Archive

2020 Vol. 19 No. 10 Previous Issue    Next Issue

---

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


  Cover illustration


Download table of contents

×

Cover illustration


As a lysine acetyltransferase, FgGCN5 in Fusarium graminearum has been functionally characterized in hyphal vegetative growth, asexual and sexual reproduction, deoxynivalenol (DON) biosynthesis and plant infection. However, the roles of the conserved motifs/domains in FgGCN5 are unclear. Here, the four conserved sequence motifs (I–IV) were presented in the catalytic domain, a bromodomain in the carboxy-terminus and a conserved E130 in FgGCN5 were identified and characterized. Each conserved motif in the catalytic domain and E130 are essential for correct functions of the gene. The conserved bromodomain plays important roles in DON production and pathogen virulence. This was the first report to identify the functions of conserved motifs/domains in FgGCN5, which will contribute to our understanding of the mechanism(s) by which FgGCN5 regulates F. graminearum. The photo was provided by Associate Prof. ZHOU Shanyue from Qingdao Agricultural University, China. See pages 2477–2487 for more details.


---

For Selected:

Download Citations EndNote Ris BibTeX

Toggle Thumbnails

Crop Science

Select

Transcriptome and metabolome profiling of unheading in F1 hybrid rice WANG Jie, WEI Shao-bo, WANG Chun-chao, Najeeb Ullah KHAN, ZHANG Zhan-ying, WANG Wen-sheng, ZHAO Xiu-qin, ZHANG Hong-liang, LI Zi-chao, GAO Yong-ming 2020, 19(10): 2367-2382.  DOI: 10.1016/S2095-3119(19)62838-8 Abstract ( )   PDF in ScienceDirect   Heading date is a crucial agronomic trait.  However, rice usually delays heading due to the photoperiod, temperature, hormones or age.  The present research was conducted to analyze the mechanism controlling heading date in F1 hybrid rice.  We constructed two test-crossing populations using two introgression lines (ILs), P20 and P21 coming from SH527/FH838 as the male parent, respectively, and male sterile line Jin23A as the female parent.  Meanwhile, the F1 hybrids of H20, obtained by mating P20 with Jin23A and having no heading, and H21, from the crossing between P21 and Jin23A having normal heading, were both observed under long days.  Here, we analyzed the photoperiodic response of F1 hybrids by transcriptome and metabolome profiling.  The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod (exogenous) instead of genes (endogenous).  The coping mechanism resulted from long days (LD) in H20, leading to differences in the circadian rhythm and glutathione metabolism relative to other samples.  The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis, and both of them are responsible for modulating ROS in H20 under LD condition.  Both circadian rhythm genes and the reported genes related to heading date function via the DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18 pathway and the glutathione metabolism pathway by regulating oxidative reduction processes.  Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation, and all of them collectively modulated the heading process.  The results of this study will be helpful for unraveling the mechanism of F1 hybrid responses to unheading under LD condition.

Select

Identification of main effect and epistatic QTLs controlling initial flowering date in cultivated peanut (Arachis hypogaea L.) WANG Liang, YANG Xin-lei, CUI Shun-li, WANG Ji-hong, HOU Ming-yu, MU Guo-jun, LI Zi-chao, LIU Li-feng 2020, 19(10): 2383-2393.  DOI: 10.1016/S2095-3119(20)63211-7 Abstract ( )   PDF in ScienceDirect   Initial flowering date (IFD) is closely related to mature period of peanut pods.  In present study, a population of recombinant inbred lines (RIL) derived from the cross between Silihong (female parent) and Jinonghei 3 (male parent) was used to map QTLs associated with IFD.  The RIL population and its two parental cultivars were planted in two locations of Hebei Province, China from 2015 to 2018 (eight environments).  Based on a high-density genetic linkage map (including 2 996 SNP and 330 SSR markers) previously constructed in our laboratory, QTLs were analyzed using phenotypic data and the best linear unbiased prediction (BLUP) value of initial flowering date by inclusive composite interval mapping (ICIM) method.  Interaction effects between every two QTLs and between individual QTL and environment were also analyzed.  In cultivated peanut, IFD was affected by genotypic factor and environments simultaneously, and its broad sense heritability (h2) was estimated as 86.8%.  Using the IFD phenotypic data from the eight environments, a total of 19 QTLs for IFD were detected, and the phenotypic variation explained (PVE) by each QTL ranged from 1.15 to 21.82%.  Especially, five of them were also detected by the BLUP value of IFD.  In addition, 12 additive QTLs and 35 pairs of epistatic QTLs (62 loci involved) were identified by the joint analysis of IFD across eight environments.  Three QTLs (qIFDB04.1, qIFDB07.1 and qIFDB08.1) located on chromosome B04, B07 and B08 were identified as main-effect QTL for IFD, which had the most potential to be used in peanut breeding.  This study would be helpful for the early-maturity and adaptability breeding in cultivated peanut.

Select

Yield characteristics of japonica/indica hybrids rice in the middle and lower reaches of the Yangtze River in China XU Dong, ZHU Ying, CHEN Zhi-feng, HAN Chao, HU Lei, QIU Shi, WU Pei, LIU Guo-dong, WEI Hai-yan, ZHANG Hong-cheng 2020, 19(10): 2394-2406.  DOI: 10.1016/S2095-3119(19)62872-8 Abstract ( )   PDF in ScienceDirect   Although a lot of researches have been done on yield characteristics of japonica/indica hybrid rice, there is little information on differences of yield characteristics between different types of hybrid.  To determine common characteristics of japonica/indica hybrid rice (JIHR) and identify the differences between different types of JIHR, the present study assessed yield characteristics, such as panicle trait, leaf area index (LAI), above-ground biomass accumulation, and nitrogen absorption and utilization, among three types of cultivar of JIHR.  In our field experiments, three types of JIHR, e.g., Yongyou, Chunyou and Jiayouzhongke, were divided, and each of them has two cultivars, which were used as materials, meanwhile, using conventional japonica rice (CJR) Wuyingjing 31 and Sujing 9 were as controls.  The results showed that the mean yield of those JIHR was above 12 t ha–1 in 2017 and 2018, and was 31.9 and 32.2%, respectively higher than that of CJR in the two years.  Spikelet number per panicle of JIHR resulted in high yield.  Higher yield of JIHR was likely contributed to greater panicle number and more spikelets per panicle.  Higher yielding JIHR showed stronger tillering capacity, larger LAI and above-ground biomass accumulation from jointing to heading stages, which likely contributed to the higher number of spikelets per panicle.  The long duration from heading to maturity stages allowed more nitrogen accumulation of higher yielding JIHR.

Select

Yield-related agronomic traits evaluation for hybrid wheat and relations of ethylene and polyamines biosynthesis to filling at the mid-grain filling stage YANG Wei-bing, QIN Zhi-lie, SUN Hui, LIAO Xiang-zheng, GAO Jian-gang, WANG Yong-bo, HOU Qi-ling, CHEN Xian-chao, TIAN Li-ping, ZHANG li-ping, MA Jin-xiu, CHEN Zhao-bo, ZHANG Feng-ting, ZHAO Chang-ping 2020, 19(10): 2407-2418.  DOI: 10.1016/S2095-3119(19)62873-X Abstract ( )   PDF in ScienceDirect   Because of the yield increase of 3.5–15% compared to conventional wheat, hybrid wheat is considered to be one of the main ways to greatly improve the wheat yield in the future.  In this study, we performed a principal component analysis (PCA) on two-line hybrids wheat and their parents using the grain weight (GW), the length of spike (LS), the kernel number of spike (KSN), and spike number (SPN) as variables.  The results showed that the variables could be classified into three main factors, the weight factor (factor 1), the quantity factor 1 (factor 2) and the quantity factor 2 (factor 3), which accounted for 37.1, 22.6 and 18.5%, respectively of the total variance in different agronomic variables, suggesting that the GW is an important indicator for evaluating hybrid combinations, and the grain weight of restorer line (RGW) could be used as a reference for parents selection.  The hybrid combination with a higher score in factor 1 direction and larger mid-parent heterosis (MPH) of the GW and its parents were used to carry out the analysis of grain filling, 1-aminocylopropane-1-carboxylicacid (ACC) and polyamine synthesis related genes.  The results suggested that the GW of superior grain was significantly higher than that of inferior grains in BS1453×JS1 (H) and its parents.  Both grain types showed a weight of H between BS1453 (M) and JS1(R), and a larger MPH, which may be caused by their differences in the active filling stage and the grain filling rate.  The ADP-glucose pyrophosphorylase (AGPase), granule bound starch synthase I (GBSSI), starch synthase III (SSS), and starch branching enzyme-I (SBE-I) expression levels of H were intermediated between M and R, which might be closely related to MPH formation of the GW.  Compared with R and H, the GW of M at maturity was the lowest.  The expression levels of spermidine synthase 2 (Spd2), ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (SAMDC) had significantly positive correlations with the grain filling rate (r=0.77*, 0.51*, 0.59*), suggesting their major roles in the grain filling and heterosis formation.  These provide a theoretical basis for improving the GW of photo-thermo-sensitive male sterile lines (PTSMSL) by changing the endogenous polyamine synthesis in commercial applications.

Select

Key indicators affecting maize stalk lodging resistance of different growth periods under different sowing dates WANG Qun, XUE Jun, CHEN Jiang-lu, FAN Ying-hu, ZHANG Guo-qiang, XIE Rui-zhi, MING Bo, HOU Peng, WANG Ke-ru, LI Shao-kun 2020, 19(10): 2419-2428.  DOI: 10.1016/S2095-3119(20)63259-2 Abstract ( )   PDF in ScienceDirect   The accurate evaluation of maize stalk lodging resistance in different growth periods enables timely management of lodging risks and ensures stable and high maize yields.  Here, we established five different sowing dates to create different conditions for maize growth.  We evaluated the effects of the different growth conditions on lodging resistance by determining stalk morphology, moisture content, mechanical strength and dry matter, and the relationship between stalk breaking force and these indicators during the silking stage (R1), milk stage (R3), physiological maturity stage (R6), and 20 days after R6.  Plant height at R1 positively affected stalk breaking force.  At R3, the coefficient of ear height and the dry weight per unit length of basal internodes were key indicators of stalk lodging resistance.  At R6, the key indicators were the coefficient of the center of gravity height and plant fresh weight.  After R6, the key indicator was the coefficient of the center of gravity height.  The crushing strength of the fourth internode correlated significantly and positively with the stalk breaking force from R1 to R6, which indicates that crushing strength is a reliable indicator of stalk mechanical strength.  These results suggest that high stalk strength and low ear height benefit lodging resistance prior to R6.  During and after R6, the coefficient of the center of gravity height and the mechanical strength of basal internodes can be used to evaluate plant lodging resistance and the appropriate time for harvesting in fields with a high lodging risk.

Select

High-throughput phenotyping identifies plant growth differences under well-watered and drought treatments Seth TOLLEY, Yang Yang, Mohsen MOHAMMADI 2020, 19(10): 2429-2438.  DOI: 10.1016/S2095-3119(20)63154-9 Abstract ( )   PDF in ScienceDirect   The ability to screen larger populations with fewer replicates and non-destructive measurements is one advantage of high-throughput phenotyping (HTP) over traditional phenotyping techniques.  In this study, two wheat accessions were grown in a controlled-environment with a moderate drought imposed from stem elongation to post-anthesis.  Red-green-blue (RGB) imaging was performed on 17 of the 22 d following the start of drought imposition.  Destructive measurements from all plants were performed at the conclusion of the experiment.  The effect of line was significant for shoot dry matter, spike dry matter, root dry matter, and tiller number, while the water treatment was significant on shoot dry matter and root dry matter.  The temporal, non-destructive nature of HTP allowed the drought treatment to be significantly differentiated from the well-watered treatment after 6 d in a line from Argentina and 9 d in a line from Chile.  This difference of 3 d indicated an increased degree of drought tolerance in the line from Chile.  Furthermore, HTP from the final day of imaging accurately predicted reference plant height (r=1), shoot dry matter (r=0.95) and tiller number (r=0.91).  This experiment illustrates the potential of HTP and its use in modeling plant growth and development.

Select

Rejuvenating soybean (Glycine max L.) growth and development through slight shading stress WEN Bing-xiao, Sajad Hussain, YANG Jia-yue, WANG Shan, ZHANG Yi, QIN Si-si, XU Mei, YANG Wen-yu, LIU Wei-guo 2020, 19(10): 2439-2450.  DOI: 10.1016/S2095-3119(20)63159-8 Abstract ( )   PDF in ScienceDirect   The impact of increased shading stress on agronomic traits, photosynthetic performance and antioxidants activities in leaves of two soybeans cultivars (D16 and E93) was studied.  Soybean seedlings were grown in pots and exposed to no shade (S0), slight shade (S1), moderate shade (S2), and heavy shade (S3).  Our findings showed that under the S3 in both cultivars, leaf fresh weight (LFW), specific leaf area (SLA) and leaf thickness decreased significantly, accompanied by a reduction in photochemical parameters including the maximum quantum yield (Fv/Fm) and electron transport rate (ETR).  Furthermore, compared to S0, S1 significantly increased the ETR, sucrose content and the activity of catalase (CAT) in both D16 and E93 cultivars while S2 and S3 decreased the activity.  However, under all treatments of shading stress, the antioxidant activities of superoxide dismutase (SOD) and peroxidase (POD) were lowered in both cultivars.  Such morphological and physiological plasticity to adapt S1 compensates for the decrease in biomass and leads to seed weight compared to that obtained with an amount of normal light.  Through configuring the space in the intercropping systems, S1 could be helpful for optimum growth and yield.  Redesigning photosynthesis through S1 for the intercropping systems could be a smart approach.

Horticulture

Select

A new species of Malus in China, Malus shizongensis Liu sp. nov LIU Zhen-zhong, LI Zhong-xing, GAO Hua, BAO Cha-na 2020, 19(10): 2451-2457.  DOI: 10.1016/S2095-3119(20)63282-8 Abstract ( )   PDF in ScienceDirect   Based on morphological, molecular biological, and molecular systematic studies, we describe here a new species of Malus from Yunnan, China.  We compared the morphology of this new species, Malus shizongensis Liu sp. nov, with three Malus species, including M. hupehensis, M. baccata, and M. micromalus.  Although the appearance of M. shizongensis was similar to these three species, it differed in height, branch color, branch hair, and flower color.  To better identify the taxonomy of this new species, genome of M. shizongensis and that of seven Malus species, including M. prunifolia, M. sylvestris, M. sieversii, M. hupehensis, M. baccata, M. robusta, and M. micromalus were analyzed.  A phylogenetic tree based on genome analysis indicated that M. shizongensis was close to M. hupehensis.  Furthermore, M. shizongensis had its species-specific SNPs, and the number of species-specific SNPs was similar to that of three close species (M. hupehensis, M. baccata, and M. micromalus).  Based on the above information, we named this new species as M. shizongensis Liu sp. nov.

Select

Efficiency of potassium-solubilizing Paenibacillus mucilaginosus for the growth of apple seedling CHEN Yan-hui, YANG Xiao-zhu, LI Zhuang, AN Xiu-hong, MA Ren-peng, LI Yan-qing, CHENG Cun-gang 2020, 19(10): 2458-2469.  DOI: 10.1016/S2095-3119(20)63303-2 Abstract ( )   PDF in ScienceDirect   Chemical potassium (K) fertilizer is commonly used in apple (Malus domestica L. Borkh) production but K is easily fixed by soil, resulting in reduced K fertilizer utilization and wasted resources.  K-solubilizing bacteria (KSB) can cost-effectively increase the soluble K content in rhizosphere soil.  Therefore, the objectives were to select high-efficiency KSB from apple orchards under various soil management models and evaluate their effects on apple seedling growth.  Maize (Zea mays L.) straw mulching (MSM) increased the total carbon (TC), total nitrogen (TN) and available potassium (AK) in the rhizosphere and improved fruit quality.  The number of KSB in the rhizosphere soil of MSM was 9.5×104 CFU g–1 soil, which was considerably higher than that in the other mulching models.  Fourteen KSB strains were isolated with relative K solubilizing ability ranging from 17 to 30%, and five strains increased the dry weight per apple seedling.  The most efficient strain was identified as Paenibacillus mucilaginosus through morphological observation and sequence analysis of 16S rDNA, named JGK.  After inoculation, the colonization of JGK in soil decreased from 4.0 to 1.5×109 CFU g–1 soil within 28 d.  The growth of the apple seedlings and the K accumulation in apple plants were promoted by irrigation with 50 mL JGK bacterial solution (1×109 CFU mL–1), but there was no significant increase in the AK content of rhizosphere soil.  High-performance liquid phase analysis (HPLC) data showed that the JGK metabolites contained phytohormones and organic acids.  Hence, the JGK strain promoted the growth of two-month-old apple seedlings by stimulating function of the produced phytohormones and enhanced K solubility by acidification for apple seedling uptake.  This study enriches the understanding of KSB and provides an effective means to increase the K utilization efficiency of apple production.

Plant Protection

Select

First report of a new potato disease caused by Galactomyces candidum F12 in China SONG Su-qin, Lü Zhuo, WANG Jing, ZHU Jing, GU Mei-ying, TANG Qi-yong, ZHANG Zhi-dong, WANG Wei, ZHANG Li-juan, WANG Bo 2020, 19(10): 2470-2476.  DOI: 10.1016/S2095-3119(20)63257-9 Abstract ( )   PDF in ScienceDirect   Potato (Solanum tuberosum L.) is an important crop throughout the world.  An uncharacterized disease has been observed on potato plants during the growing season and tubers during the storage period from Nileke County, Qitai County and other locations in Xinjiang, China.  A particular fungus was consistently isolated from the infected potato plants and tubers.  Based on its morphology, molecular characteristics, pathogenicity test and internal transcribed spacer (ITS) sequence, the pathogens was identified as Galactomyces candidum F12.  Further study also showed that the hyphae and conidia of the pathogenic fungus grew faster as the temperature was 30°C, pH was 7, soluble starch was used as optimal carbon source and yeast powder as optimal nitrogen source.  In addition, 12-h continuous illumination light was beneficial to the hyphal growth, while 24-h continuous illumination was beneficial to the sporulation of the strain at 30°C.  To our knowledge, this is the first report of Galactomyces candidum causing leaf wilt and postharvest tuber rot on potato in China.

Select

Functional characterization of the catalytic and bromodomain of FgGCN5 in development, DON production and virulence of Fusarium graminearum WANG Qian-nan, HUANG Pan-pan, ZHOU Shan-yue 2020, 19(10): 2477-2487.  DOI: 10.1016/S2095-3119(20)63219-1 Abstract ( )   PDF in ScienceDirect   FgGCN5, a GCN5 homolog in Fusarium graminearum, plays a critical role in hyphal vegetative growth, asexual and sexual reproduction, deoxynivalenol (DON) biosynthesis and plant infection.  For nuclear localized GCN5, four conserved sequence motifs (I–IV) are presented in the catalytic domain and a bromodomain in the carboxy-terminus.  As a lysine acetyltransferase, conserved negatively charged residues are present to neutralize the protons from lysine substrates.  However, the role of conserved motifs/domains and residues in FgGCN5 are unclear.  Here, we generated deletion mutant strains for each the conserved motifs/domains and a glutamate residue 130 (E130) replacement mutant.  Deletion of each conserved motif in the catalytic domain and replacement of E130 site resulted in manifold defects in hyphae growth, asexual and sexual development, DON biosynthesis, and plant infection.  Phenotypic defects in the mutant strains were similar to deletion mutants.  The deletion of the bromodomain led a significant reduction in DON production and virulence, with no effects on hyphae growth, asexual or sexual reproduction.  FgGCN5 was further found to localize to the nucleus in conidia and hyphae cells.  In conclusion, FgGCN5 encodes a nuclear localized acetyltransferase.  The conserved motifs in the catalytic domain and E130 are essential for correct functions of the gene.  The conserved bromodomain is important for DON production and pathogen virulence.  This was the first report to identify the functions of conserved motifs/domains in FgGCN5, which will contribute to our understanding of the mechanism(s) by which FgGCN5 regulates F. graminearum.

Select

Effects of a novel mesoionic insecticide, triflumezopyrim, on the feeding behavior of rice planthoppers, Nilaparvata lugens and Sogatella furcifera (Hemiptera: Delphacidae) ZHU Jun, SUN Wen-qing, LI Yao, GE Lin-quan, YANG Guo-qing, XU Jian-xiang, LIU Fang 2020, 19(10): 2488-2449.  DOI: 10.1016/S2095-3119(20)63197-5 Abstract ( )   PDF in ScienceDirect   The rice planthoppers, Nilaparvata lugens and Sogatella furcifera, are important sap-sucking pests of rice in Asia.  The mesoionic insecticide triflumezopyrim was previously shown to be highly effective in controlling both N. lugens and S. furcifera.  In this study, electropenetrography (EPG) was used to evaluate the effect of three triflumezopyrim concentrations (LC10, LC50 and LC90) on the feeding behavior of N. lugens and S. furcifera.  EPG signals of planthoppes indicated that there were six different waveforms NP, N1, N2, N3, N4, and N5, which corresponded to non-penetration, stylet penetration into epidermis, salivation, extracellular movement of stylet, sap ingestion in phloem, and water ingestion in xylem during feeding.  Compared to untreated controls, triflumezopyrim at LC50 and LC90 prolonged the duration of the non-penetration period by 105.3 to 333.7%.  The probing frequencies of N. lugens exposed to triflumezopyrim at LC10 and LC50 were significantly increased; however, the probing frequencies of S. furcifera showed a significant decrease when exposed to triflumezopyrim at all concentrations.  Triflumezopyrim exposure prolonged the duration of salivation and shortened the duration of extracellular movement.  The duration of phloem sap ingestion decreased from 37.2 to 77.7% in the LC50 and LC90 treatments, respectively.  Differences in feeding behavior in response to triflumezopyrim and pymetrozine were minimal.  In summary, the results show that the LC50 and LC90 concentrations of triflumezopyrim inhibit the feeding activities of N. lugens and S. furcifera mainly by prolonging the duration of non-penetration and by shortening the duration of phloem sap ingestion, which may foster more efficient use of triflumezopyrim in Asia.

Select

Development of an automatic monitoring system for rice light-trap pests based on machine vision YAO Qing, FENG Jin, TANG Jian, XU Wei-gen, ZHU Xu-hua, YANG Bao-jun, Lü Jun, XIE Yi-ze, YAO Bo, WU Shu-zhen, KUAI Nai-yang, WANG Li-jun 2020, 19(10): 2500-2513.  DOI: 10.1016/S2095-3119(20)63168-9 Abstract ( )   PDF in ScienceDirect   Monitoring pest populations in paddy fields is important to effectively implement integrated pest management.  Light traps are widely used to monitor field pests all over the world.  Most conventional light traps still involve manual identification of target pests from lots of trapped insects, which is time-consuming, labor-intensive and error-prone, especially in pest peak periods.  In this paper, we developed an automatic monitoring system for rice light-trap pests based on machine vision.  This system is composed of an intelligent light trap, a computer or mobile phone client platform and a cloud server.  The light trap firstly traps, kills and disperses insects, then collects images of trapped insects and sends each image to the cloud server.  Five target pests in images are automatically identified and counted by pest identification models loaded in the server.  To avoid light-trap insects piling up, a vibration plate and a moving rotation conveyor belt are adopted to disperse these trapped insects.  There was a close correlation (r=0.92) between our automatic and manual identification methods based on the daily pest number of one-year images from one light trap.  Field experiments demonstrated the effectiveness and accuracy of our automatic light trap monitoring system.

Animal Science · Veterinary Medicine

Select

Two new SINE insertion polymorphisms in pig Vertnin (VRTN) gene revealed by comparative genomic alignment ZHENG Yao, CHEN Cai, CHEN Wei, WANG Xiao-yan, WANG Wei, GAO Bo, Klaus WIMMERS, MAO Jiu-de, SONG Cheng-yi 2020, 19(10): 2514-2522.  DOI: 10.1016/S2095-3119(20)63255-5 Abstract ( )   PDF in ScienceDirect   Despite one SINE retrotransposon insertion polymorphism (sRTIP) in the vertebrae development-associated (VRTN) gene was identified in pigs, the structural variations (SVs) in VRTN gene and its proximal flank regions were largely unknown.  VRTN genic and flanking sequences from 14 breeds were assembled or downloaded from whole-genome shotgun contings (WGS) database, and aligned to identify the SVs with Clustalx, and retrotransposons in VRTN gene were annotated by RepeatMasker, the splicing patterns of VRTN gene were predicted by Genescan, and large SVs were evaluated by PCR.  A total of 12 small SVs and three large SVs in intron of VRTN, derived from SINE insertion polymorphisms, were identified, and two of them (VRTN-sRTIP2 and VRTN-sRTIP3) were not reported before.  These VRTN-sRTIPs may affect the splicing patterns of VRTN.  They displayed polymorphisms in most detected eight breeds.  VRTN-sRTIP2 and VRTN-sRTIP3 showed Hardy-Weinberg equilibrium distributions in most populations except the Chinese local Erhualian pigs, while VRTN-sRTIP1 showed genetic equilibrium in Erhualian pigs.  Three VRTN-sRTIPs were identified, and displayed polymorphisms in pigs, and two of them were not reported before.  These SVs provide a useful molecular markers for genetic analysis in pigs, and offer new information to facilitate the understanding the SVs of VRTN gene and their putative roles in the variation of vertebral number.

Select

Rapid detection of Pseudomonas aeruginosa by cross priming amplification XIANG Yong, YAN Ling, ZHENG Xiao-cui, LI Li-zhen, LIU Peng, CAO Wei-sheng 2020, 19(10): 2523-2529.  DOI: 10.1016/S2095-3119(20)63187-2 Abstract ( )   PDF in ScienceDirect   Pseudomonas aeruginosa (PA) is an opportunistic pathogen of humans and animals and a common source of nosocomial infections especially of the respiratory tract.  Pseudomonas aeruginosa is also a major bacterial disease of poultry and in particular, eggs and newly hatched chicks.  In this study, we developed a simple, accurate and rapid molecular detection method using cross priming amplification (CPA) with a nucleic acid test strip to detect P. aeruginosa.  The assay efficiently amplified the target gene within 45 min at 62°C only using a simple water bath.  The detection limit of the method was 1.18×102 copies μL–1 for plasmid DNA and 4.4 CFU mL–1 for bacteria in pure culture, and was 100 times more sensitive than conventional PCR.  We screened 83 clinical samples from yellow-feather broiler breeder chickens and hospitalized/treated dogs and cats using CPA, PCR and traditional culture methods.  The positive-sample ratios were 15.3% (13/83) by CPA, 13.3% (11/83) by PCR and 12.1% (10/83) by the culture method.  The established CPA method has significant advantages for detecting P. aeruginosa.  The method is easy to use and possesses high specificity and sensitivity without the requirements of complicated experimental equipment.  The PA-CPA assay is especially fit for outdoor and primary medical units and is an ideal system for the rapid detection and monitoring of P. aeruginosa.

Agro-ecosystem & Environment

Select

Aggregate-associated changes in nutrient properties, microbial community and functions in a greenhouse vegetable field based on an eight-year fertilization experiment of China LUAN Hao-an, GAO Wei, TANG Ji-wei, LI Ruo-nan, LI Ming-yue, ZHANG Huai-zhi, CHEN Xin-ping, Dainius MASILIUNAS, HUANG Shao-wen 2020, 19(10): 2530-2548.  DOI: 10.1016/S2095-3119(20)63269-5 Abstract ( )   PDF in ScienceDirect   Soil aggregation, microbial community, and functions (i.e., extracellular enzyme activities; EEAs) are critical factors affecting soil C dynamics and nutrient cycling.  We assessed soil aggregate distribution, stability, nutrients, and microbial characteristics within >2, 0.25–2, 0.053–0.25, and <0.053 mm aggregates, based on an eight-year field experiment in a greenhouse vegetable field in China.  The field experiment includes four treatments: 100% N fertilizer (CF), 50% substitution of N fertilizer with manure (M), straw (S), and manure plus straw (MS).  The amounts of nutrient (N, P2O5, and K2O) input were equal in each treatment.  Results showed higher values of mean weight diameter in organic-amended soils (M, MS, and S, 2.43–2.97) vs. CF-amended soils (1.99).  Relative to CF treatment, organic amendments had positive effects on nutrient (i.e., available N, P, and soil organic C (SOC)) conditions, microbial (e.g., bacterial and fungal) growth, and EEAs in the >0.053 mm aggregates, but not in the <0.053 mm aggregates.  The 0.25–0.053 mm aggregates exhibited better nutrient conditions and hydrolytic activity, while the <0.053 mm aggregates had poor nutrient conditions and higher oxidative activity among aggregates, per SOC, available N, available P, and a series of enzyme activities.  These results indicated that the 0.25–0.053 mm (<0.053 mm) aggregates provide suitable microhabitats for hydrolytic (oxidative) activity.  Interestingly, we found that hydrolytic and oxidative activities were mainly impacted by fertilization (58.5%, P<0.01) and aggregate fractions (50.5%, P<0.01), respectively.  The hydrolytic and oxidative activities were significantly (P<0.01) associated with nutrients (SOC and available N) and pH, electrical conductivity, respectively.  Furthermore, SOC, available N, and available P closely (P<0.05) affected microbial communities within >0.25, 0.25–0.053, and <0.053 mm aggregates, respectively.  These findings provide several insights into microbial characteristics within aggregates under different fertilization modes in the greenhouse vegetable production system in China.

Select

Pseudomonas sp. TK35-L enhances tobacco root development and growth by inducing HRGPnt3 expression in plant lateral root formation CAO Yuan-yuan, NI Hai-ting, LI Ting, LAY Khien-duc, LIU Dai-song, HE Xiang-yi, OU Kang-miao, TANG Xin-yun, WANG Xiao-bo, Qiu Li-juan 2020, 19(10): 2549-2560.  DOI: 10.1016/S2095-3119(20)63266-X Abstract ( )   PDF in ScienceDirect   Rhizosphere colonization is a key requirement for the application of plant growth-promoting rhizobacteria (PGPR) as a biofertilizer.  Signaling molecules are often exchanged between PGPR and plants, and genes in plants may respond to the action of PGPR.  Here, the luciferase luxAB gene was electrotransformed into Pseudomonas sp. strain TK35, a PGPR with an affinity for tobacco, and the labelled TK35 (TK35-L) was used to monitor colonization dynamics in the tobacco rhizosphere and evaluate the effects of colonization on tobacco growth and root development.  The transcript levels of the hydroxyproline-rich glycoprotein HRGPnt3 gene, a lateral root induction indicator, in tobacco roots were examined by qPCR.  The results showed that TK35-L could survive for long periods in the tobacco rhizosphere and colonize new spaces in the tobacco rhizosphere following tobacco root extension, exhibiting significant increases in root development, seedling growth and potassium accumulation in tobacco plants.  The upregulation of HRGPnt3 transcription in the inoculated tobacco suggested that TK35-L can promote tobacco root development by upregulating the transcript levels of the HRGPnt3 gene, which promotes tobacco seedling growth.  These findings lay a foundation for future studies on the molecular mechanism underlying the plant growth-promoting activities of PGPR.  Furthermore, this work provided an ideal potential strain for biofertilizer production.

Select

Contrasting resilience of soil microbial biomass, microbial diversity and ammonification enzymes under three applied soil fumigants SUN Zhen-cai, LI Gui-tong, ZHANG Cheng-lei, WANG Zhi-min, LIN Qi-mei, ZHAO Xiao-rong 2020, 19(10): 2561-2570.  DOI: 10.1016/S2095-3119(20)63201-4 Abstract ( )   PDF in ScienceDirect   Fumigation is a widely applied approach to mitigate the soil-borne diseases.  However, the potential effects of currently applied fumigants on ammonification remain unclear.  An 84-day incubation experiment was conducted based on non-fumigated soil (CK) and fumigated soil using three common fumigants, i.e., chloropicrin (CP), 1,3-dichloropropene (1,3-D), and metam sodium (MS).  The results showed that, the three fumigants all decreased the microbial C, and the largest reduction (84.7%) occurred with the application of CP.  After fumigation, the microbial diversity in the CP treatment rapidly recovered, but that in the 1,3-D treatment decreased and did not recover by the end of the experiment.  The application of MS showed no impact on the microbial diversity during the assay, indicating that significantly different microbial diversity can be achieved by choosing different fumigants.  Furthermore, the three fumigants showed divergent effects on the enzymes involved in ammonification.  The analysis showed that the enzyme variation with CP application was mainly associated with the changed microbial C and N (P<0.05), and not with the microbial community, which was different from the observed effects of 1,3-D or MS application.  In addition, the soil quality index showed that CP was still significantly harmful at the end of incubation compared with the good resilience of MS, indicating that CP may not be a suitable fumigant.

Agricultural Economics and Management

Select

Impact of cash crop cultivation on household income and migration decisions: Evidence from low-income regions in China LI Meng, Christopher GAN, Wanglin MA, Wei JIANG 2020, 19(10): 2571-2581.  DOI: 10.1016/S2095-3119(20)63161-6 Abstract ( )   PDF in ScienceDirect   This study examines the impact of cash crop cultivation on household income and migration decisions, using survey data collected from low-income regions in China.  Given farmers decide themselves whether to cultivate cash crops, an endogenous treatment regression model that accounts for potential selection bias issue is used to analyze the data.  The empirical results show that cash crop cultivation exerts a positive and statistically significant impact on household income, but it does not affect household migration decisions significantly.  The disaggregated analyses reveal that cash crop cultivation significantly increases farm income but decreases off-farm income.

Select

Research and application of real-time monitoring and early warning thresholds for multi-temporal agricultural products information XU Shi-wei, WANG Yu, WANG Sheng-wei, LI Jian-zheng 2020, 19(10): 2582-2596.  DOI: 10.1016/S2095-3119(20)63368-8 Abstract ( )   PDF in ScienceDirect   Monitoring and early warning is an important means to effectively prevent risks in agricultural production, consumption and price.  In particular, with the change of modes of national administration against the background of big data, improving the capacity to monitor agricultural products is of great significance for macroeconomic decision-making.  Agricultural product information early warning thresholds are the core of agricultural product monitoring and early warning.  How to appropriately determine the early warning thresholds of multi-temporal agricultural product information is a key question to realize real-time and dynamic monitoring and early warning.  Based on the theory of abnormal fluctuation of agricultural product information and the research of substantive impact on the society, this paper comprehensively discussed the methods to determine the thresholds of agricultural product information fluctuation in different time dimensions.  Based on the data of the National Bureau of Statistics of China (NBSC) and survey data, this paper used a variety of statistical methods to determine the early warning thresholds of the production, consumption and prices of agricultural products.  Combined with Delphi expert judgment correction method, it finally determined the early warning thresholds of agricultural product information in multiple time, and carried out early warning analysis on the fluctuation of agricultural product monitoring information in 2018.  The results show that: (1) the daily, weekly and monthly monitoring and early warning thresholds of agricultural products play an important early warning role in monitoring abnormal fluctuations with agricultural products; (2) the multi-temporal monitoring and early warning thresholds of agricultural product information identified by the research institute can provide effective early warning on current abnormal fluctuation of agricultural product information, provide a benchmarking standard for China’s agricultural production, consumption and price monitoring and early warning at the national macro level, and further improve the application of China’s agricultural product monitoring and early warning.

Short Communication

Select

Decreasing detection frequency of MITE (MCLas-A) in the population of ‘Candidatus Liberibacter asiaticus’ recently collected in southern China CUI Xue-jin, ZENG Chun-hua, LIU Ke-hong, TENG Cai-ling, ZHOU Chang-yong, WANG Xue-feng 2020, 19(10): 2597-2601.  DOI: 10.1016/S2095-3119(20)63217-8 Abstract ( )   PDF in ScienceDirect   An active miniature inverted-repeat transposable element (MITE), MCLas-A, was previously identified from ‘Candidatus Liberibacter asiaticus’ known to be associated with citrus Huanglongbing (HLB, yellow shoot disease).  To explore the recent transposition status of MCLas-A, 389 ‘Ca. L. asiaticus’ strains collected from nine regions in China were amplified using a specific primer set and three representative ‘Ca. L. asiaticus’ strains were analyzed by next-generation sequencing (NGS) approach.  PCR and genomic analysis showed that the entire MCLas-A was only present in 1.80% (7/389) and the jumping-out type of the MITE was predominant (81.23%) in samples tested, suggesting high frequency transposition occurred in ‘Ca. L. asiaticus’ strains recently collected from China.  Biological roles of transposition of the active MITE remain to be determined.