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Detection of maize tassels for UAV remote sensing image with an improved YOLOX Model
SONG Chao-yu, ZHANG Fan, LI Jian-sheng, XIE Jin-yi, YANG Chen, ZHOU Hang, ZHANG Jun-xiong
2023, 22 (6): 1671-1683.   DOI: 10.1016/j.jia.2022.09.021
Abstract361)      PDF in ScienceDirect      

Maize tassel detection is essential for future agronomic management in maize planting and breeding, with application in yield estimation, growth monitoring, intelligent picking, and disease detection.  However, detecting maize tassels in the field poses prominent challenges as they are often obscured by widespread occlusions and differ in size and morphological color at different growth stages.  This study proposes the SEYOLOX-tiny Model that more accurately and robustly detects maize tassels in the field.  Firstly, the data acquisition method ensures the balance between the image quality and image acquisition efficiency and obtains maize tassel images from different periods to enrich the dataset by unmanned aerial vehicle (UAV).  Moreover, the robust detection network extends YOLOX by embedding an attention mechanism to realize the extraction of critical features and suppressing the noise caused by adverse factors (e.g., occlusions and overlaps), which could be more suitable and robust for operation in complex natural environments.  Experimental results verify the research hypothesis and show a mean average precision (mAP@0.5) of 95.0%.  The mAP@0.5, mAP@0.5–0.95, mAP@0.5–0.95 (area=small), and mAP@0.5–0.95 (area=medium) average values increased by 1.5, 1.8, 5.3, and 1.7%, respectively, compared to the original model.  The proposed method can effectively meet the precision and robustness requirements of the vision system in maize tassel detection.

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OsMas1, a novel maspardin protein gene, confers tolerance to salt and drought stresses by regulating ABA signaling in rice

WANG Fei-bing, WAN Chen-zhong, NIU Hao-fei, QI Ming-yang, LI Gang, ZHANG Fan, HU Lai-bao, YE Yu-xiu, WANG Zun-xin, PEI Bao-lei, CHEN Xin-hong, YUAN Cai-yuan
2023, 22 (2): 341-359.   DOI: 10.1016/j.jia.2022.08.077
Abstract367)      PDF in ScienceDirect      

Drought and salt stresses, the major environmental abiotic stresses in agriculture worldwide, affect plant growth, crop productivity, and quality.  Therefore, developing crops with higher drought and salt tolerance is highly desirable.  This study reported the isolation, biological function, and molecular characterization of a novel maspardin gene, OsMas1, from rice.  The OsMas1 protein was localized to the cytoplasm.  The expression levels of OsMas1 were up-regulated under mannitol, PEG6000, NaCl, and abscisic acid (ABA) treatments in rice.  The OsMas1 gene was introduced into the rice cultivar Zhonghua 11 (wild type, WT).  OsMas1-overexpression (OsMas1-OE) plants exhibited significantly enhanced salt and drought tolerance; in contrast, OsMas1-interference (OsMas1-RNAi) plants exhibited decreased tolerance to salt and drought stresses, compared with WT.  OsMas1-OE plants exhibited enhanced hypersensitivity, while OsMas1-RNAi plants showed less sensitivity to exogenous ABA treatment at both germination and post-germination stages.  ABA, proline and K+ contents and superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and photosynthesis activities were significantly increased.  In contrast, malonaldehyde (MDA), hydrogen peroxide (H2O2), superoxide anion radical (O2-·), and Na+ contents were significantly decreased in OsMas1-OE plants compared with OsMas1-RNAi and WT plants.  Overexpression of OsMas1 up-regulated the genes involved in ABA signaling, proline biosynthesis, reactive oxygen species (ROS)-scavenging system, photosynthesis, and ion transport under salt and drought stresses.  Our results indicate that the OsMas1 gene improves salt and drought tolerance in rice, which may serve as a candidate gene for enhancing crop resistance to abiotic stresses.

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Virucidal activity of MICRO-CHEM PLUS against African swine fever virus
JIANG Cheng-gang, SUN Ying, ZHANG Fan, AI Xin, LU Ming, QIN Jia-lin, ZHANG Xian-feng, WANG Jing-fei, BU Zhi-gao, ZHAO Dong-ming, HE Xi-jun
2023, 22 (11): 3560-3563.   DOI: 10.1016/j.jia.2023.09.021
Abstract270)      PDF in ScienceDirect      
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Detection of quantitative trait loci (QTL) associated with spring regrowth in alfalfa (Medicago sativa L.)
JIANG Xue-qian, ZHANG Fan, WANG Zhen, LONG Rui-cai, LI Ming-na, HE Fei, YANG Xi-jiang, YANG Chang-fu, JIANG Xu, YANG Qing-chuan, WANG Quan-zhen, KANG Jun-mei
2022, 21 (3): 812-818.   DOI: 10.1016/S2095-3119(21)63671-7
Abstract231)           
Spring regrowth is an important trait for perennial plants including alfalfa, the most cultivated forage legume worldwide.  However, the genetic and genomic basis of the trait is largely unknown in alfalfa due to its complex genetic background of the tetroploid genome.  The objective of this study was to identify quantitative trait loci (QTLs) associated with spring regrowth using high-resolution genetic linkage maps we constructed previously.  In total, 36 significant additive effect QTLs for the trait were detected.  Among them, 10 QTLs individually explained more than 10% of the phenotypic variation (PVE) with four in P1 and six in P2.  Six overlapped QTLs intervals were detected with two and four intervals distributed in P1 and P2, respectively.  In P1, both overlapped genomic regions were located on homolog 7D.  In P2, the four QTLs with PVE>10% were co-localized on homolog 6D.  Meanwhile, six pairs of significant epistatic QTLs were identified in P2.  Screening of potential candidate genes associated with four overlapped QTLs (qCP2019-8, qLF2019-5, qLF2020-4, and qBLUP-3) narrowed down one candidate annotated as MAIL1.  The Arabidopsis homolog gene has been reported to play an important role in plant growth.  Therefore, the detected QTLs are valuable resources for genetic improvement of alfalfa spring vigor using marker-assisted selection (MAS), and further identification of the associated genes would provide insights into genetic control of spring regrowth in alfalfa.
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Viricidal activity of several disinfectants against African swine fever virus
JIANG Cheng-gang, SUN Ying, ZHANG Fan, AI Xin, FENG Xiao-ning, HU Wei, ZHANG Xian-feng, ZHAO Dong-ming, BU Zhi-gao, HE Xi-jun
2021, 20 (11): 3084-3088.   DOI: 10.1016/S2095-3119(21)63631-6
Abstract114)      PDF in ScienceDirect      
Prevention of African swine fever, a disease caused by African swine fever virus (ASFV), requires maintenance of high biosecurity standards, which principally relies on disinfection.  Finding the perfect disinfectant against ASFV is difficult because of the lack of relevant data.  Therefore, we aimed to find the most effective disinfectant and to optimise its concentration as well as contact time to confirm the viricidal effect against ASFV in vitro.  We evaluated the viricidal activity of three concentrations each of six common disinfectants against ASFV using immersion disinfection assay (IDA) and spray disinfection assay (SDA); the concentrations of these disinfectants at which complete viral inactivation occurred were almost same as the manufacturer-recommended concentrations, but the exposure times for viral inactivation are different.  The following disinfectants (assay: concentration, exposure time) showed complete inactivation: iodine and acid mixed solution (IDA/SDA: 0.5%, 10 min); compound potassium peroxymonosulfate (IDA: 0.25%, 30 min; SDA: 0.25%, 60 min); citric acid (IDA: 0.25%, 60 min; SDA: 0.5%, 60 min); sodium dichloroisocyanurate (IDA: 0.125%, 60 min; SDA: 0.25%, 60 min); and glutaral ang deciquam (IDA/SDA: 0.2%, 60 min); and deciquam (IDA/SDA: 0.5%, 60 min).  However, in the presence of organic material contamination, disinfectants did not show a marked inactivation effect.  Therefore, disinfection procedures should be performed in two steps: thorough mechanical cleaning followed by application of disinfectant.  In conclusion, all the tested disinfectants can inactivate ASFV; these can be used as alternative disinfectants to enhance biosecurity.
 
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Glycosylation of the hemagglutinin protein of H9N2 subtype avian influenza virus influences its replication and virulence in mice
TAN Liu-gang, CHEN Zhao-kun, MA Xin-xin, HUANG Qing-hua, SUN Hai-ji, ZHANG Fan, YANG Shao-hua, XU Chuan-tian, CUI Ning
2019, 18 (7): 1443-1450.   DOI: 10.1016/S2095-3119(19)62669-9
Abstract209)      PDF in ScienceDirect      
N-Linked glycosylation of hemagglutinin (HA) has been demonstrated to regulate the virulence and receptor-binding specificity of avian influenza virus (AIV).  In this study, we characterized the variation trend of naturally isolated H9N2 viruses for the potential N-linked glycosylation sites in HA proteins, and explored any important role of some glycosylation sites.  HA genes of 19 H9N2 subtype AIV strains since 2001 were sequenced and analyzed for the potential glycosylation sites.  The results showed that the viruses varied by losing one potential glycosylation site at residues 200 to 202, and having an additional one at residues 295 to 297 over the past few years.  Further molecular and single mutation analysis revealed that the N200Q mutation lost an N-linked glycosylation at positions 200 to 202 of the HA protein and affected the human-derived receptor affinity.  We further found that this N-linked glycosylation increased viral productivity in the lung of the infected mice.  These findings provide a novel insight on understanding the determinants of host adaption and virulence of H9N2 viruses in mammals.
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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
Abstract807)      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.
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Linkage map construction and QTL mapping for cold tolerance in Oryza rufipogon Griff. at early seedling stage
LUO Xiang-dong, ZHAO Jun, DAI Liang-fang, ZHANG Fan-tao, ZHOU Yi, WAN Yong, XIE Jian-kun
2016, 15 (12): 2703-2711.   DOI: 10.1016/S2095-3119(16)61465-X
Abstract1012)      PDF in ScienceDirect      
    Cold stress is one of the major restraints for rice production. Cold tolerance is controlled by complex genetic factor. In this study, a backcross inbred lines (BILs) population derived from an inter-specific cross (Oryza sativa L.×O. rufipogon Griff.) was used for genetic linkage map construction and quantitative trait locus (QTL) mapping. A linkage map consisting of 153 markers was constructed, spanning 1 596.8 cM with an average distance of 11.32 cM between the adjacent markers. Phenotypic evaluation of the parents and BILs under (6±1)°C cold stress revealed that the ability of cold tolerance in BILs at early seedling obeyed a skewed normal and continuous distribution. Fifteen QTLs on chromosomes 6, 7, 8, 11, and 12 were identified using survival percent (SP) and non death percent (NDP) as indicators of cold tolerance, which could explain 5.99 to 40.07% of the phenotypic variance, of which the LOD values ranged from 3.04 to 11.32. Four QTLs on chromosomes 3, 5 and 7 were detected using leaf conductivity (LC) and root conductivity (RC) as indicators of cold tolerance, ranging from 19.54 to 33.53% for the phenotypic variance explained and 2.54 to 6.12 for the LOD values. These results suggested that there might be multi major QTLs in O. rufipogon and some useful genes for cold tolerance have been transferred into cultivated rice, which would be helpful for cloning and utilizing the cold tolerance-responsive genes from wild rice.
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Overexpression of a maize SNF-related protein kinase gene, ZmSnRK2.11, reduces salt and drought tolerance in Arabidopsis
ZHANG Fan, CHEN Xun-ji, WANG Jian-hua, ZHENG Jun
2015, 14 (7): 1229-1241.   DOI: 10.1016/S2095-3119(14)60872-8
Abstract1976)           
Sucrose non-fermenting-1 related protein kinase 2 (SnRK2) is a unique family of protein kinases associated with abiotic stress signal transduction in plants. In this study, a maize SnRK2 gene ZmSnRK2.11 was cloned and characterized. The results showed that ZmSnRK2.11 is up-regulated by high-salinity and dehydration treatment, and it is expressed mainly in maize mature leaf. A transient expression assay using onion epidermal cells revealed that ZmSnRK2.11-GFP fusion proteins are localized to both the nucleus and cytoplasm. Overexpressing-ZmSnRK2.11 in Arabidopsis resulted in salt and drought sensitivity phenotypes that exhibited an increased rate of water loss, reduced relative water content, delayed stoma closure, accumulated less free proline content and increased malondialdehyde (MDA) content relative to the phenotypes observed in wild-type (WT) control. Furthermore, overexpression of ZmSnRK2.11 up-regulated the expression of the genes ABI1 and ABI2 and decreased the expression of DREB2A and P5CS1. Taken together, our results suggest that ZmSnRK2.11 is a possible negative regulator involved in the salt and drought stress signal transduction pathways in plants.
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Identification and validation of root-specific promoters in rice
HUANG Li-yu, ZHANG Fan, QIN Qiao, WANG Wen-sheng, ZHANG Ting, FU Bin-ying
2015, 14 (1): 1-10.   DOI: 10.1016/S2095-3119(14)60763-2
Abstract2238)      PDF in ScienceDirect      
Novel promoters that confer root-specific expression would be useful for engineering resistance against problems of nutrient and water absorption by roots. In this study, the reverse transcriptase polymerase chain reaction was used to identify seven genes with root-specific expression in rice. The isolation and characterization of upstream promoter regions of five selected genes rice root-specific promoter (rRSP) 1 to 5 (rRSP1-rRSP5) and A2P (the promoter of OsAct2) revealed that rRSP1, rRSP3, and rRSP5 are particularly important with respect to root-specific activities. Furthermore, rRSP1, rRSP3, and rRSP5 were observed to make different contributions to root activities in various species. These three promoters could be used for root-specific enhancement of target gene(s).
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Using the Phosphomannose Isomerase (PMI) Gene from Saccharomyces cerevisiae for Selection in Rice Transformation
WANG Tao, LIU Liang-yu, TANG Yong-yan, ZHANG Xiao-bo, ZHANG Mei-dong, ZHENG Yong-lian, ZHANG Fang-dong
2012, 12 (9): 1391-1398.   DOI: 10.1016/S1671-2927(00)8670
Abstract1465)      PDF in ScienceDirect      
The phosphomannose isomerase (PMI) gene from Saccharomyces cerevisiae acted as selectable marker and mannose acted as selective agent for the production of transgenic plants of rice (Oryza sativa L.) via Agrobacterium-mediated transformation. The concentration of mannose during the selection was stepwise increased, 5 g L-1 mannose combined with 15 g L-1 sucrose and 500 mg L-1 cefotaxime was used in the initial selection stage, then the concentration of mannose was increased to 11 g L-1, the highest transformation rate was 20.0%. The integration of PMI gene was confirmed by PCR, and the result of RT-PCR assay proved that the intron of PMI gene can be excised correctly during RNA splicing. β- Glucuronidase (GUS) activity analysis confirmed the expression of GUS gene. All those means the PMI gene from yeast can be used as a selectable marker in rice transformation.
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Diversity and Genetic Differentiation of the Whitefly Bemisia tabaci Species Complex in China Based on mtCOI and cDNA-AFLP Analysis
GUO Xiao-jun, RAO Qiong, ZHANG Fan, LUO Chen, ZHANG Hong-yu , GAO Xi-wu
2012, 11 (2): 206-214.   DOI: 10.1016/S1671-2927(00)8538
Abstract2016)      PDF in ScienceDirect      
The whitefly Bemisia tabaci are considered as a taxonomically complex that contained some destructive pests. Two of the most prevalent cryptic species are B. tabaci Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED). In an extensive field survey of the B. tabaci complex present throughout part of China from 2004 to 2007, we obtained 93 samples of B. tabaci from 22 provinces. We determined that these Chinese haplotypes included 2 invasive species (MEAM1 and MED), and 4 indigenous cryptic species (Asia II 1, Asia II 3, China 3 and Asia II 7) by sequencing mitochondrial cytochrome oxidose one gene (mtCOI). The diversity and genetic differentiation of a subset of 19 populations of B. tabaci were studied using cDNA amplified fragment length polymorphism (AFLP). Prior to 2007, MEAM1 was a dominant species in many provinces in China. By 2007, MED was dominant in 11 provinces. Both invasive and indigenous species were simultaneously found in some regions. Indigenous species of B. tabaci were found in six provinces in southern China. MED and MEAM1 have broad ranges of host plants, and indigenous species appeared to have much narrower host ranges. All Asia II 3 samples were found on cotton except one on aubergine. China 3 has more host plants than Asia II 3. Twelve samples of China 3 were collected from sweet potato, Japanese hop, squash and cotton. A total of 677 reproducible bands amplified with 5 AFLP primer combinations were obtained. The highest proportion of polymorphic bands was 98.7% and the lowest was 91.9%. Unweighted pair-group method analysis indicated that the clustering was independent of the different species. MED showed the lowest degree of similarity than the other species. The data indicate that both MEAM1and MED were rapidly established in China.
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Relationship Among Yield Components and Selection Criteria for Yield Improvement in Early Rapeseed (Brassica napus L.)
LU Guang-yuan, ZHANG Fang, ZHENG Pu-ying, CHENG Yong, LIU Feng-lan, FU Gui-ping, ZHANG , Xue-kun
2011, 10 (7): 997-1003.   DOI: 10.1016/S1671-2927(11)60086-2
Abstract1873)      PDF in ScienceDirect      
The objective of this study was to determine the relationship between seed yield and other important agronomic traits ofearly-maturing rapeseed as a rotation crop in a double-cropping rice area using Pearson’s correlation coefficient as well asto estimate direct and indirect effects of specific yield component traits on seed yield via path analysis. Nineteen rapeseedgenotypes were grown at ten environments in South China during 2008-2009 and 12 characters were evaluated. Analysisof variance showed that environment had a significant impact on all characters. For most characters the genotype byenvironment interaction was weak and not statistically significant. Simple correlation analysis indicated that the numberof primary branches (PB), number of pods on the main raceme (PR), and number of seeds per pod made significantcontributions to seed yield per plant (SYP), while 1 000-seed weight was negatively correlated with SYP (r=-0.485, P<0.05).Furthermore, number of pods per plant (PP), PB, and PR had the greatest direct effects on SYP. In addition, PP and PB werethe best indicators to predict seed yield in stepwise regression analysis. Finally, yield component differences betweenearly- and medium-maturity varieties were compared; this showed that to improve the seed yield of early varieties, moreemphasis should be given to increase PP, PB, and PR, and reduce plant height and shortening of growth duration inbreeding practice.
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