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    Recent advances in understanding the role of miRNAs in exosomes and their therapeutic potential
    MIAO Xiang-yang
    2017, 16(04): 753-761.  DOI: 10.1016/S2095-3119(16)61530-7
    Abstract ( )   PDF in ScienceDirect  
    MicroRNAs (miRNAs) are small endogenous non-protein coding RNAs that range in size from 19–25 nucleotides.  Thousands of miRNA genes have been identified in a variety of organisms, suggesting genetic exchange and distribution among species.  miRNAs negatively regulate gene expression by binding to the 3´-untranslated regions (3´-UTRs) of their target genes and play an important role in growth, development and the occurrence of diseases.  In this review, we summarize the recent advances in the understanding of the role of miRNAs in exosomes and their therapeutic potential, as well as provide an overview of the basic characteristics of miRNAs.
    Recognizing production options for pearl millet in Pakistan under changing climate scenarios
    Asmat Ullah, Ashfaq Ahmad, Tasneem Khaliq, Javaid Akhtar
    2017, 16(04): 762-773.  DOI: 10.1016/S2095-3119(16)61450-8
    Abstract ( )   PDF in ScienceDirect  
    Climate change is making the lands a harsher environment all over the world including Pakistan.  It is expected to oppose us with three main challenges: increase in temperature up to 2–5°C (heat stress), increasing water stress and severe malnourishment due to climate change.  It has been foreseen that there will be a 10% increase of dryland areas with climate change in the world, with more variability and incidences of short periods of extreme events (drought and heat stress).  Pearl millet is a hardy, climate smart grain crop, idyllic for environments prone to drought and heat stresses.  The crop continues to produce highly nutritious grain sustainably, thereby encouraging the fight against poverty and food insecurity due to its resilience.  The crop is more responsive to good production options (planting time, planting density, inter/intra row spacing, nitrogen application and irrigation).  It has high crop growth rate, large leaf area index and high radiation use efficiency that confers its high potential yield.  In most of the cases, pearl millet is remained our agricultural answer to the climate calamity that we are facing, because it is selected as water saving, drought tolerant and climate change complaint crop.  In view of circumstances, pearl millet cultivation must be retrieved by recognizing production options in context to changing climate scenarios of Pakistan using crop modeling techniques.
    Crop Genetics · Breeding · Germplasm Resources
    Transgenic rice expressing a novel phytase-lactoferricin fusion gene to improve phosphorus availability and antibacterial activity
    WANG Zuo-ping, DENG Li-hua, WENG Lü-shui, DENG Xiang-yang, FU Xi-qin, XIN Ye-yun, XIAO Guo-ying
    2017, 16(04): 774-788.  DOI: 10.1016/S2095-3119(16)61468-5
    Abstract ( )   PDF in ScienceDirect  
    The developing trends of livestock production are efficiency, safety and sustainability, which face two major challenges: low availability of phytate phosphorus and abuse of antibiotics.  As a solution phytases and antimicrobial peptides are applied as feed additives.  However, phytases and antimicrobial peptides are susceptible to proteases, costly by fermentation and potential toxic to production hosts.  We transformed an optimized phytase-lactoferricin fusion gene PhyLf driven by an endosperm-specific promoter Gt13aP and Bar (bialaphos resistance) gene as a selection maker into rice.  The Bar and PhyLf genes were integrated into the rice genome, stably inherited and expressed.  Their phosphinothricin acetyl transferase (PAT) protein content of transgenic plants with glufosinate resistance varied between 50.45–93.39 μg g–1.  Fusion protein expressed especially in the seeds of transgenic rice had a summit phytase activity at 32.30 U g–1, which increased by 61.71-fold compared to the control/check group (CK) and 7.54-fold compared to un-optimized transgenic plant.  The highest inorganic phosphorus (Pi) content of the transgenic seeds reached 13.15 mg g–1, increased by 12.77-fold compared to that of CK.  Preliminary antibacterial experiments showed that the enterokinase hydrolysate product of fusion protein could inhibit the growth of Escherichia coli DH5α.  These results indicated that the protein PhyLf has the potential to increase availability of feed phytate phosphorus, improve consumer’s immunity and reduce the use of antibiotics.
    Single-nucleotide polymorphisms, mapping and association analysis of 1-FFT-A1 gene in wheat
    YUE Ai-qin, LI Ang, MAO Xin-guo, CHANG Xiao-ping, LI Run-zhi, JING Rui-lian
    2017, 16(04): 789-799.  DOI: 10.1016/S2095-3119(16)61471-5
    Abstract ( )   PDF in ScienceDirect  
    Fructans are major nonstructural carbohydrates in wheat (Triticum aestivum L.).  Fructan 1-fructosyltransferase (1-FFT) is the key enzyme in fructan biosynthesis.  In the present study, 96 sequence variants were detected in the 1-FFT-A1 gene among 26 wheat accessions including UR208, and 15 of them result in amino acid substitutions, forming four haplotypes.  Two markers M39 and M2164 were developed based on the InDel21-39 and SNP-2164 polymorphisms to distinguish the three haplotypes in the 1-FFT-A11-FFT-A1 was located on chromosome 4A using marker M2164 and was flanked by markers Xcwm27 and 6-SFT-A1.  By association analysis using a natural wheat population consisted of 154 accessions, the results showed that the two markers were significantly associated with water-soluble carbohydrate (WSC) content in the lower internode stem and total stem at the early and middle grain filling stages, 1 000-grain weight (TGW) at different grain filling stages and peduncle length (PLE).  Comparison of the effects of three haplotypes on agronomic traits indicated that TGW, PLE and total number of spikelets per spike (TNSS) were signi?cantly influenced by haplotypes.  HapIII showed a significant positive effect on TGW, PLE and TNSS.
    QTL mapping for leaf area in maize (Zea mays L.) under multi-environments
    CUI Ting-ting, HE Kun-hui, CHANG Li-guo, ZHANG Xing-hua, XUE Ji-quan, LIU Jian-chao
    2017, 16(04): 800-808.  DOI: 10.1016/S2095-3119(16)61524-1
    Abstract ( )   PDF in ScienceDirect  
    Leaves are the main organs of photosynthesis in green plants.  Leaf area plays a vital role in dry matter accumulation and grain yield in maize (Zea mays L.).  Thus, investigating the genetic basis of leaf area will aid efforts to breed maize with high yield.  In this study, a total of 150 F7 recombinant inbred lines (RILs) derived from a cross between the maize lines Xu 178 and K12 were used to evaluate three ear-leaves area (TELA) under multi-environments.  Inclusive composite interval mapping (ICIM) was used to identify quantitative trait loci (QTLs) for TELA under a single environment and estimated breeding value (EBV).  A total of eight QTLs were detected under a single environmental condition, and four QTLs were identified for EBV which also can be detected in single environment.  This indicated that the EBV-detected QTLs have high genetic stability.  A major QTL (qTELA_2-9) located in chromosome bin 2.04/2.05 could be detected in four environments and has a high phenotypic contribution rate (ranging from 10.79 to 16.51%) that making it a good target for molecular breeding.  In addition, joint analysis was used to reveal the genetic basis of leaf area in six environments.  In total, six QTL×environment interactions and nine epistatic interactions were identified.  Our results reveal that the genetic basis of the leaf area is not only mainly determined by additive effects, but also affected by epistatic effects environmental interaction effects.
    Identification of suitable reference genes in leaves and roots of rapeseed (Brassica napus L.) under different nutrient deficiencies
    HAN Pei-pei, QIN Lu, LI Yin-shui, LIAO Xiang-sheng, XU Zi-xian, HU Xiao-jia, XIE Li-hua, YU Chang-bing, WU Yan-feng, LIAO Xing
    2017, 16(04): 809-819.  DOI: 10.1016/S2095-3119(16)61436-3
    Abstract ( )   PDF in ScienceDirect  
    Nutrient deficiency stresses often occur simultaneously in soil.  Thus, it’s necessary to investigate the mechanisms underlying plant responses to multiple stresses through identification of some key stress-responsive genes.  Quantitative real-time PCR (qRT-PCR) is essential for detecting the expression of the interested genes, of which the selection of suitable reference genes is a crucial step before qRT-PCR.  To date, reliable reference genes to normalize qRT-PCR data under different nutrient deficiencies have not been reported in plants.  In this study, expression of ten candidate reference genes was detected in leaves and roots of rapeseed (Brassica napus L.) after implementing different nutrient deficiencies for 14 days.  These candidate genes, included two traditionally used reference genes and eight genes selected from an RNA-Seq dataset.  Two software packages (GeNorm, NormFinder) were employed to evaluate candidate gene stability.  Results showed that VHA-E1 was the highest-ranked gene in leaves of nutrient-deficient rapeseed, while VHA-G1 and UBC21 were most stable in nutrient-deficient roots.  When rapeseed leaves and roots were combined, UBC21, HTB1, VHA-G1 and ACT7 were most stable among all samples.  To evaluate the stabilities of the highest-ranked genes, the relative expression of two target genes, BnTrx1;1 and BnPht1;3 were further determined.  The results showed that the relative expression of BnTrx1;1 depended on reference gene selection, suggesting that it’s necessary to evaluate the stability of reference gene prior to qRT-PCR.  This study provides suitable reference genes for gene expression analysis of rapeseed responses to different nutrient deficiencies, which is essential for elucidation of mechanisms underlying rapeseed responses to multiple nutrient deficiency stresses.
    Genome-wide identification of the radiation sensitivity protein-23 (RAD23) family members in apple (Malus×domestica Borkh.) and expression analysis of their stress responsiveness
    WANG Na, GONG Xiao-qing, MA Feng-wang
    2017, 16(04): 820-827.  DOI: 10.1016/S2095-3119(16)61517-4
    Abstract ( )   PDF in ScienceDirect  
    Radiation sensitivity proteins-23 (RAD23) are DNA repair factors participate in the ubiquitin/proteasome system (UPS).  Although the genome-wide analysis of RAD23 family members has been conducted in some species, little is known about RAD23 genes in apple (Malus×domestica Borkh.).  We analyzed this gene family in M. domestica in terms of genomic locations, protein and promoter structures, and expressions in response to stresses.  Various members showed a ubiquitous pattern of expression in all selected apple parts.  Their expressions were altered under chilling, heat, and hydrogen peroxide treatments, as well as abscisic acid (ABA) treatment and water deficiency, suggesting their possible roles in plant stress responses.  These results provide essential information about RAD23 genes in apple and will contribute to further functional studies
    Comparative transcriptome analysis of shortened fruit mutant in woodland strawberry (Fragaria vesca) using RNA-Seq
    WANG Shou-ming, LI Wei-jia, LIU Yue-xue, LI He, MA Yue, ZHANG Zhi-hong
    2017, 16(04): 828-844.  DOI: 10.1016/S2095-3119(16)61448-X
    Abstract ( )   PDF in ScienceDirect  
    Genes controlling fruit appearance determine fruit shape and size.  In ethylmethane sulfonate (EMS)-mutagenized lines of Fragaria vesca accession Yellow Wonder (YW), two fruit shapes are observed: wild-type long fruit and mutated shortened fruit (sf).  In this study, we first characterized sf based on morphology, histology, cytology and physiology.  The sf was identified as a gibberellin (GA)-deficient mutant, and four complementary DNA (cDNA) libraries separately constructed from flower buds and small green fruits of YW and sf were sequenced to comparatively analyze transcriptome differences.  A total of 29 differentially expressed GA pathway genes were identified by comparisons between YW1 and sf1, and 28 differentially expressed GA pathway genes were identified between YW2 and sf 2.  In addition, the expression patterns of 45 differentially expressed genes were validated by quantificational real-time PCR (qRT-PCR), and the results were highly concordant with the RNA-Seq results.  This transcriptome analysis provides valuable information for understanding the molecular mechanisms of fruit development of strawberry.
    Quantifying the spatial variation in the potential productivity and yield gap of winter wheat in China
    ZHANG Shi-yuan, ZHANG Xiao-hu, QIU Xiao-lei, TANG Liang, ZHU Yan, CAO Wei-xing, LIU Lei-lei
    2017, 16(04): 845-857.  DOI: 10.1016/S2095-3119(16)61467-3
    Abstract ( )   PDF in ScienceDirect  
    Despite the improvement in cultivar characters and management practices, large gaps between the attainable and potential yields still exist in winter wheat of China.  Quantifying the crop potential yield is essential for estimating the food production capacity and improving agricultural policies to ensure food security.  Gradually descending models and geographic information system (GIS) technology were employed to characterize the spatial variability of potential yields and yield gaps in winter wheat across the main production region of China.  The results showed that during 2000–2010, the average potential yield limited by thermal resource (YGT) was 23.2 Mg ha–1, with larger value in the northern area relative to the southern area.  The potential yield limited by the water supply (YGW) generally decreased from north to south, with an average value of 1.9 Mg ha–1 across the entire study region.  The highest YGW in the north sub-region (NS) implied that the irrigation and drainage conditions in this sub-region must be improved.  The averaged yield loss of winter wheat from nutrient deficiency (YGN) varied between 2.1 and 3.1 Mg ha–1 in the study area, which was greater than the yield loss caused by water limitation.  The potential decrease in yield from photo-thermal-water-nutrient-limited production to actual yield (YGO) was over 6.0 Mg ha–1, ranging from 4.9 to 8.3 Mg ha–1 across the entire study region, and it was more obvious in the southern area than in the northern area.  These findings suggest that across the main winter wheat production region, the highest yield gap was induced by thermal resources, followed by other factors, such as the level of farming technology, social policy and economic feasibility.  Furthermore, there are opportunities to narrow the yield gaps by making full use of climatic resources and developing a reasonable production plan for winter wheat crops.  Thus, meeting the challenges of food security and sustainability in the coming decades is possible but will require considerable changes in water and nutrient management and socio-economic policies.
    Simple nonlinear model for the relationship between maize yield and cumulative water amount
    LIU Cheng SUN Bao-cheng, TANG Huai-jun, WANG Tian-yu LI Yu, ZHANG Deng-feng, XIE Xiao-qing, SHI Yun-su, SONG Yan-chun, YANG Xiao-hong, LI Jian-sheng
    2017, 16(04): 858-866.  DOI: 10.1016/S2095-3119(16)61493-4
    Abstract ( )   PDF in ScienceDirect  
    Both the additive and multiplicative models of crop yield and water supply are polynomial equations, and the number of parameters increases linearly when the growing period is specified.  However, interactions among multiple parameters occasionally lead to unreasonable estimations of certain parameters, which were water sensitivity coefficients but with negative value.  Additionally, evapotranspiration must be measured as a model input.  To facilitate the application of these models and overcome the aforementioned shortcomings, a simple model with only three parameters was derived in this paper based on certain general quantitative relations of crop yield (Y) and water supply (W).  The new model, Y/YmWk/(Wk+whk), fits an S or a saturated curve of crop yield with the cumulative amount of water.  Three parameters are related to biological factors: the yield potential (Ym), the water requirement to achieve half of the yield potential (half-yield water requirement, wh), and the water sensitivity coefficient (k).  The model was validated with data from 24 maize lines obtained in the present study and 17 maize hybrids published by other authors.  The results showed that the model was well fit to the data, and the normal root of the mean square error (NRMSE) values were 2.8 to 17.8% (average 7.2%) for the 24 maize lines and 2.7 to 12.7% (average 7.4%) for the 17 maize varieties.  According to the present model, the maize water-sensitive stages in descending order were pollen shedding and silking, tasselling, jointing, initial grain ?lling, germination, middle grain ?lling, late grain ?lling, and end of grain ?lling.  This sequence was consistent with actual observations in the maize field.  The present model may be easily used to analyse the water use efficiency and drought tolerance of maize at specific stages.
    A method to evaluate the bioactive function of fruit extracts of Chinese wild Citrus with microtubular activity
    GUAN Xin, TAN Si, Günther Buchholz, Peter Nick, ZHOU Zhi-qin
    2017, 16(04): 867-873.  DOI: 10.1016/S2095-3119(16)61463-6
    Abstract ( )   PDF in ScienceDirect  
    China is one of the most important centers of origin for Citrus genetic resources.  Due to the high content of secondary metabolites, mining wild Chinese Citrus for novel medical applications is promising.  In this study, extracts of Chinese wild species from different taxonomical groups were screened for potential effects on microtubules (MTs) in vitro.  MT density as a readout for nucleation, and frequency distribution over MT lengths as a readout for elongation and decay were determined by quantitative image analysis via a standardized coverslip assay using fluorescently labelled neurotubulin.  Extract from peels of Citrus ichangensis Swing. strongly increased the density of MTs; whereas, extract from peels of Citurs limon (L.) Burm.f. exerted the opposite effect.  Extract from pulp of Citrus limonia Osbeck promoted MT elongation, and in addition induced a small population of very long MTs.  These data suggest that wild Chinese Citrus harbour compounds that act specifically on different aspects of MT nucleation, elongation, and decay.
    Plant Protection
    Sod gene of Curvularia lunata is associated with the virulence in maize leaf
    GAO Shi-gang, NI Xuan, LI Ying-ying, FU Ke-he, YU Chuan-jin, GAO Jin-xin, WANG Meng, LI Ya-qian, CHEN Jie
    2017, 16(04): 874-883.  DOI: 10.1016/S2095-3119(16)61513-7
    Abstract ( )   PDF in ScienceDirect  
    Curvularia leaf spot, caused mainly by Curvularia lunata, is a widespread plant disease in China.  In the recent years, directional host selection by the pathogen, which likely results in the virulence differentiation in pathogens, is widely reported.  Among the hallmarks potentially associated to pathogen variation in virulence, superoxide dismutase gene Sod has been found to be closely related to the enhancement of virulence.  In the present study, the full-length of Sod was obtained via Blastn alignment against GenBank and the whole genome of C. lunata.  In order to understand the role of Sod in the virulence variation in C. lunata, targeted gene disruption was performed to construct Sod mutants.  The cell wall degrading enzyme (CWDE) activities and toxin production of ΔSod were not distinctly different from wild-type strain CX-3 and its complon.  However, at an early stage of infection, ΔSod virulence appeared to be lower than CX-3 and the complon, while at a later stage, its virulence gradually returned to the level of CX-3 and the complon.  Furthermore, the melanin production of ΔSod was significantly reduced compared to CX-3 and the complon, suggesting that Sod gene influences the virulence by regulating melanin production at an early stage of infection but is not essential for pathogenicity.  However, the disruption of Sod did not significantly affect the transcriptional expression of the melanin biosynthesis-associated genes, brn1 and scd.  Therefore, we infer that Sod in C. lunata are involved, to some extent, with the virulence in maize leaf, but still needs further studies to have a clear understanding of its mechanism.
    Monoclonal antibody-based serological detection of Citrus yellow vein clearing virus in citrus groves
    LIU Zhen, SUNZHU Yuan-ji, ZHOU Xue-ping, HONG Jian, WU Jian-xiang
    2017, 16(04): 884-891.  DOI: 10.1016/S2095-3119(16)61475-2
    Abstract ( )   PDF in ScienceDirect  
    Citrus yellow vein clearing virus (CYVCV) is considered as the causal agent of Citrus yellow vein clearing disease and belongs to the genus Mandarivirus in the family Alphaflexiviridae.  Capsid protein (CP) of CYVCV Chongqing isolate (CYVCV-CQ) was produced using a prokaryotic expression system and used as the immunogen for monoclonal antibody (MAb) production.  Four highly specific and sensitive murine MAbs and one polyclonal antibody were prepared in this study.  Titers of the four MAbs in ascites fluids ranged from 10–6 to 10–7 as determined by indirect enzyme-linked immunosorbent assay (ELISA).  Three serological assays, including dot enzyme-linked immunosorbent assay (dot-ELISA), tissue blot-ELISA, and double-antibody sandwich (DAS)-ELISA, were developed for quick and reliable detections of CYVCV in citrus samples.  The developed dot-ELISA and DAS-ELISA methods could detect CYVCV in the infected citrus leaf crude extracts diluted at 1:2 560 and 1:10 240 (w/v, g mL–1), respectively.  The detection result of 125 citrus leaf samples collected from citrus groves in Yunnan Province and Chongqing Municipality of China showed that approximately 36% samples were positive for CYVCV.  This virus was, however, not detected in any sample collected from Zhejiang or Jiangxi Province, China.
    Identification of the key chitinase genes in Tetranychus cinnabarinus (Boisduval) based on the expression and sequence characteristic analysis
    XU Hao-ran, HE Lin, XIAO Wei, SHEN Guang-mao
    2017, 16(04): 892-899.  DOI: 10.1016/S2095-3119(16)61480-6
    Abstract ( )   PDF in ScienceDirect  
    Chitin is an important content in the exoskeletons of arthropods, and its hydrolyzation is catalyzed by chitinases during the process of molting, thus, the chitinases are considered as ideal target to interfere the growth of arthropods.  This study intends to clarify the characteristic of the chitinases during the development of Tetranychus cinnabarinus, and screen out important genes as potential control targets.  The results showed that the total enzyme concentration of chitinases was significantly higher in larva, the first and second nymph than that in egg and adult.  Base on the transcriptome data, six unigenes encoding chitinases were identified and their expression patterns in different developmental stages were detected. The expressions of TcCHIT1 and TcCHIT10 showed high abundance during the molting process and their expression change during the developmental stages was consistent with the enzyme concentration.  The full-length of these two genes were further cloned, and the structural characteristics of their proteins were analyzed by constructing the three-dimensional structure model.  The results provide basic information to understand the characteristic of chitinases in T. cinnabarinus and might be considered as target for control.
    Animal Science · Veterinary Science
    Consuming fermented distillers’ dried grains with solubles (DDGS) feed reveals a shift in the faecal microbiota of growing and fattening pigs using 454 pyrosequencing
    WANG Jin, HAN Ye, ZHAO Jin-zhao, ZHOU Zhi-jiang, FAN Huan
    2017, 16(04): 900-910.  DOI: 10.1016/S2095-3119(16)61523-X
    Abstract ( )   PDF in ScienceDirect  
    The objective of this study was to investigate pig fed by Bacillus coagulans-fermented distillers’ dried grains with solubles (DDGS) on the faecal microbial composition and diversity using 454 pyrosequencing.  Healthy crossbred (Duroc×Yorkshire×Landrace) growing and fattening pigs (n=48), with an average initial body weight of 65 kg, were divided into two groups (24 replicates per group; four pens per group; six pigs per pen), and given either DDGS feed as the control, or B. coagulans-fermented DDGS feed as the treatment.  Faecal samples were collected on day 0, 7, 14, 21, and 28.  DNA was extracted, and the V3–V6 region of the 16S rRNA gene was amplified.  The fermented DDGS feed affected the relative abundance of bacteria populations at the phylum, genus, and species levels.  At the genus level, the consumption of fermented DDGS feed led to higher relative abundances of faecal Prevotella, Lactobacillus, Clostridium, Bifidobacterium, Roseburia, and Bacillus, and lower relative abundances of faecal Escherichia, Ruminococcus, Dialister, unclassified Lachnospiraceae, unclassified Ruminococcaceae, and unclassified Enterobacteriaceae than in the control.  At the species level, the consumption of fermented DDGS feed led to higher relative abundances of faecal Prevotella sp., Lactobacillus johnsonii, Lactobacillus fermentum, Lactobacillus mucosae, Lactobacillus reuteri, Clostridium butyricum, Bifidobacterium sp., and Roseburia sp., and lower relative abundances of faecal Prevotella copri, Escherichia coli, Ruminococcus gnavus, Ruminococcus flavefaciens, and Dialister sp. than in the control.  Principal coordinates analysis indicated a distinct separation in the faecal microbial communities of pigs that were fed the fermented and unfermented DDGS feed.  Fermented DDGS feed significantly increased the average daily gain (ADG) of pigs, and significantly decreased the average daily feed intake (ADFI) of feed and feed/gain (F/G).  Thus, our results demonstrate a beneficial shift in the faecal microbiota of pigs consuming fermented DDGS feed, with potential applications in livestock production.
    Effects of marker density and minor allele frequency on genomic prediction for growth traits in Chinese Simmental beef cattle
    ZHU Bo, ZHANG Jing-jing, NIU Hong, GUAN Long, GUO Peng, XU Ling-yang, CHEN Yan, ZHANG Lu-pei, GAO Hui-jiang, GAO Xue, LI Jun-ya
    2017, 16(04): 911-920.  DOI: 10.1016/S2095-3119(16)61474-0
    Abstract ( )   PDF in ScienceDirect  
    Genomic selection has been demonstrated as a powerful technology to revolutionize animal breeding.  However, marker density and minor allele frequency can affect the predictive ability of genomic estimated breeding values (GEBVs).  To investigate the impact of marker density and minor allele frequency on predictive ability, we estimated GEBVs by constructing the different subsets of single nucleotide polymorphisms (SNPs) based on varying markers densities and minor allele frequency (MAF) for average daily gain (ADG), live weight (LW) and carcass weight (CW) in 1 059 Chinese Simmental beef cattle.  Two strategies were proposed for SNP selection to construct different marker densities: 1) select evenly-spaced SNPs (Strategy 1), and 2) select SNPs with large effects estimated from BayesB (Strategy 2).  Furthermore, predictive ability was assessed in terms of the correlation between predicted genomic values and corrected phenotypes from 10-fold cross-validation.  Predictive ability for ADG, LW and CW using autosomal SNPs were 0.13±0.002, 0.21±0.003 and 0.25±0.003, respectively.  In our study, the predictive ability increased dramatically as more SNPs were included in analysis until 200K for Strategy 1.  Under Strategy 2, we found the predictive ability slightly increased when marker densities increased from 5K to 20K, which indicated the predictive ability of 20K (3% of 770K) SNPs with large effects was equal to the predictive ability of using all SNPs.  For different MAF bins, we obtained the highest predictive ability for three traits with MAF bin 0.01–0.1.  Our result suggested that designing a low-density chip by selecting low frequency markers with large SNP effects sizes should be helpful for commercial application in Chinese Simmental cattle.
    Accuracy comparison of dry matter intake prediction models evaluated by a feeding trial of lactating dairy cows fed two total mixed rations with different forage source
    PAN Xiao-hua, YANG Liang, Yves Beckers, XIONG Ben-hai, JIANG Lin-shu
    2017, 16(04): 921-929.  DOI: 10.1016/S2095-3119(16)61483-1
    Abstract ( )   PDF in ScienceDirect  
    Dry matter intake (DMI) prediction models of NRC (2001), Fox et al. (2004) and Fuentes-Pila et al. (2003) were targeted in the present study, and the objective was to evaluate their prediction accuracy with feeding trial data of 32 lactating Holstein cows fed two total mixed rations with different forage source.  Thirty-two cows were randomly assigned to one of two total mixed ration groups: a ration containing a mixed forage (MF) of 3.7% Chinese wildrye, 28.4% alfalfa hay and 26.5% corn silage diet and another ration containing 33.8% corn stover (CS) as unique forage source.  The actual DMI was greater in MF group than in CS group (P=0.064).  The NRC model to predict DMI resulted in the lowest root mean square prediction error for both MF and CS groups (1.09 kg d–1 vs. 1.28 kg d–1) and the highest accuracy and precision based on concordance correlation coefficient for both MF and CS diet (0.89 vs. 0.87).  Except the NRC model, the other two models presented mean and linear biases in both MF and CS diets when prediction residuals were plotted against predicted DMI values (P<0.001).  The DMI variation in MF was caused by week of lactation (55.6%), milk yield (13.9%), milk fat percentage (7.1%) and dietary neutral detergent fiber (13.3%), while the variation in CS was caused by week of lactation (50.9%), live body weight (28.2%), milk yield (8.4%), milk fat percentage (5.2%) and dietary neutral detergent fibre (3.8%).  In a brief, the NRC model to predict DMI is comparatively acceptable for lactating dairy cows fed two total mixed rations with different forage source.
    Establishment of an avian leukosis virus subgroup A-resistant cell line
    FENG Min, DAI Man-man, LIAO Ming, CAO Wei-sheng
    2017, 16(04): 930-936.  DOI: 10.1016/S2095-3119(16)61453-3
    Abstract ( )   PDF in ScienceDirect  
    Rapid diagnostic methods for classifying avian leukosis subgroups in the field were needed for routine, large-scale screening.  As a first step in method development, we inserted the avian leukosis virus subgroup A (ALV-A) env gene into plasmid pcDNA3.1/Zeo (+) and used this construct to transfect DF-1 cells.  Zeocin-resistant cells were obtained after 2 weeks of zeocin selection.  Then, the cells were analyzed using PCR, immunofluorescence, and Western blot for expression of the envA-encoded envelope protein after 30 serial passages.  The DF-1/A cell line was completely resistant to 104 TCID50/0.1 mL (50% tissue culture infective dose) ALV-A and was partially resistant to 105 TCID50/0.1 mL ALV-A viral particles.  By comparing the DF-1/A and DF-1 cell lines, an ALV-A isolate was identified using a gag-specific ELISA for capsid protein p27.  Thus, we established a DF-1/A cell line that was resistant to ALV-A infection.  This cell line will be useful as a diagnostic tool.
    Soil & Fertilization﹒Irrigation﹒Plant Nutrition﹒ Agro-Ecology & Environment
    Chemical fertilizers could be completely replaced by manure to maintain high maize yield and soil organic carbon (SOC) when SOC reaches a threshold in the Northeast China Plain
    LI Hui, FENG Wen-ting, HE Xin-hua, ZHU Ping, GAO Hong-jun, SUN Nan, XU Ming-gang
    2017, 16(04): 937-946.  DOI: 10.1016/S2095-3119(16)61559-9
    Abstract ( )   PDF in ScienceDirect  
    The combined use of chemical and organic fertilizers is considered a good method to sustain high crop yield and enhance soil organic carbon (SOC), but it is still unclear when and to what extent chemical fertilizers could be replaced by organic fertilizers.  We selected a long-term soil fertility experiment in Gongzhuling, Northeast China Plain to examine the temporal dynamics of crop yield and SOC in response to chemical nitrogen, phosphorus, and potassium (NPK) fertilizers and manure, applied both individually and in combination, over the course of three decades (1980–2010).  We aimed to test 1) which fertilizer application is the best for increasing both maize yield and SOC in this region, and 2) whether chemical fertilizers can be replaced by manure to maintain high maize yield and enhance SOC, and if so, when this replacement should be implemented.  We observed that NPK fertilizers induced a considerable increase in maize yield in the first 12 years after the initiation of the experiment, but manure addition did not.  In the following years, the addition of both NPK fertilizers and manure led to an increase in maize yield.  SOC increased considerably in treatments with manure but remained the same or even declined with NPK treatments.  The increase in maize yield induced by NPK fertilizers alone declined greatly with increasing SOC, whereas the combination of NPK and manure resulted in high maize yield and a remarkable improvement in SOC stock.  Based on these results we suggested that NPK fertilizers could be at least partially replaced by manure to sustain high maize yield after SOC stock has reached 41.96 Mg C ha–1 in the Northeast China Plain and highly recommend the combined application of chemical fertilizers and manure (i.e., 60 Mg ha–1).
    Ground cover management and farmyard manure effects on soil nitrogen dynamics, productivity and economics of organically grown lettuce (Lactuca sativa L. subsp. secalina)
    Manojlovi? Maja, ?abilovski Ranko, Nikoli? Ljiljana, D?igurski Dejana, ?ereme?i? Sr?an, Bavec Martina
    2017, 16(04): 947-958.  DOI: 10.1016/S2095-3119(16)61565-4
    Abstract ( )   PDF in ScienceDirect  
    Ground cover management and farmyard manure (FYM) management have important roles in organic lettuce production.  However, there is not enough information about their combined effects.  In order to assess the effects of individual and combined ground cover and FYM management on soil mineral N (NH4-N and NO3-N) dynamics, lettuce yield and economics in organic farming, a two-year field experiment was conducted on a certified organic farm in Kisa? (Vojvodina, Serbia).  The experiment had a two-factorial split-plot completely randomized block design.  FYM was applied on the half of the experimental field as a whole-plot factor, while ground cover management included the following four treatments: (I) control, without ground cover management (Ø); (II) hoeing (H); (III) agrotextile cover; (IV) straw mulch (SM), which were applied on split plots.  The applied SM and AT increased soil moisture by 12.83 and 3.73%, respectively, compared to the control treatment.   FYM increased soil mineral N concentration, the lettuce fresh matter (FM) yield and nitrate concentration in lettuce.  However, nitrate concentration in lettuce in all treatments was below the limit required by the European Commission (EC) (2001).  The highest lettuce yield was obtained by AT (39 122 kg), followed by SM (33 925 kg), and it was higher with FYM application by 16.85%.  Hoeing did not positively affect the yield, probably due to its negative effect on soil moisture.  Additional profit was higher with FYM, showing the following decreasing order: AT>H>SM>Ø.  However, value/cost ratio (VCR) was in the order Ø>H>SM>AT on FYM fertilized plots.  FYM application led to higher lettuce yield and higher profit and VCR.  In case a farm does not have FYM, SM is the best alternative due to its positive effect on the yield and low investment costs.
    Effects of long-term application of different green manures on ferric iron reduction in a red paddy soil in Southern China
    GAO Song-juan CAO Wei-dong, GAO Ju-sheng, HUANG Jing, BAI Jin-shun, ZENG Nao-hua, CHANG Dan-na, SHIMIZU Katsuyoshi
    2017, 16(04): 959-966.  DOI: 10.1016/S2095-3119(16)61509-5
    Abstract ( )   PDF in ScienceDirect  
    Dissimilatory Fe(III) reduction is an important process in the geochemical cycle of iron in anoxic environment.  As the main products of dissimilatory iron reduction, the Fe(II) species accumulation could indicate the reduction ability.  The effects of different green manures on Fe(III) reduction in paddy soil were explored based on a 31-year rice-rice-winter green manure cropping experiment.  Four treatments were involved, i.e., rice-rice-milk vetch (RRV), rice-rice-rape (RRP), rice-rice-ryegrass (RRG) and rice-rice-winter fallow (RRF).  Soils were sampled at flowering stage of milk vetch and rape (S1), before transplantation (S2), at tillering (S3), jointing (S4), and mature (S5) stages of the early rice, and after the harvest of the late rice (S6).  The contents of TFeHCl (HCl-extractable total Fe), Fe(II)HCl (HCl-extractable Fe(II) species) and Fe(III)HCl (HCl-extractable Fe(III) species) were measured.  The correlations among those Fe species with selected soil environmental factors and the dynamic characteristics of Fe(II)HCl accumulation were investigated.  The results showed that TFeHCl in RRF was significantly higher than those in the green manure treatments at most of the sampling stages.  Fe(II)HCl increased rapidly after the incorporation of green manures in all treatments and kept rising with the growth of early rice.  Fe(II)HCl in RRG was quite different from those in other treatments, i.e., it reached the highest at the S2 stage, then increased slowly and became the lowest one at the S4 and S5 stages.  Fe(III)HCl showed oppositely, and Fe(II)HCl/Fe(III)HCl performed similarly to Fe(II)HCl.  The maximum accumulation potential of Fe(II)HCl was significantly higher in RRF, while the highest maximum reaction rate of Fe(II)HCl accumulation appeared in RRG.  Significant correlations were found between the indexes of Fe(II)HCl accumulation and soil pH, oxidation-reduction potential (Eh) and total organic acids, respectively.  In together, we found that long-term application of green manures decreased the TFeHCl in red paddy soils, but promoted the ability of Fe(III) reduction, especially the ryegrass; Fe(II)HCl increased along with the growth of rice and was affected by soil conditions and environmental factors, especially the water and redox ability.
    Effect of experimental warming on soil respiration under conventional tillage and no-tillage farmland in the North China Plain
    TU Chun, LI Fa-dong, QIAO Yun-feng, ZHU Nong, GU Cong-ke, ZHAO Xin
    2017, 16(04): 967-979.  DOI: 10.1016/S2095-3119(16)61449-1
    Abstract ( )   PDF in ScienceDirect  
    Understanding the response of soil respiration to global warming in agro-ecosystem is crucial for simulating terrestrial carbon (C) cycle.  We conducted an infrared warming experiment under conventional tillage (CT) and no-tillage (NT) farmland for winter wheat and summer maize rotation system in North China Plain (NCP).  Treatments include CT with and without warming (CTW and CTN), NT with and without warming (NTW and NTN).  The results indicated that warming had no significant effect on soil moisture in irrigated farmland of NCP (P>0.05).  The elevated average soil temperature of 1.1–1.6°C in crop growing periods could increase annual soil CO2 emission by 10.3% in CT filed (P>0.05), but significantly increase it by 12.7% in NT field (P<0.05), respectively.  The disturbances such as plowing, irrigation and precipitation resulted in the obvious soil CO2 emission peaks, which contributed 36.6–40.8% of annual soil cumulative CO2 emission.  Warming would enhance these soil CO2 emission peaks; it might be associated with the warming-induced increase of autotrophic respiration and heterotrophic respiration.  Compared with un-warming treatments, dissolved organic carbon (DOC) and soil microbial biomass carbon (MBC) in warming treatments were significantly increased by 11.6–23.4 and 12.9–23.6%, respectively, indicating that the positive responses of DOC and MBC to warming in both of two tillage systems.  Our study highlights that climate warming may have positive effects on soil C release in NCP in association with response of labile C substrate to warming.