2018 Vol. 17 No. 2 Previous Issue    Next Issue

    Crop Science
    Plant Protection
    Animal Science · Veterinary Medicine
    Agro-ecosystem & Environment
    Agricultural Economics and Management
    Short Communication

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    Crop Science
    Rapid mapping of candidate genes for cold tolerance in Oryza rufipogon Griff. by QTL-seq of seedlings
    LUO Xiang-dong, LIU Jian, ZHAO Jun, DAI Liang-fang, CHEN Ya-ling, ZHANG Ling, ZHANG Fan-tao, HU Biao-lin, XIE Jian-kun
    2018, 17(2): 265-275.  DOI: 10.1016/S2095-3119(17)61712-X
    Abstract ( )   PDF in ScienceDirect  
    Cold stress is a major problem in rice production.  To rapidly identify genes for cold tolerance in Dongxiang wild rice (DWR, Oryza rufipogon Griff.), sequencing-based bulked segregant analysis of QTL-seq method was used to resequence the extremely resistant (R) and susceptible (S) bulks of a backcross inbred lines (BILs) population (derived from Oryza sativa×O. rufipogon) and their parents.  Single nucleotide polymorphisms (SNP)-index graphs and corresponding Δ(SNP-index) graphs (at 99 and 95% confidence levels) for R- and S-bulks detected a total of 2 609 candidate SNPs, including 58 candidate cold-tolerance genes.  Quantitative real-time PCR analysis revealed that 5 out of the 58 candidate genes had significant differences in expression between O. sativa and O. rufipogon.  Structural variation and functional annotations of the 5 candidate genes were also analyzed, and allowed us to identify 2 insertion-deletion (InDel) markers (12-7 and 12-16) that were linked with candidate genes on chromosome 12 in DWR.  These results are helpful for cloning and using cold tolerance genes from common wild rice in cultivated rice.
    A dCAPS marker developed from a stress associated protein gene TaSAP7-B governing grain size and plant height in wheat
    WANG Yi-xue, XU Qiao-fang, CHANG Xiao-ping, HAO Chen-yang, LI Run-zhi, JING Rui-lian
    2018, 17(2): 276-284.  DOI: 10.1016/S2095-3119(17)61685-X
    Abstract ( )   PDF in ScienceDirect  
    Stress associated proteins (SAPs) are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants.  In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat (Triticum aestivum L.).  Sequencing analysis on TaSAP7-B illustrated one InDel (insertion-deletion) and one SNP (single nucleotide polymorphism) in the promoter region while no diversity was observed in the coding region.  On the basis of SNP in the promoter region (–260 bp), a dCAPS (derived cleaved amplified polymorphic sequences) marker SNP-260 was developed for TaSAP7-B.  Using a natural population consisting of 262 wheat accessions, significant associations were detected between the marker SNP-260 and agronomic traits, such as plant height (PH), peduncle length (PL), length of penultimate internode (LPI), number of spike per plant (NSP), and 1 000-grain weight (TGW).  Two genotypes were identified using marker SNP-260 in the natural population.  Among them, the genotypes possessing C allele exhibited a higher TGW and shorter PH than the T genotypes.  Hence, base C was considered as the superior allele.  The dCAPS marker of TaSAP7-B can be instrumental for marker-assisted selection for high grain size and short plant height.  
    A major quantitative trait locus controlling phosphorus utilization efficiency under different phytate-P conditions at vegetative stage in barley
    GAO Shang-qing, CHEN Guang-deng, HU De-yi, ZHANG Xi-zhou, LI Ting-xuan, LIU Shi-hang, LIU Chun-ji
    2018, 17(2): 285-295.  DOI: 10.1016/S2095-3119(17)61713-1
    Abstract ( )   PDF in ScienceDirect  
    Organic phosphorus (P) is an important component of the soil P pool, and it has been proven to be a potential source of P for plants.  The phosphorus utilization efficiency (PUE) and PUE related traits (tiller number (TN), shoot dry weight (DW), and root dry weight) under different phytate-P conditions (low phytate-P, 0.05 mmol L–1 and normal phytate-P, 0.5 mmol L–1) were investigated using a population consisting of 128 recombinant inbred lines (RILs) at the vegetative stage in barley.  The population was derived from a cross between a P-inefficient genotype (Baudin) and a P-efficient genotype (CN4027, a Hordeum spontaneum accession).  A major locus (designated Qpue.sau-3H) conferring PUE was detected in shoots and roots from the RIL population.  The quantitative trait locus (QTL) was mapped on chromosome 3H and the allele from CN4027 confers high PUE.  This locus explained up to 30.3 and 28.4% of the phenotypic variance in shoots under low and normal phytate-P conditions, respectively.  It also explains 28.3 and 30.7% of the phenotypic variation in root under the low and normal phytate-P conditions, respectively.  Results from this study also showed that TN was not correlated with PUE, and a QTL controlling TN was detected on chromosome 5H.  However, dry weight (DW) was significantly and positively correlated with PUE, and a QTL controlling DW was detected near the Qpue.sau-3H locus.  Based on a covariance analysis, existing data indicated that, although DW may affect PUE, different genes at this locus are likely involved in controlling these two traits.
    Overexpression of IbSnRK1 enhances nitrogen uptake and carbon assimilation in transgenic sweetpotato
    REN Zhi-tong, ZHAO Hong-yuan, HE Shao-zhen, ZHAI Hong, ZHAO Ning, LIU Qing-chang
    2018, 17(2): 296-305.  DOI: 10.1016/S2095-3119(16)61611-8
    Abstract ( )   PDF in ScienceDirect  
    Nitrogen is an important nutrient for plant development.  Nitrogen and carbon metabolisms are tightly linked to physiological functions in plants.  In this study, we found that the IbSnRK1 gene was induced by Ca(NO3)2.  Its overexpression enhanced nitrogen uptake and carbon assimilation in transgenic sweetpotato.  After Ca(15NO3)2 treatment, the 15N atom excess, 15N and total N content and nitrogen uptake efficiency (NUE) were significantly increased in the roots, stems, and leaves of transgenic plants compared with wild type (WT) and empty vector control (VC).  After Ca(NO3)2 treatment, the increased nitrate N content, nitrate reductase (NR) activity, free amino acid content, and soluble protein content were found in the roots or leaves of transgenic plants.  The photosynthesis and carbon assimilation were enhanced.  These results suggest that the IbSnRK1 gene play a important role in nitrogen uptake and carbon assimilation of sweetpotato.  This gene has the potential to be used for improving the yield and quality of sweetpotato.
    Collision detection of virtual plant based on bounding volume hierarchy: A case study on virtual wheat
    TANG Liang, SONG Wei-guo, HOU Tian-cheng, LIU Lei-lei, CAO Wei-xing, ZHU Yan
    2018, 17(2): 306-314.  DOI: 10.1016/S2095-3119(17)61769-6
    Abstract ( )   PDF in ScienceDirect  
    Visualization of simulated crop growth and development is of significant interest to crop research and production.  This study aims to address the phenomenon of organs cross-drawing by developing a method of collision detection for improving vivid 3D visualizations of virtual wheat crops.  First, the triangular data of leaves are generated with the tessellation of non-uniform rational B-splines surfaces.  Second, the bounding volumes (BVs) and bounding volume hierarchies (BVHs) of leaves are constructed based on the leaf morphological characteristics and the collision detection of two leaves are performed using the Separating Axis Theorem.  Third, the detecting effect of the above method is compared with the methods of traditional BVHs, Axis-Aligned Bounding Box (AABB) tree, and Oriented Bounding Box (OBB) tree.  Finally, the BVs of other organs (ear, stem, and leaf sheath) in virtual wheat plant are constructed based on their geometric morphology, and the collision detections are conducted at the organ, individual and population scales.  The results indicate that the collision detection method developed in this study can accurately detect collisions between organs, especially at the plant canopy level with high collision frequency.  This collision detection-based virtual crop visualization method could reduce the phenomenon of organs cross-drawing effectively and enhance the reality of visualizations.
    Integrated management strategy for improving the grain yield and nitrogen-use efficiency of winter wheat
    XU Hai-cheng, DAI Xing-long, CHU Jin-peng, WANG Yue-chao, YIN Li-jun, MA Xin, DONG Shu-xin, HE Ming-rong
    2018, 17(2): 315-327.  DOI: 10.1016/S2095-3119(17)61805-7
    Abstract ( )   PDF in ScienceDirect  
    Understanding of how combinations of agronomic options can be used to improve the grain yield and nitrogen use efficiency (NUE) of winter wheat is limited.  A three-year experiment involving four integrated management strategies was conducted from 2013 to 2015 in Tai’an, Shandong Province, China, to evaluate changes in grain yield and NUE.  The integrated management treatments were as follows: current practice (T1); improvement of current practice (T2); high-yield management (T3), which aimed to maximize grain yield regardless of the cost of resource inputs; and integrated soil and crop system management (T4) with a higher seeding rate, delayed sowing date, and optimized nutrient management.  Seeding rates increased by 75 seeds m–2 with each treatment from T1 (225 seeds m–2) to T4 (450 seeds m–2).  The sowing dates were delayed from T1 (5th Oct.) to T2 and T3 (8th Oct.), and to T4 treatment (12th Oct.).  T1, T2, T3, and T4 received 315, 210, 315, and 240 kg N ha–1, 120, 90, 210 and 120 kg P2O5 ha–1, 30, 75, 90, and 45 kg K2O ha–1, respectively.  The ratio of basal application to topdressing for T1, T2, T3, and T4 was 6:4, 5:5, 4:6, and 4:6, respectively, with the N topdressing applied at regreening for T1 and at jointing stage for T2, T3, and T4.  The P fertilizers in all treatments were applied as basal fertilizer.  The K fertilizer for T1 and T2 was applied as basal fertilizer while the ratio of basal application to topdressing (at jointing stage) of K fertilizer for both T3 and T4 was 6:4.  T1, T2, T3, and T4 were irrigated five, four, four and three times, respectively.  Treatment T3 produced the highest grain yield among all treatments over three years and the average yield was 9 277.96 kg ha–1.  Grain yield averaged across three years with the T4 treatment (8 892.93 kg ha–1) was 95.85% of that with T3 and was 21.72 and 6.10% higher than that with T1 (7 305.95 kg ha–1) and T2 (8 381.41 kg ha–1), respectively.  Treatment T2 produced the highest NUE of all the integrated treatments.  The NUE with T4 was 95.36% of that with T2 and was 51.91 and 25.62% higher than that with T1 and T3, respectively.  The N uptake efficiency (UPE) averaged across three years with T4 was 50.75 and 16.62% higher than that with T1 and T3, respectively.  The N utilization efficiency (UTE) averaged across three years with T4 was 7.74% higher than that with T3.  The increased UPE with T4 compared with T3 could be attributed mostly to the lower available N in T4, while the increased UTE with T4 was mainly due to the highest N harvest index and low grain N concentration, which consequently led to improved NUE.  The net profit for T4 was the highest among four treatments and was 174.94, 22.27, and 28.10% higher than that for T1, T2, and T3, respectively.  Therefore, the T4 treatment should be a recommendable management strategy to obtain high grain yield, high NUE, and high economic benefits in the target region, although further improvements of NUE are required.
    Exogenous application of a low concentration of melatonin enhances salt tolerance in rapeseed (Brassica napus L.) seedlings
    ZENG Liu, CAI Jun-song, LI Jing-jing, LU Guang-yuan, LI Chun-sheng, FU Gui-ping, ZHANG Xue-kun, MA Hai-qing, LIU Qing-yun, ZOU Xi-ling, CHENG Yong
    2018, 17(2): 328-335.  DOI: 10.1016/S2095-3119(17)61757-X
    Abstract ( )   PDF in ScienceDirect  
    Melatonin is a naturally occurring compound in plants.  Here, we tested the effect of exogenous melatonin on rapeseed (Brassica napus L.) grown under salt stress.  Application of 30 μmol L–1 melatonin alleviated salt-induced growth inhibition, and the shoot fresh weight, the shoot dry weight, the root fresh weight, and the root dry weight of seedlings treated with exogenous melatonin increased by 128.2, 142.9, 122.2, and 124.2%, respectively, compared to those under salt stress.  In addition, several physiological parameters were evaluated.  The activities of antioxidant enzymes including peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) were enhanced by 16.5, 19.3, and 14.2% compared to their activities in plants without exogenous melatonin application under salt stress, while the H2O2 content was decreased by 11.2% by exogenous melatonin.  Furthermore, melatonin treatment promoted solute accumulation by increasing the contents of proline (26.8%), soluble sugars (15.1%) and proteins (58.8%).  The results also suggested that higher concentrations (>50 μmol L–1) of melatonin could attenuate or even prevent the beneficial effects on seedling development.  In conclusion, application of a low concentration of exogenous melatonin to rapeseed plants under salt stress can improve the H2O2-scavenging capacity by enhancing the activities of antioxidant enzymes such as POD, CAT and APX, and can also alleviate osmotic stress by promoting the accumulation of osmoregulatory substances such as soluble proteins, proline, and water soluble glucan.  Ultimately, exogenous melatonin facilitates root development and improves the biomass of rapeseed seedlings grown under salt stress, thereby effectively alleviating the damage of salt stress in rapeseed seedlings.
    Influence of drought hardening on the resistance physiology of potato seedlings under drought stress
    ZHANG Shu-han, XU Xue-feng, SUN Ye-min, ZHANG Jun-lian, LI Chao-zhou
    2018, 17(2): 336-347.  DOI: 10.1016/S2095-3119(17)61758-1
    Abstract ( )   PDF in ScienceDirect  
    In this paper, the influence of drought hardening on the growth, development, resistance physiology, leaf microstructure and stomatal behavior of potato seedlings under drought stress was studied, and the mechanism of drought hardening improvement of potato seedling drought resistance was elucidated.  We found that drought stress had several adverse effects on potato seedlings, yet drought hardening alleviated the decrease in relative water content (RWC), net photosynthetic rate (Pn) and chlorophyll content and inhibited the increase in relative electric conductivity and malondialdehyde (MDA) content.  Compared with contrast seedlings, drought-hardened seedlings also had enhanced root vigor, increased antioxidant enzyme activity and higher levels of abscisic acid (ABA), proline (Pro), soluble sugars and polyamines (PAs) under drought stress.  In addition, the stomatal density of potato seedling leaves increased significantly, while the leaf area, stomatal size and stomatal aperture decreased with drought hardening treatment.  These changes led to reduced leaf transpiration rate (Tr) and improved water utilization efficiency (WUE).  The changes in leaf microstructure also had a positive effect on the drought resistance of the drought-hardened potato seedlings. So it can be concluded that through increasing the content of some endogenous hormones, osmotic regulatory substances and the activities of antioxidant enzymes, the resistance physiology of drought-hardened potato seedlings was enhanced. 
    Identification and expression of the CEP gene family in apple (Malus×domestica)
    LI Rui, AN Jian-ping, YOU Chun-xiang, SHU Jing, WANG Xiao-fei, HAO Yu-jin
    2018, 17(2): 348-358.  DOI: 10.1016/S2095-3119(17)61653-8
    Abstract ( )   PDF in ScienceDirect  
    Plant peptide hormones play important roles in plant growth and development.  Among these hormones, the C-TERMINALLYENCODED PEPTIDE (CEP) belongs to a newly found peptide family that regulates root development in Arabidopsis as well as in other species.  However, nothing is known about the CEP genes in apple (Malus×domestica, MdCEP).  In this study, a total of 27 apple CEP genes were identified through a genome-wide analysis and were phylogenetically divided into three classes (I, II and III).  The predicted MdCEP genes were distributed across 10 of 17 chromosomes with different densities.  Next, the gene structures and motif compositions of the MdCEP genes were analyzed.  Subsequently, the expression analysis suggested that the MdCEP genes were highly activated in roots and that MdCEP23 may play an important role in regulating the growth and development of roots.  Moreover, all of the MdCEP genes were responsive to multiple abiotic stresses, indicating that MdCEP genes may be involved with various aspects of physiological processes in apple.  Nearly one-third of MdCEP genes had a significant response to low nitrogen treatment.  Most of the MdCEP genes were up-regulated under stress, including mannitol, polyethylene glycol (PEG) and abscisic acid (ABA), suggesting that MdCEP genes may be involved in the drought stress response.  This study provides insight into the putative functions of the MdCEP genes using a genome-wide analysis of the CEP gene family. 
    Comparison of rhizosphere and endophytic microbial communities of Chinese leek through high-throughput 16S rRNA gene Illumina sequencing
    HUANG Yong-hong
    2018, 17(2): 359-367.  DOI: 10.1016/S2095-3119(17)61731-3
    Abstract ( )   PDF in ScienceDirect  
    Chinese leek (Allium tuberosum Rottler ex Sprengel) is a common vegetable in China.  In our previous study, Chinese leek in rotation was found to have significant antifungal and nematicidal activity.  This study’s aim was to investigate the potential antifungal and nematicidal activity associated with rhizosphere or endophytic microbes of Chinese leek.  Thus, a total of 79 261 high-quality sequences were obtained from Chinese leek rhizosphere soil, leaf and root samples.  In the rhizosphere soil, the bacterial community comprised five dominant phyla: Proteobacteria (37.85%), Acidobacteria (10.99%), Bacteroidetes (8.24%), Cyanobacteria (7.79%) and Planctomycetes (7.1%).  The leaf and root bacterial communities comprised two dominant phyla: Cyanobacteria (83.42% in leaf and 75.44% in root) and Proteobacteria (14.75% in leaf and 21.04% in root).  Microbial diversity, richness and evenness in the rhizosphere soil bacterial community were higher than that in the endophytic bacterial communities.  The rhizosphere bacterial community was significantly different from the endophytic bacterial communities.  The endophytic bacterial communities from the leaf and the root were slightly, but not significantly different from each other.  This study’s findings would contribute to the isolation and identification of nematicidal and antifungal bacterial communities in Chinese leek.
    Plant Protection
    Multi-functional roles of TaSSI2 involved in Fusarium head blight and powdery mildew resistance and drought tolerance
    HU Li-qin, MU Jing-jing, SU Pei-sen, WU Hong-yan, YU Guang-hui, WANG Gui-ping, WANG Liang, MA Xin, LI An-fei, WANG Hong-wei, ZHAO Lan-fei, KONG Ling-rang
    2018, 17(2): 368-380.  DOI: 10.1016/S2095-3119(17)61680-0
    Abstract ( )   PDF in ScienceDirect  
    The mutation of the gene encoding a stearoyl-acyl carrier protein fatty acid desaturase (ssi2) has been proved to enhance pathogen resistance in several plants, while it’s potential to regulate biotic and abiotic stresses in wheat is still unclear.  In this study, we cloned TaSSI2 gene in wheat and provided several evidences of its involvement in multiple biological functions.  By using barley stripe mosaic virus (BSMV)-induced gene silencing (VIGS) in wheat, it was found that TaSSI2 negatively regulated both powdery mildew and Fusarium head blight (FHB) resistance, which was consistent with the phenotype observed in knock-out mutants of Kronos.  The expression of TaSSI2 was down-regulated by in vitro treatments of methyl jasmonate (MeJA), but positively regulated by salicylic acid (SA) and abscisic acid (ABA), implying the cross-talk between different hormone signaling pathways involved in wheat to regulate biotic stresses is still to be elucidated.  Furthermore, the up-regulated expression of PR4 and PR5 indicated that TaSSI2 probably regulated FHB resistance by depressing the SA signaling pathway in wheat.  In addition, the over-expression of TaSSI2 increased the content of linolenic acid (18:3) and subsequently enhanced drought tolerance of transgenic Brachypodium.  This phenomenon might be associated with its subcellular localization in the whole cytosol, partly overlapping with Golgi apparatus and the secreted vesicles.  As a stearoyl-acyl carrier protein fatty acid desaturase, TaSSI2 was proposed to be involved in cell lipid metabolism and carried targets out of the cell from membrane or wax synthesis, resulting in enhanced drought tolerance in plant.
    Host status of Brachypodium distachyon to the cereal cyst nematode
    CHEN Chang-long, LIU Shu-sen, LIU Qian, NIU Jun-hai, LIU Pei, ZHAO Jian-long, LIU Zhi-yong, LI Hong-jie, JIAN Heng
    2018, 17(2): 381-388.  DOI: 10.1016/S2095-3119(17)61745-3
    Abstract ( )   PDF in ScienceDirect  
    Cereal cyst nematode (Heterodera avenae, CCN) distributes worldwide and has caused severe damage to cereal crops, and a model host will greatly aid in the study of this nematode.  In this research, we assessed the sensitivity of 25 inbred lines of Brachypodium distachyon to H. avenae from Beijing, China.  All lines of B. distachyon were infested by second-stage juveniles (J2s) of H. avenae from Daxing District of Beijing population, but only 13 inbred lines reproduced 0.2–3 cysts/plant, showing resistance.  The entire root system of the infested B. distachyon appeared smaller and the fibrous roots were shorter and less numerous.  We found that a dose of 1 000 J2s of H. avenae was sufficient for nematode infestation.  We showed that Koz-1 of B. distachyon could reproduce more cysts than TR2A line.  Line Koz-1 also supported the complete life cycles of 5 CCN geographical populations belonging to the Ha1 or Ha3 pathotype group.  Our results suggest that B. distachyon is a host for CCN.
    Effects of Aschersonia aleyrodis on the life table and demographic parameters of Bemisia tabaci
    ZHANG Can, SHAO Zhen-fang, HAN Yue-ye, WANG Xing-min, WANG Ze-qing, Peter Dennis Musa, QIU Bao-li, Shaukat Ali
    2018, 17(2): 389-396.  DOI: 10.1016/S2095-3119(17)61773-8
    Abstract ( )   PDF in ScienceDirect  
    The present study reports the sublethal effects of the entomopathogenic fungus, Aschersonia aleyrodis (Webber) on Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae).  A fungal suspension of A. aleyrodis isolate Aa005 containing 1×107 conidia mL–1 was sprayed against B. tabaci on eggplant leaves under greenhouse conditions.  The effects of fungal application on survival as well as life table parameters of the whitefly were observed at different post inoculation periods.  The results indicated that A. aleyrodis can significantly affect the survival of 1st, 2nd, and 3rd nymphal instars of B. tabaci.  Developmental periods of different instar nymphs were not affected by fungal application.  A. aleyrodis spores persisted well and significantly affected the survivorship of young instar nymphs of B. tabaci at different post incubation periods.  Life table results suggested that A. aleyrodis has no impact on general fecundity and longevity of B. tabaci.  When the pathogen was exposed to the open environment and maintained for a relatively longer period, a reduction in the reproductive rate and intrinsic rate of increase was caused by the fungal spores, though the sublethal effects were not as good as the control treatment.  The results suggest that the ability of spores to suppress an increase in whitefly population persists well after incubation of spores to the external environment (up to 9 days).  
    Including predator presence in a refined model for assessing resistance of alfalfa cultivar to aphids
    TU Xiong-bing, FAN Yao-li, Mark McNeill, ZHANG Ze-hua
    2018, 17(2): 397-405.  DOI: 10.1016/S2095-3119(17)61708-8
    Abstract ( )   PDF in ScienceDirect  
    The aphid quantity ratio (AQR) is defined as the number of aphids on each cultivar divided by the number of aphids on all cultivars.  AQR is based on the correlation between aphid populations and their host plants and is an important tool that has been utilized in evaluating Medicago sativa (alfalfa) cultivar resistance to aphids.  However, assessment of alfalfa resistance to aphids can be confused by the presence of aphid predators, causing the assessment of plant resistance to aphids to be based on incorrect aphid population data.  To refine the AQR and account for the effect of predators on aphid population assessments, we introduced a parameter ‘α’, corresponding to the predator quantity ratio, and used αAQR as the ratio to quantify aphid populations.  Populations of both aphids (4 species) and their predators (12 species) occurring in 28 M. sativa cultivars were sampled over two years at a research station near Cangzhou, Hebei Province, China.  Results showed that the most suitable evaluation period was from May to June, as the aphid population was stable during this period.  Compared with the AQR method, the predator population numbers based on the αAQR had a significant inverse relationship with aphid population numbers and the 28 cultivars were clustered into three classes: the resistant class, tolerant class, and susceptible class.  In addition, 17 cultivars were reassigned when evaluated using αAQR.  All numerical values calculated by αAQR were displayed as a Gaussian distribution, which showed that the 28 cultivars could be clustered into nine groups using a median value (±SE) of 1±0.1.  Hence, ongoing alfalfa breeding trials will be assessed using the αAQR to establish a robust system that includes agronomic performance parameters in order to generalize the new method for further studies.
    Animal Science · Veterinary Medicine
    Comparing successful gene knock-in efficiencies of CRISPR/Cas9 with ZFNs and TALENs gene editing systems in bovine and dairy goat fetal fibroblasts
    LIU Hui, LIU Chang, ZHAO Yu-hang, HAN Xue-jie, ZHOU Zheng-wei, WANG Chen, LI Rong-feng, LI Xue-ling
    2018, 17(2): 406-414.  DOI: 10.1016/S2095-3119(17)61748-9
    Abstract ( )   PDF in ScienceDirect  
    This study aimed to compare the efficiencies of clustered regulatory interspaced short palindromic repeat (CRISPR)/Cas9-mediated gene knock-ins with zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) in bovine and dairy goat fetal fibroblasts.  To test the knock-in efficiency, a set of ZFNs and CRISPR/Cas9 plasmids were designed to edit the bovine myostatin (MSTN) gene at exon 2, while a set of TALENs and CRISPR/Cas9 plasmids were designed for editing the dairy goat β-casein gene at exon 2.  Donor plasmids utilizing the ZFNs, TALENs, and CRISPR/Cas9 cutting sites were constructed in the GFP-PGK-NeoR plasmid background, including a 5´ and 3´ homologous arm flanking the genes humanized Fat-1 (hFat-1) or enhanced green fluorescent protein (eGFP).  Subsequently, the ZFNs, TALENs, or CRISPR/Cas9 and the hFat-1 or eGFP plasmids were co-transfected by electroporation into bovine and dairy goat fetal fibroblasts.  After G418 (Geneticin) selection, single cells were obtained by mouth pipetting, flow cytometry or a cell shove.  The gene knock-in events were screened by PCR across the homologous arms.  The results showed that in bovine fetal fibrobalsts, the efficiencies of ZFNs-mediated eGFP and hFat-1 gene knock-ins were 13.68 and 0%, respectively.  The efficiencies of CRISPR/Cas9-mediated eGFP and hFat-1 gene knock-ins were 77.02 and 79.01%, respectively.  The eGFP gene knock-in efficiency using CRISPR/Cas9 was about 5.6 times higher than when using the ZFNs gene editing system.  Additionally, the hFat-1 gene knock-in was only obtained when using the CRISPR/Cas9 system.  The difference of knock-in efficiencies between the ZFNs and CRISPR/Cas9 systems were extremely significant (P<0.01).  In the dairy goat fetal fibroblasts, the efficiencies of TALENs-mediated eGFP and hFat-1 gene knock-ins were 32.35 and 26.47%, respectively.  The efficiencies of eGFP and hFat-1 gene knock-ins using CRISPR/Cas9 were 70.37 and 74.29%, respectively.  The knock-in efficiencies difference between the TALENs and CRISPR/Cas9 systems were extremely significant (P<0.01).  This study demonstrated that CRISPR/Cas9 was more efficient at gene knock-ins in domesticated animal cells than ZFNs and TALENs.  The CRISPR/Cas9 technology offers a new era of precise gene editing in domesticated animal cell lines. 
    Effects of dietary forage to concentrate ratio and wildrye length on nutrient intake, digestibility, plasma metabolites, ruminal fermentation and fecal microflora of male Chinese Holstein calves
    XIA Chuan-qi, Aziz-Ur-Rahman Muhammad, NIU Wen-jing, SHAO Tao-qi, QIU Qing-hua, SU Hua-wei, CAO Bing-hai
    2018, 17(2): 415-427.  DOI: 10.1016/S2095-3119(17)61779-9
    Abstract ( )   PDF in ScienceDirect  
    Twenty-eight male, weaned Chinese Holstein calves ((156.8±33.4) kg) were used to investigate the effects of dietary forage to concentrate ratio (F:C) and forage length on nutrient digestibility, plasma metabolites, ruminal fermentation, and fecal microflora. Animals were randomly allocated to four treatments in a 2×2 factorial arrangement: whole-length forage (WL) with low F:C (50:50); WL with high F:C (65:35); short-length forage (SL) with high F:C (65:35); and SL with low F:C (50:50).  Chinese wildrye was used as the only forage source in this trial.  The grass in the SL treatments was chopped using a chaff cutter to achieve small particle size (~50% particles >19 mm).  Dry matter intake (DMI) and organic matter (OM) intake was increased by increasing both F:C (P<0.01) and forage length (FL) (P<0.05), while acid detergent fiber (ADF) and neutral detergent fiber (NDF) intakes were only increased by increasing the F:C (P<0.01).  The digestibility of NDF was increased as the FL increased (P<0.01), and it was also affected by interaction between F:C and FL (P<0.05).  Cholesterol (CHO) (P<0.01), leptin (LP) (P<0.05), and growth hormone (GH) (P<0.01) concentrations in plasma were increased as dietary F:C increased.  A significant increase in plasma triglyceride (TG) (P<0.01), insulin (INS) (P<0.05), and GH (P<0.01) levels was observed with decreasing dietary FL.  Ruminal pH values of calves fed with low F:C diets were significantly lower than those in high F:C treatment (P<0.05).  Increasing the F:C enhanced ruminal acetic acid (P<0.05) and acetic acid/propionic acid (P<0.01).  Fecal Lactobacillus content was significantly higher, while Escherichia coli and Salmonella contents were significantly lower in WL and high F:C groups (P<0.05).  Lower fecal scores (higher diarrhea rate) were observed in calves fed with SL hay compared to WL hay (P<0.05).  Denatured gradient gel electrophoresis (DGGE) bands and richness index (S) were significantly affected by the interaction between F:C and FL (P<0.05), under high F:C, band numbers and richness index from WL group were higher than that from SL group (P<0.05), whereas there were no differences between WL and SL groups under low F:C (P>0.05).  Microflora similarity was 50–73% among the different treatments.  It is concluded that the WL with high F:C (65:35) diet is suitable for weaned calves.
    Understanding the metabolism of Mycoplasma mycoides subsp. capri in vitro by a transcriptomic analysis
    WANG Xiao-hui, WANG Yan-fang, HUANG Hai-bi, BAI Fan, SHI Xiao-na, MA Chang-jiao, GAO Yuan, ZHANG Jian-hua, ZHANG Wen-guang, HAO Yong-qing
    2018, 17(2): 428-435.  DOI: 10.1016/S2095-3119(17)61747-7
    Abstract ( )   PDF in ScienceDirect  
    It is generally known that the culture for mycoplasma is time-consuming and a variety of nutrients are needed in the culture medium.  This brings a lot of difficulties to mycoplasma research and application, including Mycoplasma mycoides subsp. capri (Mmc).  Furthermore, little research on the characteristics of Mmc metabolism has been reported.  In this study, Mmc PG3 strain cultures were investigated for dynamic gene expression.  Culture samples were harvested during logarithmic phase (PG3-1), stationary phase (PG3-2), decline phase (PG3-3) and late decline phase (PG3-4).  Twelve RNA samples (three replicates for each of the four growth stages considered) from these cultures were collected and sequenced.  Paired comparison between consecutive growth phases in the four growth stages showed 45 significant differentially expressed genes (P<0.01) were linked to PG3 metabolism.  The enzymes these genes coded were mainly involved in ATP synthase, pyrimidine metabolism, nicotinate and nicotinamide metabolism, arginine and proline metabolism.  Among these, cytidylate kinase, fructose 1,6-bisphosphate aldolases Class II, nicotinate-nucleotide adenylyltransferase and dihydrolipoamide dehydrogenase play a key role in Mmc metabolism.  These results provide a baseline to build our understanding of the metabolic pathway of Mmc.  
    Agro-ecosystem & Environment
    The efficiency of long-term straw return to sequester organic carbon in Northeast China's cropland
    WANG Shi-chao, ZHAO Ya-wen, WANG Jin-zhou, ZHU Ping, CUI Xian, HAN Xiao-zeng, XU Ming-gang, LU Chang-ai
    2018, 17(2): 436-448.  DOI: 10.1016/S2095-3119(17)61739-8
    Abstract ( )   PDF in ScienceDirect  
    Black soil is one of the most precious soil resources on earth because it has abundant carbon stocks and a relatively high production capacity.  However, decreasing organic matter after land reclamation, and the effects of long-term inputs of organic carbon have made it less fertile black soil in Northeast China.  Straw return could be an effective method for improving soil organic carbon (SOC) sequestration in black soils.  The objective of this study was to evaluate whether straw return effectively increases SOC sequestration.  Long-term field experiments were conducted at three sites in Northeast China with varying latitudes and SOC densities.  Study plots were subjected to three treatments: no fertilization (CK); inorganic fertilization (NPK); and NPK plus straw return (NPKS).  The results showed that the SOC stocks resulting from NPKS treatment were 4.0 and 5.7% higher than those from NPK treatment at two sites, but straw return did not significantly affect the SOC stocks at the third site.  Furthermore, at higher SOC densities, the NPKS treatment resulted in significantly higher soil carbon sequestration rates (CSR) than the NPK treatment.  The equilibrium value of the CSR for the NPKS treatment equated to cultivation times of 17, 11, and 8 years at the different sites.  Straw return did not significantly increase the SOC stocks in regions with low SOC densities, but did enhance the C pool in regions with high SOC densities.  These results show that there is strong regional variation in the effects of straw return on the SOC stocks in black soil in Northeast China.  Additional cultivations and fertilization practices should be used when straw return is considered as an approach for the long-term improvement of the soil organic carbon pool.
    The effects of aeration and irrigation regimes on soil CO2 and N2O emissions in a greenhouse tomato production system
    CHEN Hui, HOU Hui-jing, WANG Xiao-yun, ZHU Yan, Qaisar Saddique, WANG Yun-fei, CAI Huan-jie
    2018, 17(2): 449-460.  DOI: 10.1016/S2095-3119(17)61761-1
    Abstract ( )   PDF in ScienceDirect  
    Aerated irrigation has been proven to increase crop production and quality, but studies on its environmental impacts are sparse.  The effects of aeration and irrigation regimes on soil CO2 and N2O emissions in two consecutive greenhouse tomato rotation cycles in Northwest China were studied via the static closed chamber and gas chromatography technique.  Four treatments, aerated deficit irrigation (AI1), non-aerated deficit irrigation (CK1), aerated full irrigation (AI2) and non-aerated full irrigation (CK2), were performed.  The results showed that the tomato yield under aeration of each irrigation regime increased by 18.8% on average compared to non-aeration, and the difference was significant under full irrigation (P<0.05).  Full irrigation significantly increased the tomato yield by 23.9% on average in comparison to deficit irrigation.  Moreover, aeration increased the cumulative CO2 emissions compared to non-aeration, and treatment effects were significant in the autumn-winter season (P<0.05).  A slight increase of CO2 emissions in the two seasons was observed under full irrigation (P>0.05).  There was no significant difference between aeration and non-aeration in soil N2O emissions in the spring-summer season, whereas aeration enhanced N2O emissions significantly in the autumn-winter season.  Furthermore, full irrigation over the two seasons greatly increased soil N2O emissions compared to the deficit irrigation treatment (P<0.05).  Correlation analysis indicated that soil temperature was the primary factor influencing CO2 fluxes.  Soil temperature, soil moisture and NO3 were the primary factors influencing N2O fluxes.  Irrigation coupled with particular soil aeration practices may allow for a balance between crop production yield and greenhouse gas mitigation in greenhouse vegetable fields.
    Agricultural Economics and Management
    Designing price-contingent vegetable rotation schedules using agent-based simulation
    LI Jing, Daniel Rodriguez, WANG Hao-xiang, WU Liu-san
    2018, 17(2): 461-472.  DOI: 10.1016/S2095-3119(17)61741-6
    Abstract ( )   PDF in ScienceDirect  
    Chinese vegetable production cooperatives supply their members, mostly smallholder farmers, with a rotation schedule for the year.  Since vegetable prices are not stable throughout the year, designing a rotation schedule that maximizes expected profits, distributes farmers’ profits more equitably, maintains the diversity of produce in the market, and reduces the risk of pests and diseases, requires adaptive, price-contingent rotation schedules (here, called “self-adaptive adjustment”).  This study uses an agent-based simulation (ABS) to design self-adaptive rotation schedules that deliver these aims.  The self-adaptive adjustment strategy was more profitable for farmers when faced with price volatility, and more equitable as well.  This work provides a decision-support tool for managers of Chinese vegetable production cooperatives to provide farmers with more profitable and equitable rotation schedules.   
    One size fits all?  Contract farming among broiler producers in China
    HUANG Ze-ying, XU Ying, ZENG Di, WANG Chen, WANG Ji-min
    2018, 17(2): 473-482.  DOI: 10.1016/S2095-3119(17)61752-0
    Abstract ( )   PDF in ScienceDirect  
    Contract farming has been increasingly found to benefit smallholders in developing countries, yet much less is known about its role in the poultry industry where economies of scale could be more prominent.  This study aims to narrow this gap by analysing the choice of contract farming among Chinese broiler producers using a nationally representative survey.  Simply cost-benefit analysis and multinomial logit regression modelling are jointly employed to explain contract farming decision making especially among small producers.  In contrast to many recent studies, we find that small producers, though not passively excluded, usually opt out of contract farming due to limited profitability when large producers are coexistent.  Such relationship is appropriately identified through a control function approach to correct for possible endogeneity.  Therefore, contract farming may not help achieve higher welfare goals for small broiler producers who actually instead seek alternative market opportunities that better realise their comparative advantages. 
    Short Communication
    Development of a sensitive and reliable droplet digital PCR assay for the detection of ‘Candidatus Liberibacter asiaticus’
    ZHONG Xi, LIU Xue-lu, LOU Bing-hai, ZHOU Chang-yong, WANG Xue-feng
    2018, 17(2): 483-487.  DOI: 10.1016/S2095-3119(17)61815-X
    Abstract ( )   PDF in ScienceDirect  
    Citrus Huanglongbing (HLB, yellow shoot disease) is one of the most serious citrus diseases worldwide.  To better improve the detection sensitivity, a droplet digital PCR (ddPCR) assay was developed for the rapid detection of ‘Candidatus Liberibacter asiaticus’ (Las), the putative causal agent of HLB.  The detection of sensitivity comparison using positive plasmid indicated that ddPCR was superior to quantitative PCR (qPCR) for detecting and quantifying Las at low concentrations.  The Las detection of 40 field samples also showed that six of 13 asymptomatic samples (46.15%) with high Ct value (>35) were positive by ddPCR.  This methodology showed great potential for early HLB infection diagnosis.
    Experimental infectivity of Theileria luwenshuni and Theileria uilenbergi in Chinese Kunming mice
    LI You-quan, GUO Peng-fei, LIU Jun-long, LIU Zhi-jie, HAN Yuan, LI Xuan, LIU Ai-hong, GUAN Gui-quan, LIU Guang-yuan, LUO Jian-xun, YIN Hong
    2018, 17(2): 488-492.  DOI: 10.1016/S2095-3119(17)61812-4
    Abstract ( )   PDF in ScienceDirect  
    Theileria luwenshuni and Theileria uilenbergi are important tick-borne pathogens and cause substantial losses to the sheep industry in China.  The improvement in detection techniques has allowed the identification of multi-homing parasitism in Theileria parasites.  Herein we evaluated the experimental infectivity of T. luwenshuni and T. uilenbergi in Chinese Kunming mice by screening blood samples of experimentally inoculated mice by microscopic examination (ME) and PCR.  T. luwenshuni infected Chinese Kunming mice and 20 mice inoculated with this parasite were positive by ME and PCR.  In addition, T. uilenbergi infected mice and 20 mice inoculated with this species were positive by ME and PCR.  However, the number of red blood cells and the levels of hemoglobin of 40 infected mice had no obvious changes in the course of infection.  Our results demonstrated the multi-homing parasitism of T. luwenshuni and T. uilenbergi, which were believed to be parasites of sheep and goats.  This study was the first to demonstrate the infection of T. luwenshuni and T. uilenbergi in Kunming mice.