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Monthly composites from Sentinel-1 and Sentinel-2 images for regional major crop mapping with Google Earth Engine
LUO Chong, LIU Huan-jun, LU Lü-ping, LIU Zheng-rong, KONG Fan-chang, ZHANG Xin-le
2021, 20 (7): 1944-1957.   DOI: 10.1016/S2095-3119(20)63329-9
Abstract131)      PDF in ScienceDirect      
Rapid and accurate access to large-scale, high-resolution crop-type distribution maps is important for agricultural management and sustainable agricultural development.  Due to the limitations of remote sensing image quality and data processing capabilities, large-scale crop classification is still challenging.  This study aimed to map the distribution of crops in Heilongjiang Province using Google Earth Engine (GEE) and Sentinel-1 and Sentinel-2 images.  We obtained Sentinel-1 and Sentinel-2 images from all the covered study areas in the critical period for crop growth in 2018 (May to September), combined monthly composite images of reflectance bands, vegetation indices and polarization bands as input features, and then performed crop classification using a Random Forest (RF) classifier.  The results show that the Sentinel-1 and Sentinel-2 monthly composite images combined with the RF classifier can accurately generate the crop distribution map of the study area, and the overall accuracy (OA) reached 89.75%.  Through experiments, we also found that the classification performance using time-series images is significantly better than that using single-period images.  Compared with the use of traditional bands only (i.e., the visible and near-infrared bands), the addition of shortwave infrared bands can improve the accuracy of crop classification most significantly, followed by the addition of red-edge bands.  Adding common vegetation indices and Sentinel-1 data to the crop classification improved the overall classification accuracy and the OA by 0.2 and 0.6%, respectively, compared to using only the Sentinel-2 reflectance bands.  The analysis of timeliness revealed that when the July image is available, the increase in the accuracy of crop classification is the highest.  When the Sentinel-1 and Sentinel-2 images for May, June, and July are available, an OA greater than 80% can be achieved.  The results of this study are applicable to large-scale, high-resolution crop classification and provide key technologies for remote sensing-based crop classification in small-scale agricultural areas.
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Development and characterization of new allohexaploid resistant to web blotch in peanut
WANG Si-yu, LI Li-na, FU Liu-yang, LIU Hua, QIN Li, CUI Cai-hong, MIAO Li-juan, ZHANG Zhong-xin, GAO Wei, DONG Wen-zhao, HUANG Bing-yan, ZHENG Zheng, TANG Feng-shou, ZHANG Xin-you, DU Pei
2021, 20 (1): 55-64.   DOI: 10.1016/S2095-3119(20)63228-2
Abstract101)      PDF in ScienceDirect      
Peanut diseases seriously threaten peanut production, creating disease-resistant materials via interspecific hybridization is an effective way to deal with this problem.  In this study, the embryo of an interspecific F1 hybrid was obtained by crossing the Silihong (Slh) cultivar with Arachis duranensis (ZW55), a diploid wild species.  Seedlings were generated by embryo rescue and tissue culture.  A true interspecific hybrid was then confirmed by cytological methods and molecular markers.  After treating seedlings with colchicine during in vitro multiplication, the established interspecific F1 hybrid produced seeds which were named as Am1210.  With oligonucleotide fluorescence in situ hybridization (Oligo FISH), molecular marker evaluations, morphological and web blotch resistance characterization, we found that: 1) Am1210 was an allohexaploid between Slh and ZW55; 2) the traits of spreading lateral branches, single-seeded or double-seeded pods and red seed coats were observed to be dominant compared to the erect type, multiple-seeded pods and brown seed coats; 3) the web blotch resistance of Am1210 was significantly improved than that of Slh, indicating the contribution of the web blotch resistance from the wild parent A. duranensis.  In addition, 69 dominant and co-dominant molecular markers were developed which could be both used to verify the hybrid in this study and to identify translocation or introgression lines with A. duranensis chromosome fragments in future studies as well.
 
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Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding
REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng
2021, 20 (1): 35-45.   DOI: 10.1016/S2095-3119(20)63256-7
Abstract226)      PDF in ScienceDirect      
Hybrid rice significantly contributes to the food supply worldwide.  Backbone parents play important roles in elite hybrid rice breeding systems.  In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding.  Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array.  Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives.  These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study.  This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.
 
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Mapping the fallowed area of paddy fields on Sanjiang Plain of Northeast China to assist water security assessments
LUO Chong, LIU Huan-jun, FU Qiang, GUAN Hai-xiang, YE Qiang, ZHANG Xin-le, KONG Fan-chang
2020, 19 (7): 1885-1896.   DOI: 10.1016/S2095-3119(19)62871-6
Abstract147)      PDF in ScienceDirect      
Rice growth requires a large amount of water, and planting rice will increase the contradiction between supply and demand of water resources.  Paddy field fallowing is important for the sustainable development of an agricultural region, but it remains a great challenge to accurately and quickly monitor the extent and area of fallowed paddy fields.  Paddy fields have unique physical features associated with paddy rice during the flooding and transplanting phases.  By comparing the differences in phenology before and after paddy field fallowing, we proposed a phenology-based fallowed paddy field mapping algorithm.  We used the Google Earth Engine (GEE) cloud computing platform and Landsat 8 images to extract the fallowed paddy field area on Sanjiang Plain of China in 2018.  The results indicated that the Landsat8, GEE, and phenology-based fallowed paddy field mapping algorithm can effectively support the mapping of fallowed paddy fields on Sanjiang Plain of China.  Based on remote sensing monitoring, the total fallowed paddy field area of Sanjiang Plain is 91 543 ha.  The resultant fallowed paddy field map is of high accuracy, with a producer (user) accuracy of 83% (81%), based on validation using ground-truth samples.  The Landsat-based map also exhibits high consistency with the agricultural statistical data.  We estimated that paddy field fallowing reduced irrigation water by 384–521 million cubic meters on Sanjiang Plain in 2018.  The research results can support subsidization grants for fallowed paddy fields, the evaluation of fallowed paddy field effects and improvement in subsequent fallowed paddy field policy in the future. 
 
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Invasion, expansion, and control of Bactrocera dorsalis (Hendel) in China
LIU Huan, ZHANG Dong-ju, XU Yi-juan, WANG Lei, CHENG Dai-feng, QI Yi-xiang, ZENG Ling, LU Yong-yue
2019, 18 (4): 771-787.   DOI: 10.1016/S2095-3119(18)62015-5
Abstract355)      PDF (818KB)(287)      
The Oriental fruit fly, Bactrocera dorsalis (Hendel), is among the most destructive fruit/vegetable-eating agricultural pests in the world, particularly in Asian countries such as China.  Because of its widespread distribution, invasive ability, pest status, and economic losses to fruit and vegetable crops, this insect species is viewed as an organism warranting severe quarantine restrictions by many countries in the world.  To understand the characteristics and potential for expansion of this pest, this article assembled current knowledge on the occurrence and comprehensive control of the Oriental fruit fly in China concerning the following key aspects: invasion and expansion process, biological and ecological characteristics, dynamic monitoring, chemical ecology, function of symbionts, mechanism of insecticide resistance, control index, and comprehensive control and countermeasures.  Some suggestions for the further control and study of this pest are also proposed.
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Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions
WANG Jiang-xu, SUN Jian, LI Cheng-xin, LIU Hua-long, WANG Jing-guo, ZHAO Hong-wei, ZOU De-tang
2016, 15 (12): 2688-2702.   DOI: 10.1016/S2095-3119(16)61427-2
Abstract1019)      PDF in ScienceDirect      
    Plant height (PH) is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line (RIL) derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr (2013 and 2014), respectively (regarded as four environments), was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL×environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between gene×gene interactions and gene×environment interactions in specific growth period. A total of 26 additive QTLs (A-QTLs) and 37 epistatic QTLs (E-QTLs) associated with PH were detected by unconditional and conditional mapping over seven growth periods. qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses. qPH-4-3 and qPH-7-5 were detected in four stages (periods) to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects (A-QTLs) were mostly expressed in the period S3|S2 (the time interval from stages 2 to 3), and QTL×environment interactions performed actively in the first three stages (periods) which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly influenced by environments as well. Many QTLs (qPH-1-2, qPH-3-5, qPH-4-1, qPH-2-3) coincident with previously identified drought resistance genes. The result of this study is helpful to elucidating the genetic mechanism and regulatory network underlying the development of PH in rice and providing references to marker assisted selection.
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Chromosome painting of telomeric repeats reveals new evidence for genome evolution in peanut
DU Pei, LI Li-na, ZHANG Zhong-xin, LIU Hua, QIN Li, HUANG Bing-yan, DONG Wen-zhao, TANG Feng-shou, QI Zeng-jun, ZHANG Xin-you
2016, 15 (11): 2488-2496.   DOI: 10.1016/S2095-3119(16)61423-5
Abstract1287)      PDF in ScienceDirect      
    Interspecific hybridization is an important approach to improve cultivated peanut varieties. Cytological markers such as tandem repeats will facilitate alien gene introgression in peanut. Telomeric repeats have also been frequently used in chromosome research. Most plant telomeric repeats are (TTTAGGG)n that are mainly distributed at the chromosome ends, although interstitial telomeric repeats (ITRs) are also commonly identified. In this study, the telomeric repeat was chromosomally localized in 10 Arachis species through sequential GISH (genomic in situ hybridization) and FISH (fluorescence in situ hybridization) combined with 4’,6-diamidino-2-phenylindole (DAPI) staining. Six ITRs were identified such as in the centromeric region of chromosome Bi5 in Arachis ipaënsis, pericentromeric regions of chromosomes As5 in A. stenosperma, Bho7 in A. hoehnei and Av5 in A. villosa, nucleolar organizer regions of chromosomes As3 in A. stenosperma and Adi3 in A. diogoi, subtelomeric regions of chromosomes Bho9 in A. hoehnei and Adu7 in A. duranensis, and telomeric region of chromosome Es7 in A. stenophylla. The distributions of the telomeric repeat, 5S rDNA, 45S rDNA and DAPI staining pattern provided not only ways of distinguishing different chromosomes, but also karyotypes with a higher resolution that could be used in evolutionary genome research. The distribution of telomeric repeats, 5S rDNA and 45S rDNA sites in this study, along with inversions detected on the long arms of chromosomes Kb10 and Bho10, indicated frequent chromosomal rearrangements during evolution of Arachis species.
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Highly Sensitive and Specific Monoclonal Antibody-Based Serological Methods for Rice Ragged Stunt Virus Detection in Rice Plants and Rice Brown Planthopper Vectors
LIU Huan, SONG Xi-jiao, NI Yue-qun, LU Li-na, ZHOU Xue-ping , WU Jian-xiang
2014, 13 (9): 1943-1951.   DOI: 10.1016/S2095-3119(13)60533-X
Abstract1765)      PDF in ScienceDirect      
Rice ragged stunt virus (RRSV) is a serious rice disease in Asia, causing serious yield losses on rice. The capsid protein (CP) gene of the major outer capsid protein of RRSV was expressed in Escherichia coli BL21 (DE3) using the pMAL-C2X expression vector. The recombinant protein was used as the immunogen to immunize BALB/c mice. A hybridoma cell line 8A12 secreting monoclonal antibody (MAb) against RRSV was obtained by fusing mouse myeloma cells (Sp 2/0) with spleen cells from the immunized BALB/c mice. Western blot analysis showed that the MAb 8A12 can specifically react with RRSV CP. Using the MAb, an antigen-coated-plate enzyme-linked immunosorbent assay (ACP-ELISA), a dot enzyme-linked immunosorbent assay (dot-ELISA), and immunocapture-RT-PCR (IC-RT-PCR) assay were developed to detect RRSV. The established ACP-ELISA, dot-blot ELISA and IC-RT-PCR methods could detect RRSV in infected rice tissue crude extracts with dilutions of 1:40 960, 1:1280 and 1:655360 (w/v, g mL-1), respectively. The ACP-ELISA and dot-blot ELISA methods could detect RRSV in infected insect vector crude extracts with dilutions of 1:12800 and 1:1600 (an individual planthopper μL-1), respectively. The field survey revealed that Rice ragged stunt disease occurs on rice in Hainan, Yunnan, Guangxi, Sichuan, Guizhou, Fujian, Hunan, Jiangxi and Zhejiang in China.
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Changes in Organic Carbon Index of Grey Desert Soil in Northwest China After Long-Term Fertilization
XU Yong-mei, LIU Hua, WANG Xi-he, XU Ming-gang, ZHANG Wen-ju , JIANG Gui-ying
2014, 13 (3): 554-561.   DOI: 10.1016/S2095-3119(13)60712-1
Abstract1620)      PDF in ScienceDirect      
Soil organic carbon (SOC), soil microbial biomass carbon (SMBC) and SMBC quotient (SMBC/SOC, qSMBC) are key indexes of soil biological fertility because of the relationship to soil nutrition supply capacity. Yet it remains unknown how these three indexes change, which limits our understanding about how soil respond to different fertilization practices. Based on a 22-yr (1990-2011) long-term fertilization experiment in northwest China, we investigated the dynamics of SMBC and qSMBC during the growing period of winter wheat, the relationships between the SMBC, qSMBC, soil organic carbon (SOC) concentrations, the carbon input and grain yield of wheat as well. Fertilization treatments were 1) nonfertilization (control); 2) chemical nitrogen plus phosphate plus potassium (NPK); 3) NPK plus animal manure (NPKM); 4) double NPKM (hNPKM) and 5) NPK plus straw (NPKS). Results showed that the SMBC and qSMBC were significantly different among returning, jointing, flowering and harvest stages of wheat under long-term fertilization. And the largest values were observed in the flowering stage. Values for SMBC and qSMBC ranged from 37.5 to 106.0 mg kg-1 and 0.41 to 0.61%, respectively. The mean value rank of SMBC during the whole growing period of wheat was hNPKM>NPKM>NPKS>CK>NPK. But there were no statistically significant differences between hNPKM and NPKM, or between CK and NPK. The order for qSMBC was NPKS>NPKM>CK>hNPKM>NPK. These results indicated that NPKS significantly increased the ratio of SMBC to SOC, i.e., qSMBC, compared with NPK fertilizer or other two NPKM fertilizations. Significant linear relationships were observed between the annual carbon input and SOC (P<0.01) or SMBC (P<0.05), and between the relative grain yield of wheat and the SOC content as well (P<0.05). But the qSMBC was not correlated with the annual carbon input. It is thus obvious that the combination of manure, straw with mineral fertilizer may be benefit to increase SOC and improve soil quality than using only mineral fertilizer.
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The Role of Radical Burst in Plant Defense Responses to Necrotrophic Fungi
Mahesh S Kulye, LIU Hua, QIU De-wen
2012, 12 (8): 1305-1312.   DOI: 10.1016/S1671-2927(00)8659
Abstract1690)      PDF in ScienceDirect      
Necrotrophic fungi, being the largest class of fungal plant pathogens, pose a serious economic problem to crop production. Nitric oxide (NO) is an essential regulatory molecule in plant immunity in synergy with reactive oxygen species (ROS). Most experimental data available on the roles of NO and ROS during plant-pathogen interactions are from studies of infections by potential biotrophic pathogens, including bacteria and viruses. However, there are several arguments about the role of ROS in defense responses during plants and necrotrophic pathogens interaction and little is known about the role of NO as a counterpart of ROS in disease resistance to necrotrophic pathogens. This review focuses on the recent knowledge about the role of oxidative burst in plant defense response to necrotrophic fungi.
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Arsenic Distribution, Species, and Its Effect on Maize Growth Treated with Arsenate
CI Xiao-ke, LIU Hua-lin, HAO Yu-bo, LIU Peng, DONG Shu-ting
2012, 12 (3): 416-423.   DOI: 10.1016/S1671-2927(00)8559
Abstract2238)      PDF in ScienceDirect      
A pot experiment was conducted to investigate the effect of different arsenic (As) levels on maize (Zea mays L.) growth and As accumulation and species in different parts of maize plants, as a guideline for production of maize in As-polluted areas with the objective of preventing As from entering the food chain, and improving understanding of the mechanisms of effect of As on plant. Zhengdan 958 was grown at five As levels added to soil (0, 12.5, 25, 50, and 100 mg kg-1 As). As concentration in maize tissues increased in the order of grain<stalk<leaf<<root. The As concentration in maize grain exceeded the maximum permissible concentration of 0.7 mg kg-1 in China at levels of 50 and 100 mg kg-1. As species were presented in root, stalk, and grain, but organic As was the major As species identified in the grain. Maize plants were able to reduce arsenate to arsenite. Low As levels of 12.5 and 25 mg kg-1 improved maize growth and grain nutrition quality, while high levels of As 50 or 100 mg kg-1 inhibited them. Yield reduction at high As levels resulted mainly from reduced ear length, kernel number per row, and kernel weight.
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Utilization of Chinese Herbal Feed Additives in Animal Production
LIU Hua-wei, TONG Jian-ming, ZHOU Dao-wei
2011, 10 (8): 1262-1272.   DOI: 10.1016/S1671-2927(11)60118-1
Abstract4337)      PDF in ScienceDirect      
The experimental knowledge on efficacy, possible modes of action and aspects of application of Chinese herbs as feedadditives for animal production are reviewed in this article. Chinese herbs commonly contain protein, carbohydrate, fat,vitamins, and mineral which are necessary nutrients to the growth of animal. Polysaccharide, organic acid, alkaloids, andessential oils involved in Chinese herbs can improve the immune function of livestock. Currently, numerous studies havedemonstrated anti-oxidative and anti-microbial efficacy and the assumption that Chinese herbs may improve the flavor ofmeat, which has been confirmed by some observations, but the mode of this action is still unclear. Moreover, severalobservations support the hypothesis that herbal feed additives may favorably affect gut functions (e.g., enzyme activity,microbial eubiosis) in vitro. Such effects may explain a considerable number of practical studies with livestock reportingimproved production performance after providing herbal feed additives. In summary, available evidence indicates thatherbal feed additives may have the potential to add to the set of non-antibiotic growth promoters for use in livestock, suchas organic acids and probiotics. However, a systematic approach toward the efficacy, mode of action and safety of herbalcompounds used as feed additives for animal production seems to be required in the future.
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Effect of Host Plants on Development, Fecundity and Enzyme Activity of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae)
ZHANG Bin, LIU Huai, Helen Hull-Sanders, WANG Jin-jun
2011, 10 (8): 1232-1240.   DOI: 10.1016/S1671-2927(11)60114-4
Abstract3306)      PDF in ScienceDirect      
The beet armyworm, Spodoptera exigua (Lepidoptera: Noctuidae), is an economically important pest of crops worldwide,attacking plants from over 20 families including trans-continental agricultural cotton, corn and citrus crops. In this study,performance and subsequent enzyme activity of beet armyworm reared on host plants from five families were investigated.Significant differences were found in development, fecundity and enzyme activity on different host plants. Survival ratewas the highest (42.8%) on asparagus lettuce (Lactuca sativar var. asparagina) and the lowest (17.0%) on sweet pepper(Capsicum annuum). Larval duration was the shortest on asparagus lettuce (12.0 d), and was 43.4% longer on sweetpeppers (21.2 d). The activity of acetylcholine esterase (AChE) and carboxylesterase (CarE) in 3rd instar larvae, andsoluble carbohydrate and crude protein contents in different host plants were determined. AChE activity was the highestin the larvae feeding on Chinese cabbage (Brassica rapa), but declined by nearly 60% on maize (Zea mays) seedlings. Theratio of soluble carbohydrate content to crude protein content in host plants was found to have a positive effect onoviposition and a negative correlation with larval duration and life time (from larval to adult stages) of the insect.
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Identification of oil content QTL on Arahy12 and Arahy16 and development of KASP markers in cultivated peanut (Arachis hypogaea L.)
HUANG Bing-yan, LIU Hua, FANG Yuan-jin, MIAO Li-juan, QIN Li, SUN Zi-qi, QI Fei-yan, CHEN Lei, ZHANG Feng-ye, LI Shuan-zhu, ZHENG Qing-huan, SHI Lei, WU Ji-hua, DONG Wen-zhao, ZHANG Xin-you
DOI: 10.1016/j.jia.2023.11.010 Online: 10 November 2023
Abstract74)      PDF in ScienceDirect      

Peanut kernels rich in oil, particularly those with oleic acid as their primary fatty acid, are sought after by consumers, the food industry, and farmers due to their superior nutritional content, extended shelf life, and health benefits.  The oil content and fatty acid composition are governed by multiple genetic factors.  Identifying the quantitative trait loci (QTL) related to these attributes would facilitate marker-assisted selection or genomic selection, thus enhancing the quality-focused peanut breeding program.  For this purpose, we developed a population of 521 recombinant inbred lines (RIL) and tested their kernel quality traits across five different environments. We identified two major and stable QTLs for oil content (qOCAh12.1 and qOCAh16.1).  The markers linked to these QTLs were designed by competitive allele-specific PCR (KASP) and were subsequently validated.  Moreover, we found that the superior haplotype of oil content in the qOCAh16.1 region was conserved within the PI germplasm cluster, as evidenced by a diverse peanut accession panel.  In addition, we determined that qAh09 and qAh19.1, which harbor the key gene encoding fatty acid desaturase 2 (FAD2), influence all seven fatty acids, including palmitic, stearic, oleic, linoleic, arachidic, gadoleic, and behenic acids.  As for protein content and the long-chain saturated fatty acid behenic acid, qAh07 emerged as the major and stable QTLs, accounting for over 10% of the phenotypic variation explained (PVE).  These findings would enhance marker-assisted selection in peanut breeding, aiming to improve oil content, and deepen our understanding of the genetic mechanisms that shape fatty acid composition. 

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