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    15th Anniversary of Journal of Integrative Agriculture (JIA)
    WAN Jian-min
    2017, 16(12): 2655-2656.  DOI: 10.1016/S2095-3119(17)61828-8
    Abstract ( )   PDF (740KB) ( )  
    The year 2017 marks the 15th anniversary of Journal of Integrative Agriculture (JIA), an official journal of the Chinese Academy of Agricultural Sciences (CAAS).  JIA has experienced a successful journey during the past 15 years.  The 21st century began with great challenges in global climate change, food safety, resource scarcity, and other key issues which are closely related to the agriculture sciences.  Effective solutions for agricultural problems require an international exchange of experience via platforms such as academic journals.  To contribute to these forums, the agriculture community in China sought to establish a scholarly journal published in English.  In Jan. 2002, an agriculture journal in English was launched by CAAS and the first issue of the journal Agricultural Sciences in China was published.  From the start, it has emphasized global concerns in multi-disciplinary agricultural fields of crop science, horticulture, plant protection, animal science, veterinary medicine,  agro-ecosystem and environment science, food science and etc.  And it is a peer-reviewed international journal published monthly in English.  The first Editor-in-Chief was ZHAI Huqu, the president of CAAS at that time.

    Four years later in 2006, the journal joined Elsevier publishing and became known worldwide.  In 2012, the journal was renamed Journal of Integrative Agriculture (JIA).  This change was spearheaded by Shu Geng who was the then Executive Editor-in-Chief.  In the next few years, led by the second Editor-in-Chief LIU Xu, JIA improved greatly.  JIA has successfully provided a platform for agriculture science communication home and abroad.  I am honoured to have become the third Editor-in-Chief in 2016.  I would like to take this opportunity to thank my predecessors for all their sterling efforts.

    Over the years, JIA’s progress has been reflected in many ways.  The JCR impact factor went up from 0.449 in 2012 to 1.042 in 2016.  The downloads per year from ScienceDirect increased from 18 to 430 thousand times.  Initially, almost all the articles were translations from the Chinese journal Scientia Agriculura Sinica, also published by CAAS.  Currently, annual submissions have risen to around 1 500 articles of which 35% are from outside China with an overall rejection rate of about 85%.  Up to now, around 4 000 articles have been published in 16 volumes of the journal.  

    JIA’s achievements are also recognized widely in China.  It has received many awards including First Prize of JINLI Award of 5th National Outstanding Agricultural Journals in 2006 by Chinese Association of Agricultural Science Societies (CAASS), one of the Top 10 High-Quality English Journals in 2007 by General Administration of Press and Publication of China (GAPPC), Outstanding Science and Technology Journal of China 2 times in 2008 and 2017 by Institute of Scientific & Technical Information of China (ISTIC).  One article was selected for inclusion among “The 100 Most Influential Articles” by ISTIC in 2012, and it has been listed as among the Highest International Impact Academic Journals of China 6 times consistently in 2012–2017 by China Academic Journal Electronic Publishing House, China Scientific Literature Evaluation and Measuring Research Center and Tsinghua University Library jointly.  

    The internet is changing the world, revolutionizing scientific communication and publishing.  To keep pace with this revolution, JIA has constructed its own dynamically changing website.  Now one week after a manuscript’s acceptance, JIA has advanced online publication on its own website.  By cooperating with Elsevier B. V., the journal’s full texts are available globally on ScienceDirect.  Since 2016, 30% of the articles have been open access, freely available to readers.  Since 2010, JIA has had a ScholarOne Manuscripts portal with embedded CrossCheck for all communications among authors, editors, and reviewers.  This helps not only reduce the manuscripts’ handling time, but effectively avoid plagiarism.  In addition, with the aid of the journal’s Wechat, circles of scientists-friends have been built covering key agricultural scientists in China.  Among these circles are the plant protection circle, the agro-ecology circle, and the editorial board circle, etc.  Wechat is having a marked effect for JIA’s work, for example, distributing articles, releasing news, initiating a discussion, calling for articles, etc.

    To cope with this increasing demand, JIA reconstructed its Editorial Board this year to include a new team of 10 Section Editors (SE), who are responsible for acting as editors.  The SE handles submissions and solicit special issues and contributions within their areas of specialization.  Accordingly, the journal changed its procedures from having the Editor-in-Chief bearing the major responsibility for making manuscript decisions to having the SE do a majority of the work.  The aim was to spread the work load and involve more people in the effort.  On the other hand, we try by this means to tell our authors as quickly as possible whether their manuscripts could be further reviewed or not, and thereby to give them enough time to consider other journals.  It has been successful.  

    To spread and promote the journal, JIA has hosted five international conferences on various agricultural sciences each with about 400 persons in attendance.  JIA also conducts many other activities every year including meetings, seminars, news briefings, and author trainings at different levels.  

    Fifteen years is not a long time for journal development, but JIA has progressed rapidly and never has been in a stronger position than what it is now.  This is due to the combined efforts of a strong Editorial Board, a dedicated Editorial staff team, the publisher Elsevier B.V., but certainly not least, the great number of the referees whose entirely voluntary work not only maintains the scientific standards of the journal, but also provides the authors with the opportunity to improve their research manuscripts.  And I thank all our authors and readers most sincerely for their enthusiasm and support to JIA.  

    JIA has been strengthened by grants and foundations including the 2013–2014 Special Fund on Key Academic Journals by the National Natural Science Foundation of China (NSFC), the 2016–2018 Promoting Project for Leading Journals in China by China Association for Science and Technology (CAST), and the 2016–2018 Climbing Peaking Program for Elite Journals in China by CAST.  And it also has been funded by CAAS and Agricultural Information Institute of CAAS.  

    Within this 15th anniversary issue, 25 themes are addressed in crop science, plant protection, animal science and veterinary medicine, agro-ecosystem & environment, food science, agricultural economics and management.  The significant scientific advances and the important methods within the specialists’ areas are highlighted.  I thank all contributors to this special issue.  They have devoted a hard work for it.  This issue celebrates both our past and JIA’s developing promotion in publishing.  Looking ahead, JIA is determined to be at the forefront of world agriculture and to provide effective and efficient publication to its authors and readers.
    Crop Science
    Transgenic approaches for improving use efficiency of nitrogen, phosphorus and potassium in crops
    TENG Wan, HE Xue, TONG Yi-ping
    2017, 16(12): 2657-2673.  DOI: 10.1016/S2095-3119(17)61709-X
    Abstract ( )   PDF (364KB) ( )  
    The success of the Green Revolution largely relies on fertilizers, and a new Green Revolution is very much needed to use fertilizers more economically and efficiently, as well as with more environmental responsibility. The use efficiency of nitrogen, phosphorus, and potassium is controlled by complex gene networks that co-ordinate uptake, re-distribution, assimilation, and storage of these nutrients. Great progress has been made in breeding nutrient-efficient crops by molecularly engineering root traits desirable for efficient acquisition of nutrients from soil, transporters for uptake, redistribution and homeostasis of nutrients, and enzymes for efficient assimilation. Regulatory and transcription factors modulating these processes are also valuable in breeding crops with improved nutrient use efficiency and yield performance.
    Genomics-assisted breeding - A revolutionary strategy for crop improvement
    LENG Peng-fei, Thomas Lübberstedt, XU Ming-liang
    2017, 16(12): 2674-2685.  DOI: 10.1016/S2095-3119(17)61813-6
    Abstract ( )   PDF (279KB) ( )  
    Food shortages arise more frequently owing to unpredictable crop yield losses caused by biotic and abiotic stresses.  With advances in molecular biology and marker technology, a new era of molecular breeding has emerged that has greatly accelerated the pace of plant breeding.  High-throughput genotyping technology and phenotyping platforms have enabled large-scale marker-trait association analysis, such as genome-wide association studies, to precisely dissect the genetic architecture of plant traits.  Large-scale mapping of agronomically important quantitative trait loci, gene cloning and characterization, mining of elite alleles/haplotypes, exploitation of natural variations, and genomic selection have paved the way towards genomics-assisted breeding (GAB).  With the availability of more and more informative genomic datasets, GAB would become a promising technique to expedite the breeding cycle for crop improvement.  
    The CCT domain-containing gene family has large impacts on heading date, regional adaptation, and grain yield in rice
    ZHANG Jia, HU Yong, XU Li-he, HE Qin, FAN Xiao-wei, XING Yong-zhong
    2017, 16(12): 2686-2697.  DOI: 10.1016/S2095-3119(17)61724-6
    Abstract ( )   PDF (454KB) ( )  
    There are 41 members of the CCT (CO, CO-like, and TOC1) domain-containing gene family in rice, which are divided into three subfamilies: COL (CONSTANS-like), CMF (CCT motif family), and PRR (pseudoresponse regulator).  The first flowering gene to be isolated by map-based cloning, Heading date 1 (Hd1), which is the orthologue of CO in rice, belongs to COL.  The central regulator of plant development, Ghd7, belongs to CMF.  The major role in controlling rice distribution to high latitudes, Ghd7.1/PRR37, belongs to PRR.  Both of Hd1, Ghd7 and Ghd7.1 simultaneously control grain number, plant height, and the heading date.  To date, 13 CCT family genes from these three subfamilies have been shown to regulate flowering.  Some of them have pleiotropic effects on grain yield, plant height, and abiotic stresses, and others function as circadian oscillators.  There are two independent photoperiod flowering pathways that are mediated by GI-Hd1-Hd3a/RFT and GI-Ehd1-Hd3a/RFT in rice.  CCT family genes are involved in both pathways.  The latest study reveals that protein interaction between Hd1 and Ghd7 integrates the two pathways.  CCT family genes are rich in natural variation because rice cultivars have been subjected to natural and artificial selection for different day lengths in the process of domestication and improvement.  Alleles of several crucial CCT family genes such as Hd1, Ghd7, and Ghd7.1 exhibit geographic distribution patterns and are highly associated with yield potentials.  In addition, CCT family genes are probably involved in the responses to abiotic stress, which should be emphasized in future work.  In general, CCT family genes play important roles in regulating flowering, plant growth, and grain yield.  The functional identification and elucidation of the molecular mechanisms of CCT family genes would help construct a flowering regulatory network and maximize their contribution to rice production.
    Cytogenetics and germplasm enrichment in Brassica allopolyploids in China
    LI Zai-yun, WANG You-ping
    2017, 16(12): 2698-2708.  DOI: 10.1016/S2095-3119(17)61733-7
    Abstract ( )   PDF (357KB) ( )  
    This paper reviews research advances in cytogenetics and germplasm innovation in Brassica allopolyploids, particularly oilseed rape (Brassica napus), in China.  Three naturally evolved Brassica allotetraploid species are cytologically stable but tend to preferentially lose several chromosomes from one subgenome when induced by alien chromosome elimination.  A-subgenome is extracted from B. napus, and the ancestral Brassica rapa was restituted after the total loss of C-subgenome chromosomes.  Genome-wide genetic and epigenetic alterations were observed in both natural and synthetic Brassica allotetraploids.  B. napus was subjected to extensive interspecific hybridization with landraces of B. rapa and Brassica juncea, which exhibit abundant phenotype variations, to widen the genetic diversity in breeding and select numerous elite germplasm resources and cultivars; these cultivars include the representative Zhongyou 821, which also parented numerous other varieties.  Novel B. napus genotypes were obtained using Brassica trigenomic hybrids and allohexaploids (2n=54, AABBCC) by combining subgenomes from extant allotetraploids and diploids as bridge.  Alien additions, substitutions, and translocations of the B. napus genome were developed by intergeneric/intertribal sexual and somatic hybridizations with several crucifers.  Furthermore, mitochondrial DNA recombination promoted the production of novel cytoplasmic male sterile lines.  
    Priming: A promising strategy for crop production in response to future climate
    WANG Xiao, LIU Fu-lai, JIANG Dong
    2017, 16(12): 2709-2716.  DOI: 10.1016/S2095-3119(17)61786-6
    Abstract ( )   PDF (579KB) ( )  
    Anticipated more frequent extreme events due to changes in global climatic variability requires adaptation of crop species to multi-occurrence abiotic stresses hereby sustaining the food security.  Priming, by pre-exposure of plants to an eliciting factor, enables plants to be more tolerant to later biotic or abiotic stress events.  Priming induced “stress memory” exists in both present generation and the offspring.  Thus, priming is suggested to be a promising strategy for plants to cope with the abiotic stresses under global change scenarios.  In this review, the underlying physiological and molecular mechanisms of priming induced enhancement of stress tolerance to the major abiotic stresses of drought and waterlogging, and high and low temperature in crop plants were discussed, and the potential to utilize the priming effect for sustaining crop productivity in future climates was also suggested.
    Research progress on reduced lodging of high-yield and -density maize
    XUE Jun, XIE Rui-zhi, ZHANG Wang-feng, WANG Ke-ru, HOU Peng, MING Bo, GOU Ling, LI Shao-kun
    2017, 16(12): 2717-2725.  DOI: 10.1016/S2095-3119(17)61785-4
    Abstract ( )   PDF (250KB) ( )  
    Increasing plant density is an effective way to enhance maize yield, but often increases lodging rate and severity, significantly elevating the risk and cost of maize production.  Therefore, lodging is a major factor restricting future increases in maize yield through high-density planting.  This paper reviewed previous research on the relationships between maize lodging rate and plant morphology, mechanical strength of stalks, anatomical and biochemical characteristics of stalks, root characteristics, damage from pests and diseases, environmental factors, and genomic characteristics.  The effects of planting density on these factors and explored possible ways to improve lodging resistance were also analyzed in this paper.  The results provide a basis for future research on increasing maize lodging resistance under high-density planting conditions and can be used to develop maize cultivation practices and lodging-resistant maize cultivars.
    Booming research on rice physiology and management in China: A bibliometric analysis based on three major agronomic journals
    PENG Shao-bing
    2017, 16(12): 2726-2735.  DOI: 10.1016/S2095-3119(17)61804-5
    Abstract ( )   PDF (351KB) ( )  
    Rice research has always been the top priority in China and China produces the highest number of scientific journal papers on rice, particularly on rice genetics and breeding.  In this study, we used a bibliometric approach to analyze the trends of papers published by Chinese researchers on rice physiology and management.  Data were collected from three major agronomic journals (i.e., Agronomy Journal, Crop Science, and Field Crops Research) by searching in the Web of Science on September 8, 2017.  A total of 186 rice papers were published by Chinese researchers on crop physiology and management in the three journals since their establishment.  Yearly average number of such papers was 1.6, 6.5, and 21.0 for the periods of 1993–2005, 2006–2011, and 2012–2017, respectively.  Their quality in terms of citation performance has also improved significantly in the recent decade.  Huazhong Agricultural University, Yangzhou University, and Nanjing Agricultural University were leading organizations and published 54.4% of all 186 papers.  Huang Min of Hunan Agricultural University and Peng Shaobing of Huazhong Agricultural University published the most number of rice papers on crop physiology and management as the first and corresponding authors, respectively.  Yield potential and nitrogen-related research such as nitrogen use efficiency, nitrogen management, and plant nitrogen diagnosis have been the research focuses for rice crop.  In recent years, research on global warming including high temperature stress, direct seeding, zero tillage, Bt rice, and critical nitrogen dilution curve were becoming popular.  New research is emerging on yield gap, rice ratooning, and simplified and reduced-input practices in rice production.
    Plant Protection
    Action modes of transcription activator-like effectors (TALEs) of Xanthomonas in plants
    XU Zheng-yin, ZOU Li-fang, MA Wen-xiu, CAI Lu-lu, YANG Yang-yang, CHEN Gong-you
    2017, 16(12): 2736-2745.  DOI: 10.1016/S2095-3119(17)61750-7
    Abstract ( )   PDF (1305KB) ( )  
    Plant-pathogenic Xanthomonas infects a wide variety of host plants and causes many devastating diseases on crops.  Transcription activator-like effectors (TALEs) are delivered by a type III secretion system (T3SS) of Xanthomonas into plant nuclei to directly bind specific DNA sequences (TAL effector-binding elements, EBEs) on either strand of host target genes with an unique modular DNA-binding domain and to bidirectionally drive host gene transcription.  The target genes in plants consist of host susceptibility (S) genes promoting disease (ETS) and resistance (R) genes triggering defense (ETI).  Here we generally summarized the discovery of TALEs in Xanthomonas species, their functions in bacterial pathogenicity in plants and their target genes in different host plants, and then focused on the newly revealed modes of protein action in triggering or suppressing plant defense.
    The arms race between Magnaporthe oryzae and rice: Diversity and interaction of Avr and R genes
    WANG Bao-hua, Daniel J. Ebbole, WANG Zong-hua
    2017, 16(12): 2746-2760.  DOI: 10.1016/S2095-3119(17)61746-5
    Abstract ( )   PDF (476KB) ( )  
    Rice blast disease, caused by Magnaporthe oryzae, threatens global food security.  The rice blast pathosystem is a longstanding model system for understanding plant-microbe interactions.  In order to elucidate the coevolution of the host and pathogen, and provide the appropriate methods for preventing or controlling rice blast disease, researchers have focused on the evolution of virulence factors and resistance genes.  Thus far, more than 30 rice blast resistance (R) genes and 12 avirulence (Avr) genes have been cloned.  This review summarizes the cloned rice blast R genes, cloned Avr genes of M. oryzae and the interaction between them.  This discussion also considers some of the major unanswered questions concerning this pathosystem and the opportunities for future investigations.
    Geminiviruses and their application in biotechnology
    YANG Qiu-ying, DING Bo, ZHOU Xue-ping
    2017, 16(12): 2761-2771.  DOI: 10.1016/S2095-3119(17)61702-7
    Abstract ( )   PDF (476KB) ( )  
    Being a major class of single-stranded DNA viruses, geminiviruses are mostly studied due to their catastrophic infectious effect on crops.  These DNA viruses are characteristic for their ability in quickly multiplying viral genetic materials without integrating into the genome of plants, which makes them ideal for developing viral vectors for plants bioengineering.  Geminivirus-derived vectors can be classified into expression vectors and virus-induced gene silencing (VIGS) vectors.  Details of the design, construction, application and improvements of these geminivirus vectors are summarized and discussed.  
    Progress in the development and application of plant-based antiviral agents
    LI Xiang-yang, SONG Bao-an
    2017, 16(12): 2772-2783.  DOI: 10.1016/S2095-3119(17)61788-X
    Abstract ( )   PDF (1461KB) ( )  
    Plant virus disease is one of the major causes of biological disasters in agriculture worldwide.  Given the complexity of transmission media and plant disease infection mechanisms, the prevention and control of plant viral diseases is a great challenge, and an efficient green pesticide is urgently needed.  For this reason, when developing candidate drug leads to regulate plant viruses, pesticide experts have focused on characteristics such as low pesticide resistance, eco-friendliness, and novel mechanism.  Researchers have also theoretically investigated the molecular targets of viruses infecting agricultural crops.  Antiviral screening models have been constructed based on these molecular targets, and the mechanisms of commercial drugs and high-activity compounds have been extensively investigated.  After screening, some compounds have been applied in the field and found to have good commercial prospects; these drugs may be used to create new green antiviral pesticides to control plant viruses.  This paper reviews the screening, mode of action, development and application of recently used plant-based antiviral agents.
    Animal Science · Veterinary Medicine
    Future livestock breeding: Precision breeding based on multi-omics information and population personalization
    YANG Ya-lan, ZHOU Rong, LI Kui
    2017, 16(12): 2784-2791.  DOI: 10.1016/S2095-3119(17)61780-5
    Abstract ( )   PDF (241KB) ( )  
    With the rapid development of molecular biology and related disciplines, animal breeding has moved from conventional breeding to molecular breeding.  Marker-assisted selection and genomic selection have become mainstream practices in molecular breeding of livestock.  However, these techniques only use information from genomic variation but not multi-omics information,  thus do not fully explain the molecular basis of phenotypic variations in complex traits.  In addition, the accuracy of breeding value estimation based on these techniques is occasionally controversial in different populations or varieties.  Given the rapid development of high-throughput sequencing techniques and functional genome and dramatic reductions in the overall cost of sequencing, it is possible to clarify the interactions between genes and formation of phenotypes using massive sets of omic-level data from studies of the transcriptome, proteome, epigenome, and metabolome.  During livestock breeding, multi-omics information regarding breeding populations and individuals should be taken into account.  The interactive regulatory networks governing gene regulation and phenotype formation in diverse livestock population, varieties and species should be analyzed.  In addition, a multi-omics regulatory breeding model should be constructed.  Precision, population-personalized breeding is expected to become a crucial practice in future livestock breeding.  Precision breeding of individuals can be achieved by combining population genomic information at multi-omics levels together with genomic selection and genome editing techniques.  
    Gene engineering in swine for agriculture
    WANG Yan-fang, HUANG Jiao-jiao, ZHAO Jian-guo
    2017, 16(12): 2792-2804.  DOI: 10.1016/S2095-3119(17)61766-0
    Abstract ( )   PDF (451KB) ( )  
    Domestic pigs are the second most important source of meat world-wide, and the genetic improvement of economic traits, such as meat production, growth, and disease resistance, is a critical point for efficient production in pigs.  Through conventional breeding and selection programs in pigs, which are painstakingly slow processes, some economic traits, such as growth and backfat, have been greatly improved over the past several decades.  However, the improvement of many polygenetic traits is still very slow and challenging to be improved by conventional breeding strategies.  The development of reproductive knowledge and a variety of techniques, including foreign gene transfer strategies, somatic cell nuclear transfer (SCNT) and particularly, recently developed nuclease-mediated genome editing tools, has provided efficient ways to produce genetically modified (GM) pigs for the dramatic improvement of economic traits.  In this review, we briefly discuss the progress of genomic markers used in pig breeding program, trace the history of genetic engineering, mainly focusing on the progress of recently developed genome editing tools, and summarize the GM pigs which have been generated to aim at the agricultural purposes.  We also discuss the specific challenges facing application of gene engineering in pig breeding, and future prospects.
    Current research progresses on calf rearing and nutrition in China
    DIAO Qi-yu, ZHANG Rong, TU Yan
    2017, 16(12): 2805-2814.  DOI: 10.1016/S2095-3119(17)61767-2
    Abstract ( )   PDF (262KB) ( )  
    Calves are the reserve forces for dairy cattle.  Scientific rearing strategy of calves is the basis of efficient cattle breeding.  However, many problems exist in current rearing systems of calves and restrict the sustainable development of dairy cattle in China.  The absence of basic research is the most highlighted problem among them.  Recent researches on growth performance, nutrient digestibility, blood biochemical indices and rumen development in calves were summarized in this paper.  Additionally, the optimal levels of energy and protein in milk replacer and starter diets for calves were indicated, and limiting amino acids for calves fed different diets were discussed.  A variety of additives, such as acidifiers, probiotics and polysaccharides, are regarded as promising alternatives to antibiotics to reduce disease in calves.  Dietary supplementations of these additives have positive effects on growth and health of calves.  However, studies on the nutrition of vitamins and minerals in calves have been seldom done, and deserve our further researches.  To sum up, the postnatal period is one of the most critical “windows” for rumen manipulation and epigenetic regulation.  Any changes from environments, especially early nutrition, may produce long-term effects on growth, health and milk yields in adult cattle.
    Nutritional strategies for reducing nitrogen, phosphorus and trace mineral excretions of livestock and poultry
    LU Lin, LIAO Xiu-dong, LUO Xu-gang
    2017, 16(12): 2815-2833.  DOI: 10.1016/S2095-3119(17)61701-5
    Abstract ( )   PDF (311KB) ( )  
    Animal agriculture contributes to environmental pollutions through the surplus nitrogen (N), phosphorus (P), and trace minerals that animals excrete.  Animal nutritionists have sought alternatives to formulate more efficient diets and reduce production costs and environmental concerns.  In general, element excretions may be reduced by avoiding the overfeeding of specific elements or using nutritional approaches to improve element utilizations by the animals.  Several nutritional strategies are possible for minimizing N, P, and trace mineral excretions: 1) to accurately meet dietary N, P and trace mineral requirements of animals, which includes reducing the dietary crude protein contents with synthetic amino acids or feeding high rumenally undegraded protein, minimizing the adequate levels of dietary P and trace elements, adopting phase or group-feeding program, and considering the bioavailable trace mineral contents in the feed ingredients; 2) to improve the bioavailabilities of dietary N, P, and trace elements for animals by using some additives (enzymes, growth promoters, probiotics, prebiotics, vitamin D isomers, and organic acids); 3) to use highly available P sources or organic trace elements.  In the future, nutrient strategies must be integrated into total production systems so that animal production systems are environmentally safe as well as economically viable.
    Advances in pathogenesis of Streptococcus suis serotype 2
    FAN Hong-jie
    2017, 16(12): 2834-2847.  DOI: 10.1016/S2095-3119(17)61768-4
    Abstract ( )   PDF in ScienceDirect  
    Streptococcus suis is one of the major pathogens of swine streptococcosis.  Among them, the strongest virulence and highest rate of clinical isolation serotype is S. suis serotype 2 (SS2).  Moreover, SS2 is also an important zoonosis pathogen, which caused severe public health issues in China.  It has been reported that SS2 has several virulence factors, including muramidase released protein, extracellular factors, capsule, fibronectin-binding protein, enolase, hemolysin, small RNA, biofilm, two-component regulatory systems, STK/STP, etc., whose functions involved in adhesion, anti-phagocytosis, inflammatory pathway activation, invasion, etc.  Actually, SS2 has developed a variety of ways to escape from host immune system during evolution.  In particularly, capsule could resist phagocytosis through inhibiting sphingosine dependent immune cell recognition, which plays an important role in escaping host inflammation response; moreover, superoxide dismutase encoding by sodA enables SS2 escaping reactive oxygen species (ROS) in host immune cells; besides, binding complement factor h with Fhb could suppress the activation of complement alternative pathway and bactericidal effect.  And SS2 could also hinder the formation of neutrophil extracellular traps (NETs) to avoid trapping by swine neutrophils, while host immune globulin could be degraded by IgA1 hydrolase and IgM protease.  In addition, SS2 could escape host immune defense with the help of multiple transcriptional factors and micro-RNA.  So far, the pathogenesis of meningitis, arthritis caused by SS2 infection, is still unclear, and the virulence regulatory mechanism of phosphorylation, micro-RNA need to be further clarified.  Importantly, the study of interaction mechanism of pathogen and host contribute to further demonstration the pathogenesis of SS2.  
    Agro-ecosystem & Environment
    Nitrogen cycling and environmental impacts in upland agricultural soils in North China: A review
    JU Xiao-tang, ZHANG Chong
    2017, 16(12): 2848-2862.  DOI: 10.1016/S2095-3119(17)61743-X
    Abstract ( )   PDF (730KB) ( )  
    The upland agricultural soils in North China are distributed north of a line between the Kunlun Mountains, the Qinling Mountains and the Huaihe River.  They occur in arid, semi-arid and semi-humid regions and crop production often depends on rain-fed or irrigation to supplement rainfall.  This paper summarizes the characteristics of gross nitrogen (N) transformation, the fate of N fertilizer and soil N as well as the N loss pathway, and makes suggestions for proper N management in the region.  The soils of the region are characterized by strong N mineralization and nitrification, and weak immobilization and denitrification ability, which lead to the production and accumulation of nitrate in the soil profile.  Large amounts of accumulated nitrate have been observed in the vadose-zone in soils due to excess N fertilization in the past three decades, and this nitrate is subject to occasional leaching which leads to groundwater nitrate contamination.  Under farmer’s conventional high N fertilization practice in the winter wheat-summer maize rotation system (N application rate was approximately 600 kg ha–1 yr–1), crop N uptake, soil residual N, NH3 volatilization, NO3 leaching, and denitrification loss accounted for around 27, 30, 23, 18 and 2% of the applied fertilizer N, respectively.  NH3 volatilization and NO3 leaching were the most important N loss pathways while soil residual N was an important fate of N fertilizer for replenishing soil N depletion from crop production.  The upland agricultural soils in North China are a large source of N2O and total emissions in this region make up a large proportion (approximately 54%) of Chinese cropland N2O emissions.  The “non-coupled strong ammonia oxidation” process is an important mechanism of N2O production.  Slowing down ammonia oxidation after ammonium-N fertilizer or urea application and avoiding transient high soil NH4+ concentrations are key measures for reducing N2O emissions in this region.  Further N management should aim to minimize N losses from crop and livestock production, and increase the recycling of manure and straw back to cropland.  We also recommend adoption of the 4R (Right soure, Right rate, Right time, Right place) fertilization techniques to realize proper N fertilizer management, and improving application methods or modifying fertilizer types to reduce NH3 volatilization, improving water management to reduce NO3 leaching, and controlling the strong ammonia oxidation process to abate N2O emission.  Future research should focus on the study of the trade-off effects among different N loss pathways under different N application methods or fertilizer products.  
    Effects of long-term fertilization on soil gross N transformation rates and their implications
    DAI Shen-yan, WANG Jing, CHENG Yi, ZHANG Jin-bo, CAI Zu-cong
    2017, 16(12): 2863-2870.  DOI: 10.1016/S2095-3119(17)61673-3
    Abstract ( )   PDF in ScienceDirect  
    Application of fertilizer has been found to significantly affect soil N cycling.  However, a comprehensive understanding of the effects of long-term fertilization on soil gross N transformation rates is still lacking.  We compiled data of observations from 10 long-term fertilization experiments and conducted a meta-analysis of the effects of long-term fertilization on soil gross N transformation rates.  The results showed that if chemical fertilizers of N, P and K were applied in balance, soil pH decreased very slightly.  There was a significantly positive effect of long-term fertilization, either chemical or organic fertilizers or their combinations, on gross N mineralization rate compared to the control treatment (the mean effect size ranged from 1.21 to 1.25 at 95% confidence intervals (CI) with a mean of 1.23), mainly due to the increasing soil total N content.  The long-term application of organic fertilizer alone and combining organic and chemical fertilizer could increase the mineralization-immobilization turnover, thus enhance available N for plant while reduce N losses potential compared to the control treatment.  However, long-term chemical fertilizer application did not significantly affect the gross NH4+ immobilization rate, but accelerated gross nitrification rate (1.19; 95% CI: 1.08 to 1.31).  Thus, long-term chemical fertilizer alone would probably induce higher N losses potential through NO3– leaching and runoff than organic fertilizer application compared to the control treatment.  Therefore, in the view of the effects of long-term fertilization on gross N transformation rates, it also supports that organic fertilizer alone or combination of organic and chemical fertilizer could not only improve crop yield, but also increase soil fertility and reduce the N losses potential.
    Recent progress and future prospect of digital soil mapping: A review
    ZHANG Gan-lin, LIU Feng, SONG Xiao-dong
    2017, 16(12): 2871-2885.  DOI: 10.1016/S2095-3119(17)61762-3
    Abstract ( )   PDF (778KB) ( )  
    To deal with the global and regional issues including food security, climate change, land degradation, biodiversity loss, water resource management, and ecosystem health, detailed accurate spatial soil information is urgently needed.  This drives the worldwide development of digital soil mapping.  In recent years, significant progresses have been made in different aspects of digital soil mapping.  The main purpose of this paper is to provide a review for the major progresses of digital soil mapping in the last decade.  First, we briefly described the rise of digital soil mapping and outlined important milestones and their influence, and main paradigms in digital soil mapping.  Then, we reviewed the progresses in legacy soil data, environmental covariates, soil sampling, predictive models and the applications of digital soil mapping products.  Finally, we summarized the main trends and future prospect as revealed by studies up to now.  We concluded that although the digital soil mapping is now moving towards mature to meet various demands of soil information, challenges including new theories, methodologies and applications of digital soil mapping, especially for highly heterogeneous and human-affected environments, still exist and need to be addressed in the future.
    Food Science
    Review on the processing characteristics of cereals and oilseeds and their processing suitability evaluation technology
    WANG Qiang, LIU Hong-zhi, SHI Ai-min, HU Hui, LIU Li, WANG Li, YU Hong-wei
    2017, 16(12): 2886-2897.  DOI: 10.1016/S2095-3119(17)61799-4
    Abstract ( )   PDF (1108KB) ( )  
    Cereals and oilseeds are the foundation of human survival which have attracted much attention due to their nutritional and functional properties for maintaining the healthy life.  There are abundant varieties of cereals and oilseeds, however, for a long time, their process suitabilities are still unknown, resulting in the lack of precision processing.  This paper summarized the characteristics of cereals and oilseeds, including sensory, physicochemical and processing qualities, their characteristic fingerprinting and products qualities.  Furthermore, the quality fast detection method was also analyzed.  It also explored the role of mathematical model and the standard evaluation index to determine the process suitability and discussed the opportunity for advanced model capability.  We also prospected on scientific problems for expanding the predictive capabilities for processing suitabilities of these abundant varieties, focusing on the better results and advancements towards the processing of cereals and oilseeds products and improvement of their quality.  
    Global production, processing and utilization of lentil: A review
    Matina Joshi, Yakindra Timilsena, Benu Adhikari
    2017, 16(12): 2898-2913.  DOI: 10.1016/S2095-3119(17)61793-3
    Abstract ( )   PDF (440KB) ( )  
    Lentil is a highly nutritious legume with an ample quantity of carbohydrates and good amount of proteins, minerals, vitamins, phytochemicals and fibres.  Although it has been used as staple food since ancient times, its usage has been limited in developed countries, especially due to the lower protein digestibility, presence of anti-nutritional factors, flatulence and poor cooking qualities.  Processing of lentils including dehulling and splitting and isolation of major fractions, e.g., proteins and starches are some of the strategies that can be adopted to add value and increase consumption of these legumes.  This review paper intends to provide detailed overview of lentil’s global production, nutritional composition and processing methods of lentil.  Methods of isolation/characterization of lentil protein and starch and their subsequent application in foods are also presented. 
    pH effect on the formation of THM and HAA disinfection byproducts and potential control strategies for food processing
    Yen-Con Hung, Brian W. Waters, Veerachandra K. Yemmireddy, Ching-Hua Huang
    2017, 16(12): 2914-2923.  DOI: 10.1016/S2095-3119(17)61798-2
    Abstract ( )   PDF (229KB) ( )  
    Chlorine-based sanitizers have seen wide spread use in food sanitation.  The reaction of chlorine species with organic matter is a concern for two reasons.  Available chlorine can be “used up” by organic compounds resulting in a lower amount of chlorine available for disinfection.  Another concern is that some forms of chlorine can react with some organic compounds to form toxic halogenated disinfection byproducts (DBPs).  Many studies have been conducted to evaluate the role of hypochlorous acid (HOCl) and hypochlorite ion (OCl–) in the production of DBPs with a particular interest in the production of trihalomethanes (THMs) and haloacetic acids (HAAs).  Since most of the chlorine reactions are pH dependent, pH is found to have a significant effect on the formation of chlorine DBPs.  In many cases, the concentration of THMs decreases and HAAs increases as pH decreases.  pH also plays an important role in the determination of the type and amount of DBPs formed, with lower, more acidic, pHs resulting in the formation of less chloroform. This review summarizes the information from the literature on the role of chlorine-based sanitizers as affected by pH in the formation of different types of DBPs.  Alternative novel strategies to minimize the formation of DBPs are also discussed.   
    Progress of potato staple food research and industry development in China
    ZHANG Hong, XU Fen, WU Yu, HU Hong-hai, DAI Xiao-feng
    2017, 16(12): 2924-2932.  DOI: 10.1016/S2095-3119(17)61736-2
    Abstract ( )   PDF (230KB) ( )  
    Potato is the largest non-cereal food crop worldwide and ranked as the world’s fourth most important food crop after rice, wheat, and maize.  Potato is a vital food-security crop and substitute for cereal crop considering its high yield and great nutritive value.  Therefore, by replacing wheat, rice or maize in traditional staple foods partly by potato, the nutritional value of traditional foods and the utilization of potato are expected to be improved.  China is the largest potato producer worldwide in terms of either volume or area.  However, majority of potatoes are consumed as fresh vegetables for cuisine, and the industrial processing rate is much lower than the global average.  Thus, research and development for nutritional potato stable food suitable for the dietary habits of Chinese residents are of great significance.  However, we still confronted plenty of constraints in the development of potato staple food.  In order to develop potato staple food suitable for Chinese residents’ dietary habit like noodles, Mantou (steamed bread), rice and rice noodles, also to industrialize production of potato staple foods, some transformations need to be realized.  Independent innovation is the only choice to realize the potato staple food processing and industrial development strategy on the technical level.  Thus a lot of researches have been done to promote the development of potato staple food in China.  Up to now, we already developed a series kinds of potato staple foods and some of these staple foods have already been widely promoted in Chinese markets.  
    Agricultural Economics and Management
    The prospects for China's food security and imports: Will China starve the world via imports?
    HUANG Ji-kun, WEI Wei, CUI Qi, XIE Wei
    2017, 16(12): 2933-2944.  DOI: 10.1016/S2095-3119(17)61756-8
    Abstract ( )   PDF (254KB) ( )  
    China’s food supply and demand have significant implications for both China’s own national food security and that of the world.  This study reviews China’s food security prospects and their implications, focusing on international trade in the coming decade.  The results show that China’s policies for ensuring food security will be enhanced and China will move to sustainable agriculture.  Most studies anticipate that China will increase its food and feed imports in the coming decade.  China’s overall food self-sufficiency is likely to fall from 94.5% in 2015 to around 91% by 2025.  The greatest increases in imports are likely to be soybean, maize, sugar, and dairy products.  However, within the production capacity of the major exporting countries and of many food-importing developing countries, China’s additional imports of 3 to 5% of its total food consumption in the coming decade are unlikely to threaten global food security.  Indeed, the projected imports of feed and several foods could provide opportunities for many exporting countries to expand their production and save global resources.  
    Air pollution, food production and food security: A review from the perspective of food system
    Feifei Sun, DAI Yun, Xiaohua Yu
    2017, 16(12): 2945-2962.  DOI: 10.1016/S2095-3119(17)61814-8
    Abstract ( )   PDF (370KB) ( )  
    Air pollution negatively impacts food security.  This paper reviews the current literature on the relationship between air pollution and food security from the perspective of food system.  It highlights that agricultural emissions which substantially contribute to air pollution could happen at every stage along the food supply chain.  Meanwhile, air pollution can not only affect plant growth and animal health but also shift market equilibrium of both agro-inputs and outputs in the food supply chain and thereby affect food security indirectly.  Furthermore, this study evaluates the effects of agricultural policy and energy policy on food security and air pollution, respectively, and provides an overview of potential policy instruments to reduce air pollution while ensuring food security.  Finally, we identify the remaining research and policy issues for further studies, mainly focusing on the study of household’s bounded rational behaviors and the issue of rural aging population.