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Genome-wide identification and expression analysis of GDSL esterase/lipase genes in tomato
SUN Yao-guang, HE Yu-qing, WANG He-xuan, JIANG Jing-bin, YANG Huan-huan, XU Xiang-yang
2022, 21 (2): 389-406.   DOI: 10.1016/S2095-3119(20)63461-X
Abstract480)      PDF in ScienceDirect      
The GDSL esterase/lipase family contains many functional genes that perform important biological functions in growth and development, morphogenesis, seed oil synthesis, and defense responses in plants.  The expression of GDSL esterase/lipase genes can respond to biotic and abiotic stresses.  Although GDSL esterase/lipase family genes have been identified and studied in other plants, they have not been identified and their functions remain unclear in tomato.  This study is the first to identify 80 GDSL esterase/lipase family genes in tomato, which were named SlGELP1–80.  These genes were mapped to their positions on the chromosomes and their physical and chemical properties, gene structure, phylogenetic relationships, collinear relationships, and cis-acting elements were analyzed.  The spatiotemporal expression characteristics of the SlGELP genes in tomato were diverse.  In addition, RNA-seq analysis indicated that the expression patterns of the SlGELP genes in tomato differed before and after inoculation with Stemphylium lycopersici.  qRT-PCR was used to analyze the expression of five SlGELP genes after treatments with S. lycopersici, salicylic acid and jasmonic acid.  Finally, this study was the first to identify and analyze GDSL esterase/lipase family genes in tomato via bioinformatics approaches, and these findings provide new insights for improving the study of plant disease resistance.
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Status and path of intergenerational transmission of poverty in rural China: A human capital investment perspective
BAI Yun-li, ZHANG Lin-xiu, SUN Ming-xing, XU Xiang-bo
2021, 20 (4): 1080-1091.   DOI: 10.1016/S2095-3119(20)63373-1
Abstract194)      PDF in ScienceDirect      
This paper focused on the intergenerational transmission of poverty in rural China by estimating the intergenerational transmission of earnings and stated its mechanism from the perspective of human capital investment before children participated in the labor market.  The data used in this study were longitude data collected in 2 000 households of 100 villages among 25 counties across five provinces in 2005, 2008, 2012, 2016, and 2019.  Qualitative and quantitative methods were adopted.  We found a significant intergenerational transmission of earnings in rural China, especially for the pairs of father–children and parents–children.  The intergenerational earnings’ elasticities were much less than those in urban areas, which indicated better social mobility in rural areas than that in urban China.  The children with parents who could earn much were more likely to be invested before they participated in the labor market, gain a high education and have more skills.  Three cases further showed that the mechanism of human capital investment in children breaking the intergenerational transmission of poverty and promoting social mobility.
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Silencing the SLB3 transcription factor gene decreases drought stress tolerance in tomato
WANG Zi-yu, bAO Yu-fang, PEI Tong, WU Tai-ru, DU Xu, HE Meng-xi, WANG Yue, LIU Qi-feng, YANG Huan-huan, JIANG Jing-bin, ZHANG He, LI Jing-fu, ZHAO Ting-ting, XU Xiang-yang
2020, 19 (11): 2699-2708.   DOI: 10.1016/S2095-3119(20)63350-0
Abstract128)      PDF in ScienceDirect      
BRI1-EMS-SUPPRESSOR 1 (BES1) transcription factor is closely associated with the brassinosteroid (BR) signaling pathway and plays an important role in plant growth and development.  SLB3 is a member of BES1 transcription factor family and its expression was previously shown to increase significantly in tomato seedlings under drought stress.  In the present study,we used virus-induced gene silencing (VIGS) technology to downregulate SLB3 expression to reveal the function of the SLB3 gene under drought stress further.  The downregulated expression of SLB3 weakened the drought tolerance of the plants appeared earlier wilting and higher accumulation of H2O2 and O2·, decreased superoxide dismutase (SOD) activity, and increased proline (PRO) and malondialdehyde (MDA) contents and peroxidase (POD) activity.  Quantitative real-time PCR (qRT-PCR) analysis of BR-related genes revealed that the expression of SlCPD, SlDWARF and BIN2-related genes was significantly upregulated in SLB3-silenced seedlings under drought stress, but that the expression of TCH4-related genes was downregulated.  These results showed that silencing the SLB3 gene reduced the drought resistance of tomato plants and had an impact on the BR signaling transduction which may be probably responsible for the variation in drought resistance of the tomato plants. 
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Downregulation of SL-ZH13 transcription factor gene expression decreases drought tolerance of tomato
ZHAO Ting-ting, WANG Zi-yu, BAO Yu-fang, ZHANG Xiao-chun, YANG Huan-huan, ZHANG Dong-ye, JIANG Jing-bin, ZHANG He, LI Jing-fu, CHEN Qing-shan, XU Xiang-yang
2019, 18 (7): 1579-1586.   DOI: 10.1016/S2095-3119(19)62621-3
Abstract293)      PDF in ScienceDirect      
Zinc finger-homeodomain proteins (ZF-HDs) are transcription factors that regulate plant growth, development, and abiotic stress tolerance.  The SL-ZH13 gene was found to be significantly upregulated under drought stress treatment in tomato (Solanum lycopersicum) leaves in our previous study.  In this study, to further understand the role that the SL-ZH13 gene plays in the response of tomato plants to drought stress, the virus-induced gene silencing (VIGS) method was applied to downregulate SL-ZH13 expression in tomato plants, and these plants were treated with drought stress to analyze the changes in drought tolerance.  The SL-ZH13 silencing efficiency was confirmed by quantitative real-time PCR (qRT-PCR) analysis.  In SL-ZH13-silenced plants, the stems wilted faster, leaf shrinkage was more severe than in control plants under the same drought stress treatment conditions, anyd the mean stem bending angle of SL-ZH13-silenced plants was smaller than that of control plants.  Physiological analyses showed that the activity of superoxide dismutase (SOD) and peroxidase (POD) and the content of proline (Pro) in SL-ZH13-silenced plants were lower than those in control plants after 1.5 and 3 h of drought stress treatment.  The malondialdehyde (MDA) content in SL-ZH13-silenced plants was higher than that in control plants after 1.5 and 3 h of drought stress treatment, and H2O2 and O2-· accumulated much more in the leaves of SL-ZH13-silenced plants than in the leaves of control plants.  These results suggested that silencing the SL-ZH13 gene affected the response of tomato plants to drought stress and decreased the drought tolerance of tomato plants. 
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Genomic and transcriptomic insights into cytochrome P450 monooxygenase genes involved in nicosulfuron tolerance in maize (Zea mays L.)
LIU Xiao-min, XU Xian, LI Bing-hua, YAO Xiao-xia, ZHANG Huan-huan, WANG Gui-qi, HAN Yu-jun
2018, 17 (08): 1790-1799.   DOI: 10.1016/S2095-3119(18)61921-5
Abstract375)      PDF in ScienceDirect      
Postemergence application of nicosulfuron for weed control in maize fields can cause great damage to certain maize inbred lines and hybrids.  Two maize genotypes, tolerant inbred (HBR) and sensitive inbred (HBS), were found to significantly differ in their phenotypic responses to nicosulfuron, with the EC50 (50% effective concentration) values differed statistically (763.6 and 5.9 g a.i. ha–1, respectively).  Pre-treatment with malathion, a known cytochrome P450 inhibitor, increased nicosulfuron injury in both HBR and HBS.  Our results support the hypothesis that nicosulfuron selectivity in maize is associated with cytochrome P450 metabolism.  Further analysis of the maize genome resulted in the identification of 314 full length cytochrome P450 monooxygenase (CYP) genes.  These genes were classified into 2 types, 10 clans and 44 families.  The CYP71 clan was represented by all A-type genes (168) belonging to 17 families.  Nine clans possessed 27 families containing 146 non-A-type genes.  The consensus sequences of the heme-binding regions of A-type and non-A-type CYP proteins are ‘PFGXGRRXCPG’ and ‘FXXGPRXCXG’, respectively.  Illumina transcriptome sequence results showed that there were 53 differentially expressed CYP genes on the basis of high variation in expression between HBS and HBR, nicosulfuron-treated and untreated samples.  These genes may contribute to nicosulfuron tolerance in maize.  A hierarchical clustering analysis obtained four main clusters named C1 to C4 in which 4, 15, 21, and 13 CYP genes were found in each respective cluster.  The expression patterns of some CYP genes were confirmed by RT-qPCR analysis.  The research will improve our understanding of the function of maize cytochrome P450 in herbicide metabolism.
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Insecticide resistance of the field populations of oriental armyworm, Mythimna separata (Walker) in Shaanxi and Shanxi provinces of China
ZHAO Yu-yu, SU Li, LI Shuai, LI Yi-ping, XU Xiang-li, CHENG Wei-ning, WANG Yi, WU Jun-xiang
2018, 17 (07): 1556-1562.   DOI: 10.1016/S2095-3119(17)61787-8
Abstract518)      PDF in ScienceDirect      
Resistance of five field populations of Mythimna separata (Walker) collected from Shaanxi and Shanxi provinces of China to six different insecticides was evaluated by leaf dip method in the laboratory.  The results showed that all populations were relatively sensitive to emamectin benzoate with a resistance ratio (RR) of 0.583–1.583 folds.  All populations showed susceptible or low level resistance to chlorantraniliprole and beta-cypermethrin.  Compared with a relatively susceptible strain of M. separata, the resistance level of the whole populations ranged from susceptible to moderate to chlorpyrifos and lambda-cyhalothrin, moderate to high to phoxim (RR=19.367–70.100) except for population from Sanyuan County (RR=2.567).  Pair-wise correlation analysis among different insecticides indicated that chlorpyrifos has a significantly positive and significant correlation with emamectin benzoate.  Chlorantraniliprole didn’t have significant correlation with emamectin benzoate, chlorpyrifos and phoxim.  Therefore, emamectin benzoate, chlorantraniliprole and beta-cypermethrin are recommended to control oriental armyworm.  Meanwhile, to postpone the occurrence and development of insecticide resistance in Shaanxi and Shanxi provinces, alternative and rotational application of insecticides between chlorantraniliprole and emamectin benzoate or chlorpyrifos is necessary.
 
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Effects of constant and stage-specific-alternating temperature on the survival, development and reproduction of the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)
LI Bo-liao, XU Xiang-li, JI Jia-yue, WU Jun-xiang
2018, 17 (07): 1545-1555.   DOI: 10.1016/S2095-3119(17)61841-0
Abstract479)      PDF in ScienceDirect      
Migratory insects make diverse adaptive strategies in response to changes in external environment.  Temperature has an impact on the survival, development, reproduction, and migration initiation of insects.  Previous research has primarily been focused on the effects of constant temperature on populations, but changing temperature has received less attention.  Three constant temperature treatments (20, 25 and 30°C) and three pupal-alternating temperature treatments (20–25, 25–20 and 25–30°C) were set up to study the relationship between temperature and population development by age-stage, two-sex life table analysis in the oriental armyworm, Mythimna separata Walker, a notorious migratory pest in grain crops.  The 25°C treatment was considered optimal with 20 and 30°C as low suitable temperature and high temperatures, respectively.  The survival rate was relatively low before third instar larvae at  20°C (63.0%) and 20–25°C (70.1%), and extreme low after pupal stage at 30°C (20.6%).  Developmental duration of each stage was negatively correlated with temperature.  The adult pre-oviposition period, when most migratory insects initiate migration, was the shortest at 25°C (2.69 d) but was lengthened at both low suitable (7.48 d for 20°C, 6.91 d for 25–20°C and 4.57 d for 20–25°C) and high temperatures (3.74 d for 25–30°C and 5.00 d for 30°C).  Both low suitable and high temperature decreased lifetime fecundity, net reproductive rate and the intrinsic rate of increase, with variability observed across developmental duration and stage during non-optimal temperature.  The results expand knowledge of the relationship between changing temperature and armyworm population development, and adaptive strategies in complex ambient environment.
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Effects of different feeding methods and space allowance on the growth performance, individual and social behaviors of Holstein calves
DONG Li-feng, XU Xian-cha, ZHANG Nai-feng, TU Yan, DIAO Qi-yu
2017, 16 (06): 1375-1382.   DOI: 10.1016/S2095-3119(16)61484-3
Abstract666)      PDF in ScienceDirect      
The importance of nutrient provisions and weaning methods for calves has been well established over the past few years, while as increasing interest has focused on contribution of animal behavior and their overall performance in production regimes.  The present study investigated the effects of feeding methods and space allowance on growth performance, individual and social behaviors in Holstein calves.  Twenty-four Chinese Holstein male and female calves were allocated to either an individual or group of 6 and fed either with a bucket or a teat.  Milk replacer, calf starter, and Chinese wildrye were offered during the experiment.  A fecal index used in the present study was defined as the total fecal scores/total number of calves in each treatment.  The results showed that there was no significant difference among the 4 treatments in terms of feed intake, body weight, average daily gain, and fecal index.  For the feeding behaviors, the ingesting milk time and ingesting milk rate were significantly affected by space allowance, while the feeding methods showed a significant influence on the bunting behavior of the calves.  There was no significant difference among the 4 treatments in terms of licking fixtures, self-grooming, and lying down behaviors, irrespective of the feeding method or space allowance.  However, sucking an empty bucket or the teat was significantly affected by the feeding method.  Several selected group behaviors were examined in the present study, and similar values for sniffing the other calves, social grooming, and cross-sucking behaviors were observed.  Overall, the present study demonstrated that different feeding methods and space allowances had a significant effect on the feeding behavior of calves, while the feed intake, growth performance, health condition, individual and group social behaviors were not significantly influenced.  Furthermore, under intensified production systems, Holstein calves raised in a group may obtain a similar production performance, thus reducing management input and profitability compared with those kept individually.  However, there may be competition during the feeding period.
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An improved method for RNA extraction from urediniospores of and wheat leaves infected by an obligate fungal pathogen, Puccinia striiformis f. sp. tritici
MA Li-Jie, QIAO Jia-xing, KONG Xin-yu, WANG Jun-juan, XU Xiang-ming, HU Xiao-ping
2016, 15 (06): 1293-1303.   DOI: 10.1016/S2095-3119(15)61250-3
Abstract1723)      PDF in ScienceDirect      
   Stripe rust, caused by Puccinia striiformis f. sp. tritici, is an important wheat disease in China, seriously threatening wheat production. Understanding the winter survival of the fungus is a key for predicting the spring epidemics of the disease, which determines the crop loss. Estimation of P. striiformis f. sp. tritici winter survival requires processing a large number of samples for sensitive detection of the pathogen in wheat leaf tissue using real-time quantitative reverse transcription PCR (qRT-PCR). A bottleneck for the analysis is the acquisition of a good yield of high quality RNA suitable for qRT-PCR to distinguish dead and alive fungal hyphae inside leaves. Although several methods have been described in the literatures and commercial kits are available for RNA extraction, these methods are mostly too complicated, expensive and inefficient. Thus, we modified three previously reported RNA extraction methods with common and low-cost reagents (LiCl, SDS and NaCl) to solve the problems and selected the best to obtain high quality and quantity RNA for use in qRT-PCR. In the three improved methods, the NaCl method was proven to be the best for extracting RNA from urediniospores of and wheat leaves infected by P. striiformis f. sp. tritici, although the modified LiCl and SDS methods also increased yield of RNA compared to the previous methods. The improved NaCl method has the following advantages: 1) Complete transfer of urediniospores of P. striiformis f. sp. tritici from the mortar and pestle can ensure the initial amount of RNA for the qRT-PCR analysis; 2) the use of low-cost NaCl to replace more expensive Trizol can reduce the cost; 3) the yield and quality of RNA can be increased; 4) the improved method is more suitable for a large number and high quantity of samples from fields. Using the improved NaCl method, the amount of RNA was increased three times from urediniospores of P. striiformis f. sp. tritici compared from the extraction kit. Approximately, 10.11 μg total RNA of high quality was obtained from 100 mg of infected leaves, which was 8.8, 6.5, 3.4 and 2.1 folds of the amounts obtained from the previous LiCl, SDS, NaCl and traditional Trizol methods, respectively. The method could be used to study the overwintering rates of P. striiformis f. sp. tritici over a large region of wheat production for predicting epidemic levels by determining pathogen survival levels after winter. The method can also be used in any studies which need a large number of high quality RNA samples.
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Functional prediction of tomato PLATZ family members and functional verification of SlPLATZ17
XU Min, GAO Zhao, LI Da-long, ZHANG Chen, ZHANG Yu-qi, HE Qian, QI Ying-bin, ZHANG He, JIANG Jing-bin, XU Xiang-yang, ZHAO Ting-ting
DOI: doi.org/10.1016/j.jia.2023.08.003 Online: 03 August 2023
Abstract0)      PDF in ScienceDirect      

PLATZ is a novel zinc finger DNA-binding protein that plays an important role in regulating plant growth and development and resisting abiotic stress. However, there has been very little research on the function of this family gene in tomatoes, which limits its application in germplasm resource improvement. Therefore, the PLATZ gene family was identified and analyzed in tomato, and its roles were predicted and verified to provide a basis for in-depth research on SlPLATZ gene function. In this study, the PLATZ family members of tomato were identified in the whole genome, and 19 SlPLATZ genes were obtained. Functional prediction was conducted based on gene and promoter structure analysis and RNA-seq-based expression pattern analysis. SlPLATZ genes that responded significantly under different abiotic stresses or were significantly differentially expressed among multiple tissues were screened as functional gene resources. SlPLATZ17 was selected for functional verification by experiment-based analysis. The results showed that the downregulation of SlPLATZ17 gene expression reduced the drought and salt tolerance of tomato plants. Tomato plants overexpressing SlPLATZ17 had larger flower sizes and long, thin petals, adjacent petals were not connected at the base, and the stamen circumference was smaller. This study contributes to understanding the functions of the SlPLATZ family in tomato and provides a reference for functional gene screening.

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