-xiang, LIU Xin, CHEN Hua-lan, WANG Jun...
    2019, 18(7): 1460-1472.  DOI: 10.1016/S2095-3119(19)62646-8
    Abstract ( )   PDF in ScienceDirect  
    H5N1 influenza represents one of the great challenges to public health.  Some H5N1 viruses (i.e., A/goose/Hubei/65/05, GS/65) are weakly pathogenic, while the others (i.e., A/duck/Hubei/49/05, DK/49) are highly pathogenic to their natural hosts.  Here, we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus.  We demonstrated that, compared to the GS/65 virus, the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways (i.e., RIG-I and MDA5) in ducks.  We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes, while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus.  We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis (WGCNA).  Moreover, we first demonstrated that the duck BCL2L15 and DCSTAMP in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently.  These analyses, in combination with our comprehensive transcriptomic data, provided global view of the molecular architecture for the interaction between host and H5N1 viruses. 
    Special Focus: Ecological functions of biochar
    TAN Wen-feng, LIN Qi-mei
    2019, 18(7): 1473.  DOI: 10.1016/S1671-2927(00)12350
    Abstract ( )   PDF in ScienceDirect  
    Biochar has been widely applied as a soil amendment in many parts of the world, which can enhance soil organic carbon (SOC) sequestration and nutrient availability beyond the fertilizer effect.  Enriched in poly-condensed aromatic C forms, biochar-C is difficult to be degraded and can hold carbon in soils for hundreds to thousands of years.  Biochar production and incorporation in soil would play critical roles in climate change mitigation.  Over the last decades, numerous researches have highlighted the beneficial roles of biochar in soil amendments.  The specific ecological functions of biochar have not been clearly described because of its diversities and complexities.  For example, biochar helps to ameliorate soil acidity and increase soil aggregated carbon, but the role of microbial interactions between biochar and soil has not been well understood.  In this special issue, we selected four papers contributed by Yuan et?al. (2019), Chen et?al. (2019), Guan et?al. (2019) and Shi et?al. (2019), as a window to reflect the latest research progress of this field in China.  Yuan et?al. (2019) investigated the diversity of microbial carbon use patterns in paddy soils amended with straw or straw-derived biochar in a 3-year field experiment; Chen et?al. (2019) reported that steam explosion of crop straws could improve the characteristics of biochar; Guan et?al. (2019) evaluated the effects of uncharred maize straw and charred maize straw amendments on organic carbon contents in bulk soil and in various soil aggregate-size and density fractions; Shi et?al. (2019) summarized the positive effects and mechanisms involved in the correction of soil acidity, the alleviation of aluminum toxicity and the increase of soil pH buffering capacity by applying crop residue biochar.  Through this special issue, we hope to further boost the basic and applied researches with related to the ecological functions of biochar from different aspects in soil in China and abroad. 
    Straw and biochar strongly affect functional diversity of microbial metabolism in paddy soils
    YUAN Hong-zhao, ZHU Zhen-ke, WEI Xiao-meng, LIU Shou-long, PENG Pei-qin, Anna Gunina, SHEN Jian-lin, Yakov Kuzyakov, GE Ti-da, WU Jin-shui, WANG Jiu-rong
    2019, 18(7): 1474-1485.  DOI: 10.1016/S2095-3119(18)62102-1
    Abstract ( )   PDF in ScienceDirect  
    The application of straw and biochar is widely practiced for the improvement of soil fertility.  However, its impact on microbial functional profiles, particularly with regard to paddy soils, is not well understood.  The aim of this study was to investigate the diversity of microbial carbon use patterns in paddy soils amended with straw or straw-derived biochar in a 3-year field experiment in fallow soil and at various development stages of a rice crop (i.e., tillering and blooming).  We applied the community level physiological profiling approach, with 15 substrates (sugars, carboxylic and amino acids, and phenolic acid).  In general, straw application resulted in the greatest microbial functional diversity owing to the greater number of  available C sources than in control or biochar plots.  Biochar amendment promoted the use of α-ketoglutaric acid, the mineralization of which was higher than that of any other substrate.  Principal component analyses indicated that microbial functional diversity in the biochar-amended soil was separated from those of the straw-amended and control soils.  Redundancy analyses revealed that soil organic carbon content was the most important factor regulating the pattern of microbial carbon utilization.  Rhizodeposition and nutrient uptake by rice plants modulated microbial functions in paddy soils and stimulated the microbial use of N-rich substances, such as amino acids.  Thus, our results demonstrated that the functional diversity of microorganisms in organic amended paddy soils is affected by both physicochemical properties of amendment and plant growth stage. 
    Steam explosion of crop straws improves the characteristics of biochar as a soil amendment
    CHEN Xue-jiao, LIN Qi-mei, Muhammad Rizwan, ZHAO Xiao-rong, LI Gui-tong
    2019, 18(7): 1486-1495.  DOI: 10.1016/S2095-3119(19)62573-6
    Abstract ( )   PDF in ScienceDirect  


    Five crop straws (wheat, rice, maize, oil-rape, and cotton) were first steam-exploded for 2 min at 210°C, 2.5 MPa and then pyrolyzed at 500°C for 2 h.  Steam explosion (SE) induced 47–95% and 5–16% reduction of hemicellulose and cellulose, respectively, in the crop straws.  The biochars derived from SE-treated feedstocks had a lower specific surface area (SSA) and pore volume, compared to those from pristine feedstocks, with one exception that SE enhanced SSA of oil-rape straw biochar by approximately 16 times.  After SE, biochars had significant higher anion exchange capacity (AEC) (6.88–11.44 cmol kg–1) and point of zero net charges (PZNC) (pH 3.61–5.32) values.  It can thus be speculated that these biochars may have higher potential for anions adsorption.  In addition, oil-rape straw might be suitable to SE pretreatment for preparing biochar as a soil amendment and sorbent as well.  Further work is required for testing its application in soil.
    Soil organic carbon associated with aggregate-size and density fractions in a Mollisol amended with charred and uncharred maize straw
    GUAN Song, LIU Si-jia, LIU Ri-yue, ZHANG Jin-jing, REN Jun, CAI Hong-guang, LIN Xin-xin
    2019, 18(7): 1496-1507.  DOI: 10.1016/S2095-3119(19)62643-2
    Abstract ( )   PDF in ScienceDirect  
    Straw return has been strongly recommended in China, whereas applying biochar into soil is considered to provide more benefits for agriculture as well as the environment.  In this study, a five-year (2011−2015) field experiment was conducted to evaluate the effects of uncharred maize straw amendment (MS) and charred maize straw amendment (charred MS) on organic carbon (C) contents in bulk soil and in various soil aggregate-size and density fractions.  Compared to no amendment (CK), the bulk soil organic C content significantly improved by 9.30% for MS and by 23.4% for charred MS.  Uncharred and charred maize straw applied annually at a consistent equal-C dosage resulted in 19.7 and 58.2% organic C sequestration efficiency in soil, respectively, after the five years of the field experiment.  The percentages of macroaggregates (>0.25 mm) and occluded microaggregates (0.25−0.053 mm) obviously increased by 7.73 and 18.1% for MS and by 10.7 and 19.6% for charred MS, respectively.  Moreover, significant incremental increases of 19.4 and 35.0% in macroaggregate-associated organic C occurred in MS and charred MS, respectively.  The occluded microaggregates associated organic C significantly increased by 21.7% for MS and 25.1% for charred MS.  Mineral-associated organic C (<0.053 mm) inside the macroaggregates and the occluded microaggregates obviously improved by 24.7 and 33.3% for MS and by 18.4 and 44.9% for charred MS.  Organic C associated with coarse particulate organic matter (POM) within the macroaggregates markedly increased by 65.1 and 41.2% for MS and charred MS, respectively.  Charred MS resulted in a noteworthy increment of 50.4% for organic C associated with heavy POM inside the occluded microaggregates, whereas charred MS and MS observably improved organic C associated with heavy POM inside the free microaggregates by 36.3 and 20.0%, respectively.  These results demonstrate that uncharred and charred maize straw amendments improve C sequestration by physically protecting more organic C in the macroaggregates and the occluded microaggregates.  Compared to the feedstock straw amendment, charred maize straw amendment is more advantageous to C sequestration. 
    Understanding the biochar’s role in ameliorating soil acidity
    SHI Ren-yong, LI Jiu-yu, NI Ni, XU Ren-kou
    2019, 18(7): 1508-1517.  DOI: 10.1016/S2095-3119(18)62148-3
    Abstract ( )   PDF in ScienceDirect  
    Extensive acidic soils, which suffer from accelerated soil acidification, are found in southern China.  Soil acidity, aluminum toxicity, and nutrient deficiencies severely limited crop productivity in acidic soils.  It has been widely reported that crop residue biochars can ameliorate acidic soils and increase crop productivity.  Here, we summarized the positive effects and mechanisms involved in the correction of soil acidity, the alleviation of aluminum toxicity and the increase of soil pH buffering capacity by crop residue biochars.  The carbonate, oxygen-containing functional groups and silicates in biochars are the major components responsible for their efficacy in amending acidic soils and resisting soil re-acidification.  We conclude that application of crop residue biochars may be a better option than traditional liming to ameliorate acidic soils.  Nonetheless, further researches into soil acidification are still required to address some issues that are controversial and poorly understood.
    A review: The beneficial effects and possible mechanisms of aluminum on plant growth in acidic soil
    Noor Muhammad, Gerald Zvobgo, ZHANG Guo-ping
    2019, 18(7): 1518-1528.  DOI: 10.1016/S2095-3119(18)61991-4
    Abstract ( )   PDF in ScienceDirect  
    Aluminum (Al) is the third most abundant element in the earth’s crust and a major factor inhibiting plant growth and reducing crop yield in acidic soil.  Although there is substantial research on the phytotoxic effects and the underlying mechanisms of Al by applying Al alone hydroponically, soil is a complex medium containing numerous mineral elements that can interact with Al and other elements and their bioavailability in plants.  In this review, we describe the roles of Al in promoting plant growth, enhancing phosphorus availability and efficient use in plants, and alleviating H+, iron, and manganese toxicity in acidic conditions.  Furthermore, we discuss the possible mechanisms of enhanced abiotic stress tolerance induced by Al.  We also elucidate the role of Al in attracting plant growth promoting rhizo-bacteria (PGPR) and their interactions with plants by increasing organic exudates.
    Crop Science
    Gene bank scheduling of seed regeneration: Interim report on a long term storage study
    Robert Redden, Debra Partington
    2019, 18(7): 1529-1540.  DOI: 10.1016/S2095-3119(19)62730-9
    Abstract ( )   PDF in ScienceDirect  
    A major challenge for the management of gene banks is the maintenance of good seed health in the collections.  Large germplasm collections >10 000 accessions often have been acquired from different sources over a range of dates, may differ in germination at time of deposition in the gene bank, and may have genetic differences in seed longevity.  The major storage variables affecting seed longevity are temperature and seed moisture content.  Two varieties of each pea (Pisum sativus L.), lentil (Lens culinaris Medikus subsp. culinaris), and chickpea (Cicer arietinum L.), were stored at three temperatures; 40, 20, and 2°C, each with three seed moisture levels of 10.9–13.8% (high), 7.9–10.3% (medium), and 7–7.8% (low), in the Australian Temperate Field Crops Collection gene bank.  Seed longevity at a given storage period was estimated by the corresponding germination percentage for each treatment.  This paper is an interim report on seed viability decline in the first seven years of this seed longevity study, in which viability decline towards zero was almost completed in the three seed moisture treatments at 40°C and the 20°C high seed moisture treatment, but had not declined in the other treatments.  Seed longevity positively responded to a reduction in temperature and then to a reduction in seed moisture.  The number of days in storage for seed germination decline to 85% (p85), and to 50% (p50) for mean seed viability, are reported by storage/varietal treatment.  Both p85 and p50 showed significant inverse linear responses with seed moisture at 40°C for pea and lentil varieties, with intra-specific variation for pea.  This long term trial aims to provide informed timing of seed regeneration for accessions in a gene bank.
    Assignment of unanchored scaffolds in genome of Brassica napus by RNA-seq analysis in a complete set of Brassica rapa-Brassica oleracea monosomic addition lines
    HUO Dong-ao, ZHU Bin, TIAN Gui-fu, DU Xu-ye, GUO Juan, CAI Meng-xian
    2019, 18(7): 1541-1546.  DOI: 10.1016/S2095-3119(19)62635-3
    Abstract ( )   PDF in ScienceDirect  
    The economically valuable oil crop Brassica napus (AACC, 2n=38), which arose from interspecific hybridization between the diploid ancestors Brassica rapa (AA, 2n=20) and Brassica oleracea (CC, 2n=18), has a complex genome.  More than 10% of the assembled sequences, most of which belong to the C subgenome, have not been anchored to the corresponding chromosome.  Previously, a complete set of monosomic alien addition lines (MAALs, C1–C9) with each of the nine C-subgenome chromosomes added to the extracted A subgenome was obtained from the allotetraploid B. napus donor Oro, after the ancestral B. rapa (RBR Oro) genome was restored.  These MAALs effectively reduced the complexity of the B. napus genome.  Here, we determined the expression values of genes on unanchored scaffolds in the MAALs and RBR Oro.  Then, multiple comparisons of these gene expression values were used to determine the affiliations of the non-anchored scaffolds on which the genes were located.  In total, 54.68% (44.11 Mb) of the 80.67 Mb of non-anchored scaffolds belonging to the C subgenome were assigned to corresponding C chromosomes.  This work highlights the potential value of these MAALs in improving the genome quality of B. napus.
    Global sensitivity analysis of wheat grain yield and quality and the related process variables from the DSSAT-CERES model based on the extended Fourier Amplitude Sensitivity Test method
    LI Zhen-hai, JIN Xiu-liang, LIU Hai-long, XU Xin-gang, WANG Ji-hua
    2019, 18(7): 1547-1561.  DOI: 10.1016/S2095-3119(18)62046-5
    Abstract ( )   PDF in ScienceDirect  
    A crop growth model, integrating genotype, environment, and management factor, was developed to serve as an analytical tool to study the influence of these factors on crop growth, production, and agricultural planning.  A major challenge of model application is the optimization and calibration of a considerable number of parameters.  Sensitivity analysis (SA) has become an effective method to identify the importance of various parameters.  In this study, the extended Fourier Amplitude Sensitivity Test (EFAST) approach was used to evaluate the sensitivity of the DSSAT-CERES model output responses of interest to 39 crop genotype parameters and six soil parameters.  The outputs for the SA included grain yield and quality (take grain protein content (GPC) as an indicator) at maturity stage, as well as leaf area index, aboveground biomass, and aboveground nitrogen accumulation at the critical process variables.  The key results showed that: (1) the influence of parameter bounds on the sensitivity results was slight and less than the impacts from the significance of the parameters themselves; (2) the sensitivity parameters of grain yield and GPC were different, and the sensitivity of the interactions between parameters to GPC was greater than those between the parameters to grain yield; and (3) the sensitivity analyses of some process variables, including leaf area index, aboveground biomass, and aboveground nitrogen accumulation, should be performed differently.  Finally, some parameters, which improve the model’s structure and the accuracy of the process simulation, should not be ignored when maturity output as an objective variable is studied.
    Estimating total leaf nitrogen concentration in winter wheat by canopy hyperspectral data and nitrogen vertical distribution
    DUAN Dan-dan, ZHAO Chun-jiang, LI Zhen-hai, YANG Gui-jun, ZHAO Yu, QIAO Xiao-jun, ZHANG Yun-he, ZHANG Lai-xi, YANG Wu-de
    2019, 18(7): 1562-1570.  DOI: 10.1016/S2095-3119(19)62686-9
    Abstract ( )   PDF in ScienceDirect  
    The use of remote sensing to monitor nitrogen (N) in crops is important for obtaining both economic benefit and ecological value because it helps to improve the efficiency of fertilization and reduces the ecological and environmental burden.  In this study, we model the total leaf N concentration (TLNC) in winter wheat constructed from hyperspectral data by considering the vertical N distribution (VND).  The field hyperspectral data of winter wheat acquired during the 2013–2014 growing season were used to construct and validate the model.  The results show that: (1) the vertical distribution law of LNC was distinct, presenting a quadratic polynomial tendency from the top layer to the bottom layer.  (2) The effective layer for remote sensing detection varied at different growth stages.  The entire canopy, the three upper layers, the three upper layers, and the top layer are the effective layers at the jointing stage, flag leaf stage, flowering stages, and filling stage, respectively.  (3) The TLNC model considering the VND has high predicting accuracy and stability.  For models based on the greenness index (GI), mND705 (modified normalized difference 705), and normalized difference vegetation index (NDVI), the values for the determining coefficient (R2), and normalized root mean square error (nRMSE) are 0.61 and 8.84%, 0.59 and 8.89%, and 0.53 and 9.37%, respectively.  Therefore, the LNC model with VND provides an accurate and non-destructive method to monitor N levels in the field.
    Effect of mechanical threshing on damage and vigor of maize seed threshed at different moisture contents
    GU Ri-liang, HUANG Ran, JIA Guang-yao, YUAN Zhi-peng, REN Li-sha, LI Li, WANG Jian-hua
    2019, 18(7): 1571-1578.  DOI: 10.1016/S2095-3119(18)62026-X
    Abstract ( )   PDF in ScienceDirect  
    Mechanical threshing used when preparing maize seeds for planting subjects seed to damage and reduces seed quality.  The purpose of this study was to assess the effect of mechanical threshing on the quality of maize seed threshed at different moisture contents (MCs).  Seeds of dent maize JK968 and flint maize DD2 were threshed at 12, 15, 18, 21, and 24% MC.  The damage degree was determined by iodine staining, and seed vigor was assessed by standard germination (SG), cold test germination (CTG), accelerated aging germination (AAG), seedling emergence rate, and seedling root and shoot length.  The results showed that the damage percentage increased, and the seed vigor parameters decreased with increasing seed MC during threshing in both cultivars.  For obtaining high seed quality, indicated by at least 90, 85, and 80% of SG, AAG, and CTG, respectively, JK 968 and DD2 should be threshed at MC lower than 15 and 18%, respectively.  Furthermore, the damage mainly occurred in the apical part of seeds, irrespective of the threshing MC in both cultivars.  When the embryo was damaged, seedling emergence rates were significantly reduced with great influence on shoot length.  Damage to the endosperm resulted in little effect on seedling performance.  Flint maize DD2 was more tolerant to mechanical threshing than dent maize JK968.  These results provided technical reference for the production and processing of high vigor maize seeds.
    Downregulation of SL-ZH13 transcription factor gene expression decreases drought tolerance of tomato
    ZHAO Ting-ting, WANG Zi-yu, BAO Yu-fang, ZHANG Xiao-chun, YANG Huan-huan, ZHANG Dong-ye, JIANG Jing-bin, ZHANG He, LI Jing-fu, CHEN Qing-shan, XU Xiang-yang
    2019, 18(7): 1579-1586.  DOI: 10.1016/S2095-3119(19)62621-3
    Abstract ( )   PDF in ScienceDirect  
    Zinc finger-homeodomain proteins (ZF-HDs) are transcription factors that regulate plant growth, development, and abiotic stress tolerance.  The SL-ZH13 gene was found to be significantly upregulated under drought stress treatment in tomato (Solanum lycopersicum) leaves in our previous study.  In this study, to further understand the role that the SL-ZH13 gene plays in the response of tomato plants to drought stress, the virus-induced gene silencing (VIGS) method was applied to downregulate SL-ZH13 expression in tomato plants, and these plants were treated with drought stress to analyze the changes in drought tolerance.  The SL-ZH13 silencing efficiency was confirmed by quantitative real-time PCR (qRT-PCR) analysis.  In SL-ZH13-silenced plants, the stems wilted faster, leaf shrinkage was more severe than in control plants under the same drought stress treatment conditions, anyd the mean stem bending angle of SL-ZH13-silenced plants was smaller than that of control plants.  Physiological analyses showed that the activity of superoxide dismutase (SOD) and peroxidase (POD) and the content of proline (Pro) in SL-ZH13-silenced plants were lower than those in control plants after 1.5 and 3 h of drought stress treatment.  The malondialdehyde (MDA) content in SL-ZH13-silenced plants was higher than that in control plants after 1.5 and 3 h of drought stress treatment, and H2O2 and O2-· accumulated much more in the leaves of SL-ZH13-silenced plants than in the leaves of control plants.  These results suggested that silencing the SL-ZH13 gene affected the response of tomato plants to drought stress and decreased the drought tolerance of tomato plants. 
    Genome-wide identification and expression analysis of auxin response factor (ARF) gene family in strawberry (Fragaria vesca)
    WANG Shao-xi, SHI Feng-yan, DONG Xiang-xiang, LI Yu-xiang, ZHANG Zhi-hong, LI He
    2019, 18(7): 1587-1603.  DOI: 10.1016/S2095-3119(19)62556-6
    Abstract ( )   PDF in ScienceDirect  
    Auxin signaling plays a significant role in the whole process of plant growth and development from embryogenesis to senescence. Auxin response factors (ARFs) are reported to regulate the expression of auxin response genes by binding to auxin response elements. ARF is the most critical transcription factor family which has been released in most species, but few reports in strawberry. In this study, the structure characterization of 12 FvARF genes in strawberry, their expression patterns at different development stages, different organizations, and different indole-3-acetic acid (IAA) treatments were analyzed. The expression of 12 FvARFs was found in all experiment tissues and showed almost the same trend during fruit development. All FvARFs respond to the treatment of IAA. Our study provides comprehensive information on ARF family in strawberry, including gene structures, chromosome locations, phylogenetic relationships and expression patterns. The information on FvARF genes paves the way for future research on strawberry ARF genes. Keywords:
    Molecular cloning and functional characterization of apple U-box E3 ubiquitin ligase gene MdPUB29 reveals its involvement in salt tolerance
    HAN Peng-liang, DONG Yuan-hua, JIANG Han, HU Da-gang, HAO Yu-jin
    2019, 18(7): 1604-1612.  DOI: 10.1016/S2095-3119(19)62594-3
    Abstract ( )   PDF in ScienceDirect  
    An E3 ubiquitin ligase gene (Genbank accession no.: MD01G1010900) was cloned from the Royal Gala apple genome (Malus×domestica Borkh.).  Sequence analysis showed that the length of the MdPUB29 gene was 1 275 bp, encoding 424 amino acids.  Phylogenetic tree analysis indicated that the apple E3 ubiquitin ligase exhibited the greatest sequence similarity to Pyrus×bretschneideri.  The predicted protein structural domain of MdPUB29 showed that it contained a U-box domain.  qRT-PCR analysis showed that MdPUB29 was expressed widely in different tissues of the Royal Gala apple species, and was highly expressed in the root, while the expression of MdPUB29 was significantly inhibited by exogenous NaCl.  Immunoblotting assays revealed that MdPUB29 protein abundance in tissue cultures of the Royal Gala apple accumulated under NaCl stress conditions.  Three-dimensional protein structure prediction indicated that MdPUB29 was highly homologous with AtPUB29.  The growing potential of MdPUB29-expressing apple calli and Arabidopsis were much stronger than that of the control under salt stress conditions, suggesting that MdPUB29 may positively regulate salt tolerance.
    Plant Protection
    Sublethal effects of sulfoxaflor on the fitness of two species of wheat aphids, Sitobion avenae (F.) and Rhopalosiphum padi (L.)
    XIN Juan-juan, YU Wen-xin, YI Xiao-qing, GAO Jun-ping, GAO Xi-wu, ZENG Xiao-peng
    2019, 18(7): 1613-1623.  DOI: 10.1016/S2095-3119(18)62094-5
    Abstract ( )   PDF in ScienceDirect  
    Sitobion avenae (F.) and Rhopalosiphum padi (L.) are two important pests of wheat in China.  They typically coexist in fields during the late period of wheat growth.  Sulfoxaflor is a novel sulfoximine insecticide that demonstrates broad-spectrum efficacy, especially in targeting sap-feeding insects.  This study was carried out to investigate the sublethal effects of sulfoxaflor on the development, longevity, and reproduction of two species of wheat aphids.  Our results showed that sublethal concentrations of sulfoxaflor did not cause significant effects on the fecundity or the longevity of the parent generation (F0 generation) of either S. avenae or R. padi.  However, it caused transgenerational sublethal effects.  For S. avenae, adult longevity of F1 generation was significantly decreased.  No significant differences were observed on the population parameters of S. avenae in the F1 generation.  For R. padi, the adult preoviposition period (APOP) and the total preoviposition period (TPOP) of F1 generation were significantly reduced.  The mean generation time (T) was significantly reduced in the R. padi F1 generation.  What’s more, the intrinsic rate of increase (rm) and the finite rate of increase (λ) were significantly increased in the R. padi F1 generation.  Taken together, these results suggest that exposure to the LC25 of sulfoxafl had no effects on the parent generation of S. avenae or R. padi, but it reduced adult longevity of S. avenae as a negative effect and increased the rm and λ of R. padi in the first progeny generation, which may have an impact on the population dynamics of R. padi.
    Identification and developmental expression of putative gene encoding juvenile hormone esterase (CpJHE-like) in codling moth, Cydia pomonella (L.)
    HUANG Cong, WU Qiang, JIANG Chun-yan, XING Long-sheng, SHI Guo-liang, ZHANG Bin, QIAN Wan-qiang, LI You-zhi, XI Yu, YANG Nian-wan, WAN Fang-hao
    2019, 18(7): 1624-1633.  DOI: 10.1016/S2095-3119(19)62682-1
    Abstract ( )   PDF in ScienceDirect  
    Juvenile hormone esterase (JHE) is a key enzyme for insects, playing an important role in the regulation of insect growth, development, diapause and reproduction.  We identified a complete putative JHE of Cydia pomonella (CpJHE-like) which is comprised of a 1 761 bp coding sequence (CDS) encoding 587 amino acid residues from the transcriptome data.  The deduced protein sequence of CpJHE-like showed the highest identity of 60.44% with the Adoxophyes honmai JHE (AhJHE) and the minimal identity of 25.81% with Aedes aegypti JHE (AaJHE).  CpJHE-like exhibited all the seven typical motifs of the functional JHEs and had the highly consistent tertiary structure with Manduca sexta JHE (MsJHE).  Phylogenetic analysis showed that the CpJHE-like was close to two JHEs from the family Tortricidae.  The CpJHE-like transcript level take a leap in the 3-day-old fifth instar larva, increased about 300-fold compared to the basal level.  Tissue-specific expression profile showed that the CpJHE-like transcript was expressed mainly in the fat body.  This study indicates that the CpJHE-like is the functional JHE, which may play vital roles in the development and reproduction of C. pomonella.
    Food Science
    Chemical composition, antioxidant activity and GC-MS analysis of juice and peel oil of grapefruit varieties cultivated in India
    Shahnawaz Ahmed, H S Rattanpal, Khalid Gul, Rouf Ahmad Dar, Akash Sharma
    2019, 18(7): 1634-1642.  DOI: 10.1016/S2095-3119(19)62602-X
    Abstract ( )   PDF in ScienceDirect  
    Citrus family especially Grapefruit, has attained considerable attention due to the presence of a number of essential components that have cardiovascular and anti-hypertensive properties.  The juice and essential oil extracted from eight recently released grapefruit cultivars were used to study physicochemical and antioxidant properties.  The total soluble solids (TSS), titratable acidity (TA) and pH of juice samples extracted from various grapefruit varieties differed significantly.  The refractive index, specific gravity and optical rotation values for the oil varied from 1.473 to 1.396, 0.863 to 0.847 and +93 to +86, respectively.  The percent 2,2-diphenyl-1-picrylhydrazyl radical activity (% DPPH activity) and ferric reducing antioxidant power (FRAP) values for grapefruit juice and peel oil varied from 24.06 to 18.79, 2.91 to 1.44 mmol g–1 and 84.87 to 74.73,  7.76 to 5.73 mmol g–1, respectively.  There were significant differences in physicochemical, antioxidant properties and volatile profiles of extracted juice and oil.  The oil exhibited higher DPPH and FRAP values than the juice.  Among different components identified which accounted for over 99% of the volatile fraction, limonene, myrcene, and benzopyran were major components in all oil samples.
    Phosphorylation of sarcoplasmic and myofibrillar proteins in three ovine muscles during postmortem ageing
    WANG Ying, LI Xin, LI Zheng, DU Man-ting, ZHU Jie, ZHANG She-qi, ZHANG De-quan
    2019, 18(7): 1643-1651.  DOI: 10.1016/S2095-3119(19)62653-5
    Abstract ( )   PDF in ScienceDirect  
    This study aimed to examine changes in phosphorylation of sarcoplasmic and myofibrillar proteins from longissimus lumborum, semitendinosus, and psoas major muscles during postmortem ageing for 5 d.  These sarcoplasmic and myofibrillar proteins were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and stained with phosphorous and protein specific stains.  Myofibril fragmentation index, pH, the content of lactic acid and the relative activity of μ-calpain in three ovine muscles were measured.  These results showed that the relative phosphorylation level of sarcoplasmic and myofibrillar proteins of psoas major muscle were lower compared with longissimus lumborum and semitendinosus muscles (P<0.05).  The pH of psoas major muscle was the lowest at 0.5 h postmortem, and the highest after 12 h postmortem (P<0.05).  In addition, the relative activity of μ-calpain was higher within 5 d postmortem and myofibril fragmentation index was higher after 1 d postmortem in psoas major muscle than those of longissimus lumborum and semitendinosus muscles (P<0.05).  The sarcoplasmic protein phosphorylation may regulate the rate of pH decline to influence the μ-calpain activity and then proteolysis of proteins consequently.  This study gives a new perspective of the mechanism of postmortem meat tenderization.
    Improved food environments for healthy diets and enhanced nutrition
    QIN Yong-jun, Nathanaël Pingault, Fabio Ricci, Jessica Fanzo
    2019, 18(7): 1652-1654.  DOI: 10.1016/S2095-3119(19)62678-X
    Abstract ( )   PDF in ScienceDirect  
    As illustrated by the High-Level Panel of Experts on Food Security and Nutrition of the UN Committee on World Food Security (HLPE 2017), while hunger is on the rise again, malnutrition now takes multiple forms and affects all countries.  Globally, 821 million people are still undernourished (FAO et al. 2018), over 2 billion people suffer from micronutrient deficiencies, while overweight and obesity are quickly rising which affects 1.9 billion adults and 41 million children under five.
    The HLPE, in many of its publications, called for radical transformations in our current food systems to address the multiple burdens of malnutrition.  There is already enough evidence to act.  The short-term cost of action may seem high, but the cost of inaction is likely to be much higher, carrying with it a terrible legacy affecting future generations.
    The HLPE (2017) identified three core elements in food systems (food supply chains, food environments and consumer behaviour, see Fig. 1).  Among these three elements, the HLPE illustrated the central role of food environments in shaping consumer behaviour and food choices and, finally, in determining diets and nutrition.
    The food environment refers to the “physical, economic, political and socio-cultural context in which consumers engage with the food system to make their decisions about acquiring, preparing and consuming food” (HLPE 2017).  It consists of:
    • the built environment, including: the physical food entry points (supermarkets, formal and informal markets, street kiosks, food trucks, restaurants, schools, hospitals, public canteens, etc.) where food is purchased or obtained, their location and density; the physical infrastructures that allow consumers to access these points;
    • the human environment, including: the personal determinants of consumer food choices (such as income, education, values, skills, etc.); and the political, social and cultural norms that influence these choices.
    The food environment is a space of convergence where all actors involved in food systems, from food producers to end consumers, interact and confront their interests, objectives and strategies.  Therefore, acting on food environments in the proper way can bring transformative changes across the whole food system for delivering healthy and sustainable diets1.  More specifically, the HLPE (2017) identified three key elements of food environments on which to act to improve the diet and nutrition outcomes of our current food systems: (i) physical and economic access to food (proximity and affordability); (ii) promotion, advertising and information; (iii) food quality and safety.  Considering these three elements and recognizing the evidence gaps in our current knowledge, the HLPE (2017) explored concretely two pathways towards more sustainable food systems2 for healthier diets:
    The first pathway is to improve physical and economic access to healthy diets  This first priority adopts a food system perspective.  Food supply chains impact diets and nutrition both positively and negatively.  Governments have the key responsibility to set policies, including regulations, taxes, subsidies and other forms of incentives, which enable actors in food supply chains to maximize the nutrition value of the food produced.  Government policies and programmes which specifically focus on the food environment are also key. These include: public procurement to make diverse and healthy diets more accessible and convenient3 in public places (e.g., schools, hospitals, prisons, etc.), as well as in rural marketplaces, at reasonable prices for consumers; investments and regulations (including zoning regulations) that improve the built environment; taxing junk food or sodas; regulating product formulation; regulating nutrition and health claims on food packaging; adopting an easy to interpret front-of-the-pack labelling system; limiting advertising and promotion of unhealthy foods, especially to children and adolescents; and strengthening national food safety and quality standards, etc.
    This second pathway is to strengthen consumers’ information and education on healthy diets  This second priority adopts a consumer perspective and aims at creating and strengthening the demand for heathy foods.  There is a mutual relationship between food supply chains and consumer demands.  If current food supply chains largely shape consumers’ choice, consumers can also influence food supply through their behavior and demand for specific foods.  Effective regulation, information and education have the potential to orient consumers towards healthier and more sustainable food choices.  Mass media campaigns, social and behavior change communication, social media and citizen reporting, social protection programmes and food-based dietary guidelines all serve to potentially increase awareness and influence consumer dietary choices.  Yet, information and education alone may not trigger significant changes and that communication programmes must incorporate insight on actionable steps to change habits to be more effective.   When it comes to food choices, taste, convenience, cultural norms and price often prevail over health or sustainability criteria.  The most effective way to influence demand is when healthy, palatable foods are also affordable and convenient for consumers.
    In conclusion, being the interface between food supply and food demand of consumers, food environments should be privileged as the policy entry point to transform our current food systems.