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  • CHONG Zhi-li, WEI Yun-xiao, LI Kai-li, Muhammad Aneeq Ur Rahman, LIANG Cheng-zhen, MENG Zhi-gang, WANG Yuan, GUO San-dui, HE Liang-rong, ZHANG Rui
    Journal of Integrative Agriculture. 2024, 23(10): 0. https://doi.org/10.1016/j.jia.2023.05.037

    Leaves are the main places for photosynthesis and organic synthesis of cotton.  Leaf shape has important effects on the photosynthetic efficiency and canopy formation, thereby affecting cotton yield.  Previous studies have shown that LMI1 is the main gene regulating leaf shape. In this study, the LMI1 gene (LATE MERISTEM IDENTITY1) was inserted into the 35S promoter expression vector, and cotton plants overexpressing LMI1(OE) were obtained through genetical transformation.  Statistical analysis of the biological traits of T1 and T2 populations showed that compared to wild type (WT), OE plants had significant larger leaves, thicker stems and significantly increased dry weight.  Furthermore, plant sections of the main vein and petiole showed that the number of cell in those tissues of OE plants increased significantly.  In addition, RNA-seq analysis revealed differential expression of genes related to gibberellin synthesis and NAC gene family (genes containing the NAC domain) in OE and WT plants, suggesting that LMI1 is involved in secondary wall formation and cell proliferation, and promotes stem thickening.  Moreover, GO (Gene Ontology) analysis enriched the terms of calcium ion binding, and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis enriched the terms of fatty acid degradation, phosphatidylinositol signal transduction system, and cAMP signal pathway.  These results suggested that LMI1 OE plants were responsive to gibberellin hormone signals, and altered messenger signal (cAMP, Ca2+) which amplified this function, to promote the stronger above ground vegetative growth.  This study found the LMI1 soared the nutrient growth in cotton, which is the basic for higher yield.

  • Crop Science
    Anmin Zhang, Zihong Li, Qirui Zhou, Jiawen Zhao, Yan Zhao, Mengting Zhao, Shangyu Ma, Yonghui Fan, Zhenglai Huang, Wenjing Zhang
    Journal of Integrative Agriculture. 2025, 24(1): 114-131. https://doi.org/10.1016/j.jia.2023.12.003

    Low temperature (LT) in spring has become one of the principal abiotic stresses that restrict the growth and development of wheat.  Diverse analyses were performed to investigate the mechanism underlying the response of wheat grain development to LT stress during booting.  These included morphological observation, measurements of starch synthase activity, and determination of amylose and amylopectin content of wheat grain after exposure to treatment with LT during booting.  Additionally, proteomic analysis was performed using tandem mass tags (TMT).  Results showed that the plumpness of wheat grains decreased after LT stress.  Moreover, the activities of sucrose synthase (SuS, EC 2.4.1.13) and ADP-glucose pyrophosphorylase (AGPase, EC 2.7.7.27) exhibited a significant reduction, leading to a significant reduction in the contents of amylose and amylopectin.  A total of 509 differentially expressed proteins (DEPs) were identified by proteomics analysis.  The Gene Ontology (GO) enrichment analysis showed that the protein difference multiple in the nutritional repository activity was the largest among the molecular functions, and the up-regulated seed storage protein (SSP) played an active role in the response of grains to LT stress and subsequent damage.  The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that LT stress reduced the expression of DEPs such as sucrose phosphate synthase (SPS), glucose-1-phosphate adenylyltransferase (glgC), and β-fructofuranosidase (FFase) in sucrose and starch metabolic pathways, thus affecting the synthesis of grain starch.  In addition, many heat shock proteins (HSPs) were found in the protein processing in endoplasmic reticulum pathways, which can resist some damage caused by LT stress.  These findings provide a new theoretical foundation for elucidating the underlying mechanism governing wheat yield development after exposure to LT stress in spring.

  • Yan Li, Xingkui An, Shuang Shan, Xiaoqian Pang, Xiaohe Liu, Yang Sun, Adel Khashaveh, Yong-jun Zhang
    Journal of Integrative Agriculture. 2024, 23(12): 0. https://doi.org/10.1016/j.jia.2024.03.043
    The mirid bug Apolygus lucorum (Hemiptera: Miridae) is a polyphagous pest that affects a wide range of host plants. Its control remains challenging mainly due to its rapid reproduction, necessitating an understanding of sex pheromone communication. The recognition of sex pheromones is vital for courtship and mating behaviors, and is mediated by various chemosensory-associated proteins. Among these, sensory neuron membrane protein (SNMP), a CD36-related protein, is suggested to play crucial roles in detecting sex pheromones. In this study, we employed transcriptomic and genomic data from A. lucorum and phylogenetic approaches, and identified four putative SNMP genes (AlucSNMP1a, AlucSNMP1b, AlucSNMP2a, and AlucSNMP2b) with full open reading frames. Expression analysis revealed the ubiquitous presence of AlucSNMP transcripts in multiple tissues, with only AlucSNMP1a exhibiting male-biased expression in the antennae, suggesting its potential role in male chemosensation. Functional analysis using the Xenopus oocyte expression system, coupled with two-electrode voltage clamp recording, demonstrated that the co-expression of AlucSNMP1a with specific pheromone receptors (PRs) and the co-receptor (Orco) significantly enhanced electrophysiological responses to sex pheromones compared to the co-expression of PRs and Orco alone. Moreover, the results indicated that the presence of AlucSNMP1a not only affected the responsiveness to sex pheromones but also influenced the kinetics (activation and inactivation) of the induced signals. In contrast, the co-expression of AlucSNMP1b with AlucPR/Orco complexes had no impact on the inward currents induced by two pheromone compounds. An examination of the selective pressures on SNMP1 genes across 20 species indicated strong purifying selection, implying potential functional conservation in various insects. These findings highlight the crucial role of AlucSNMP1a in the response to sex pheromones.
  • Agro-ecosystem & Environment
    Hubing Zhao, Guanfei Liu, Yingxia Dou, Huimin Yang, Tao Wang, Zhaohui Wang, Sukhdev Malhi, Adnan Anwar Khan
    Journal of Integrative Agriculture. 2024, 23(9): 3174-3185. https://doi.org/10.1016/j.jia.2024.01.008
    Amplifying drought stress and high precipitation variability impair dryland wheat production.  These problems can potentially be minimized by using plastic mulch (PM) or straw mulch (SM).  Therefore, wheat grain yield, soil water storage, soil temperature and water-use productivity of PM and SM treatments were compared with no mulch (CK) treatment on dryland wheat over a period of eight seasons.  Compared to the CK treatment, PM and SM treatments on average significantly increased grain yield by 12.6 and 10.5%, respectively.  Compared to the CK treatment, SM treatment significantly decreased soil daily temperature by 0.57, 0.60 and 0.48°C for the whole seasons, growing periods and summer fallow periods, respectively.  In contrast, compared to the CK treatment, PM treatment increased soil daily temperature by 0.44, 0.51 and 0.27°C for the whole seasons, growing periods and summer fallow periods, respectively.  Lower soil temperature under SM allowed greater soil water storage than under PM.  Soil water storage pre-seeding was 17% greater under the SM than under the PM treatment.  Soil water storage post-harvest was similar for the PM and SM treatments, but evapotranspiration was 4.5% higher in the SM than in the PM treatment.  Consequently, water-use productivity was 6.6% greater under PM than under the SM treatment.  Therefore, PM treatment increased dryland wheat yield and water-use productivity, while straw mulch increased soil water storage.


  • ZHENG Lan-jie, ZHANG Qian-long, LIU Hui-ying, WANG Xiao-qing, ZHANG Xiang-ge, HU Zhi-wei, LI Shi, JI Li, JI Man-chun, GU Yong, YANG Jia-heng, SHI Yong, HUANG Yu-bi, ZHENG Xu
    Journal of Integrative Agriculture. 2025, 24(4): 0. https://doi.org/10.1016/j.jia.2023.10.030

    Maize (Zea mays L.) is a monoecious grass species with separate male and female inflorescences which form the tassel and ear, respectively.  The mature ear inflorescences usually bear hundreds of grains, thus directly influence maize grain production and yield.  Here, we isolated a recessive maize mutant, tasselseed2016 (ts2016), which exhibits pleiotropic inflorescence defects and a reduction in grain yield.  These defects include loss of determinacy and identity in meristems and floral organs, as well as a lack of the lower floret abortion in maize ear, and the smaller grain size.  Using map-based cloning and allelic test, we identified and confirmed a microRNA gene MIR172e as the target gene controlling these related traits.  Furthermore, our evidence uncovered a new potential miR172e/ETHYLENE RESPONSIVE ELEMENT BINDING197 (EREB197) regulatory module which controls the abortion of lower floret in maize ear. Transcriptome analysis revealed that the mutation of MIR172e represses multiple biological processes, particularly the flower development and hormone-related pathways in maize ear.  Additionally, we found the mutation in the DNA sequence of MIR172e affects in RNA transcription, resulting in elongation blockage at the mutant site.  Our results reveal the function and molecular mechanism of MIR172e in maize inflorescences and grain yield, and this study deepens our knowledge of maize inflorescence development.

  • XU Ya-nan, WU Yue, HAN Yan, SONG Ji-qing, ZHANG Wen-ying, HAN Wei, LIU Bin-hui, BAI Wen-bo
    Journal of Integrative Agriculture. 2024, 23(1): 0. https://doi.org/10.1016/j.jia.2023.04.019

    Dry-hot wind stress causes losses in wheat productivity in major growing regions worldwide, especially for winter wheat in the Huang-Huai-Hai Plain of China, and both the occurrence and the severity of such events are likely to increase with global climate change.  To investigate the recovery of physiological function and yield formation using a non-commercial new chemical regulator (NCR) following dry-hot wind stress, we conducted a three-year field experiment (2018-2021), and sprayed tap water (control), monopotassium phosphate (CKP), NCR at both the jointing and flowering stage (CFS), and NCR only at the jointing stage (FSJ) or flowering stage (FSF).  The leaf physiology, biomass accumulation and translocation, grain-filling process, and yield components in winter wheat were investigated.  Among the single spraying treatments, the FSJ treatment was beneficial to accumulation of dry matter before anthesis, and to a larger increase of maximum grain-filling rate and mean grain-filling rate.  The FSF treatment performed better in maintaining a high relative chlorophyll content as SPAD value, and low rate of excised leaf water loss in flag leaves, promoting dry matter accumulation and contribution to grain after anthesis, prolonging the duration of grain filling, and inducing the period until maximum grain-filling rate to be reached earlier.  The CFS treatment was better than any other treatments in relieving effects of dry-hot wind.  The exogenous NCR treatments significantly increased grain yields by 12.45–18.20% in 2018–2019, 8.89–13.82% in 2019–2020, and 8.10–9.00% in 2020–2021.  The conventional measure of CKP treatment only increased grain yield by 6.69% in 2020–2021.  The CFS treatment had the greatest mitigating effect on loss of yield under dry-hot wind stress, following by the FSF and FSJ treatments, and the CKP treatment had a minimal effect.  In summary, the CFS treatment could be used as the main chemical control measure for wheat stress resistance and yield stability in areas with high incidence of dry-hot wind.  This can effectively regulate green retention and water status of leaves, promote dry matter accumulation and efficient translocation, improve grain-filling process, and ultimately reduce yield losses.

  • Crop Science
    Shan Sun, Wenjun Li, Yanfen Fang, Qianqian Huang, Zhibo Huang, Chengjing Wang, Jia Zhao, Yongqi He, Zhoufei Wang
    Journal of Integrative Agriculture. 2025, 24(1): 61-71. https://doi.org/10.1016/j.jia.2023.07.024

    Seed aging tolerance during storage is generally an important trait for crop production, yet the role of small auxin-up RNA genes in conferring seed aging tolerance is largely unknown in rice.  In this study, one small auxin-up RNA gene, OsSAUR33, was found to be involved in the regulation of seed aging tolerance in rice.  The expression of OsSAUR33 was significantly induced in aged seeds compared with unaged seeds during the seed germination phase.  Accordingly, the disruption of OsSAUR33 significantly reduced seed vigor compared to the wild type (WT) in response to natural storage or artificial aging treatments.  The rice OsSAUR33 gene promotes the vigor of aged seeds by enhancing their reactive oxygen species (ROS) level during seed germination, and the accumulation of ROS was significantly delayed in the aged seeds of Ossaur33 mutants in comparison with WT during seed germination.  Hydrogen peroxide (H2O2) treatments promoted the vigor of aged seeds in various rice varieties.  Our results provide timely theoretical and technical insights for the trait improvement of seed aging tolerance in rice.

  • Xingshuai Tian, Huitong Yu, Jiahui Cong, Yulong Yin, Kai He, Zihan Wang, Zhenling Cui
    Journal of Integrative Agriculture. 2025, 24(6): 0. https://doi.org/10.1016/j.jia.2024.08.023

    Cropland nitrate leaching is the major nitrogen (N) loss pathway, and it contributes significantly to water pollution. However, cropland nitrate leaching estimates show great uncertainty due to variations in input datasets and estimation methods. Here, we presented a re-evaluation of Chinese cropland nitrate leaching, and identified and quantified the sources of uncertainty by integrating three cropland area datasets, three N input datasets, and three estimation methods. The results revealed that nitrate leaching from Chinese cropland averaged 6.7±0.6 Tg N yr−1 in 2010, ranging from 2.9 to 15.8 Tg N yr−1 across 27 different estimates. The primary contributor to the uncertainty was the estimation method, accounting for 45.1%, followed by the interaction of N input dataset and estimation method at 24.4%. The results of this study emphasize the need for adopting a robust estimation method and improving the compatibility between the estimation method and N input dataset to effectively reduce uncertainty. This analysis provides valuable insights for accurately estimating cropland nitrate leaching and contributes to ongoing efforts that address water pollution concerns.

  • Horticulture
    Lin Chen, Chao Li, Jiahao Zhang, Zongrui Li, Qi Zeng, Qingguo Sun, Xiaowu Wang, Limin Zhao, Lugang Zhang, Baohua Li
    Journal of Integrative Agriculture. 2024, 23(7): 2255-2269. https://doi.org/10.1016/j.jia.2024.03.067

    Chinese cabbage is an important leafy vegetable crop with high water demand and susceptibility to drought stress.  To explore the molecular mechanisms underlying the response to drought, we performed a transcriptome analysis of drought-tolerant and -sensitive Chinese cabbage genotypes under drought stress, and uncovered core drought-responsive genes and key signaling pathways.  A co-expression network was constructed by a weighted gene co-expression network analysis (WGCNA) and candidate hub genes involved in drought tolerance were identified.  Furthermore, abscisic acid (ABA) biosynthesis and signaling pathways and their drought responses in Chinese cabbage leaves were systemically explored.  We also found that drought treatment increased the antioxidant enzyme activities and glucosinolate contents significantly.  These results substantially enhance our understanding of the molecular mechanisms underlying drought responses in Chinese cabbage.


  • Review
    LI Teng, ZHANG Xue-peng, LIU Qing, LIU Jin, CHEN Yuan-quan, SUI Peng
    Journal of Integrative Agriculture. 2022, 21(9): 2465-2476. https://doi.org/10.1016/j.jia.2022.07.013
    Maize (Zea mays L.) can exhibit yield penalties as a result of unfavorable changes to growing conditions.  The main threat to current and future global maize production is heat stress.  Maize may suffer from heat stress in all of the growth stages, either continuously or separately.  In order to manage the impact of climate driven heat stress on the different growth stages of maize, there is an urgent need to understand the similarities and differences in how heat stress affects maize growth and yield in the different growth stages.  For the purposes of this review, the maize growth cycle was divided into seven growth stages, namely the germination and seedling stage, early ear expansion stage, late vegetative growth stage before flowering, flowering stage, lag phase, effective grain-filling stage, and late grain-filling stage.  The main focus of this review is on the yield penalty and the potential physiological changes caused by heat stress in these seven different stages.  The commonalities and differences in heat stress related impacts on various physiological processes in the different growth stages are also compared and discussed.  Finally, a framework is proposed to describe the main influences on yield components in different stages, which can serve as a useful guide for identifying management interventions to mitigate heat stress related declines in maize yield.
  • Crop Science
    ZHAO Chun-hua, ZHANG Na, FAN Xiao-li, JI Jun, SHI Xiao-li, CUI Fa, LING Hong-qing, LI Jun-ming
    Journal of Integrative Agriculture. 2023, 22(9): 2603-2616. https://doi.org/10.1016/j.jia.2023.02.013
    The foundation parents play key roles in the genetic improvement of both yield potential and end-use quality in wheat.  Characterizing the genetic basis that underlies certain beneficial traits in the foundation parents will provide theoretical reference for molecular breeding by a design approach.  ‘Kenong 9204’ (KN9204) is a candidate foundation parent characterized by ideotype, high yield potential, and particularly high nitrogen fertilizer utilization.  To better understand the genetic basis of its high yield potential, high throughput whole-genome re-sequencing (10×) was performed on KN9204, its parental lines and its derivatives.  A high-resolution genetic composition map of KN9204 was constructed, which showed the parental origin of the favorable genomic segments based on the identification of excellent yield-related quantitative trait loci (QTL) from a bi-parental mapping population.  Xiaoyan 693 (XY693), a wheat–Thinopyrum ponticum partial amphidiploid, contributed a great deal to the high yield potential of KN9204, and three major stable QTLs from XY693 were fine mapped.  The transmissibility of key genomic segments from KN9204 to its derivatives were delineated, indicating that haplotype blocks containing beneficial gene combinations were conserved along with directional selection by breeders.  Evidence for selection sweeps in the breeding programs was identified.  This study provides a theoretical reference for the breeding of high-yield wheat varieties by a molecular design approach.
  • Review
    Shahid Ullah Khan, Ahmad Ali, Sumbul Saeed, Yonghai Fan, Ali Shehazd, Hameed Gul, Shah Fahad, Kun Lu
    Journal of Integrative Agriculture. 2024, 23(11): 3623-3640. https://doi.org/10.1016/j.jia.2024.02.013

    Rapeseed (Brassica napus L.) is the second most widely grown premium oilseed crop globally, mainly for its vegetable oil and protein meal.  One of the main goals of breeders is producing high-yield rapeseed cultivars with sustainable production to meet the requirements of the fast-growing population.  Besides the pod number, seeds per silique (SS), and thousand-seed weight (TSW), the ovule number (ON) is a decisive yield determining factor of individual plants and the final seed yield.  In recent years, tremendous efforts have been made to dissect the genetic and molecular basis of these complex traits, but relatively few genes or loci controlling these traits have been reported thus far.  This review highlights the updated information on the hormonal and molecular basis of ON and development in model plants (Arabidopsis thaliana).  It also presents what is known about the hormonal, molecular, and genetic mechanism of ovule development and number, and bridges our understanding between the model plant species (Athaliana) and cultivated species (Bnapus).  This report will open new pathways for primary and applied research in plant biology and benefit rapeseed breeding programs.  This synopsis will stimulate research interest to further understand ovule number determination, its role in yield improvement, and its possible utilization in breeding programs. 

  • Li Miao, Xiangyu Wang, Chao Yu, Chengyang Ye, Yanyan Yan, Huasen Wang
    Journal of Integrative Agriculture. 2024, 23(06): 0. https://doi.org/10.1016/j.jia.2024.03.058
    Plant height (PH) is one of the most important components of a plant ideotype, affecting plant biomass, yields, lodging resistance, and the ability to use mechanized harvesting. As many complex pathways controlling plant growth and development remain poorly understood, we are still unable to obtain the most ideal plants solely through breeding efforts. Plant height can be influenced by genotypes, plant hormone regulations, environmental conditions, and interaction with other plants. Here, we comprehensively review the factors influenced PH, including the regulation of PH-related development processes, the genetics and QTLs contributing to PH, and the hormone-regulated molecular mechanisms for PH. Additionally, the symbiotic influence of grafting on PH was discussed focusing on molecular regulation of gene expressions and genetics. Finally, we proposed strategies on how to apply recent findings to breeding for better PH, highlighted some knowledge gaps, and suggested potential directions for future studies.
  • Meixi Wang, Jitao Chang, Yuxin Han, Chaonan Wang, Songkang Qin, Jun Wang, Lulu Zhang, Yuanmao Zhu, Fei Xue, Fang Wang, Hongliang Chai, Yulong Wang, Xinjie Wang, Xin Yin
    Journal of Integrative Agriculture. 2024, 23(8): 0. https://doi.org/10.1016/j.jia.2024.03.074
    牛病毒性腹泻(BVD)是由牛病毒性腹泻病毒(BVDV)引起的一种在世界范围内广泛流行的传染病。牛感染BVDV后导致产奶量下降、产肉质量降低及繁殖能力下降,给全球畜牧业带来巨大负担。BVDV感染妊娠期母畜后,可通过胎盘传播至胎儿。若胎儿幸存则成为持续感染(PI)牛,其分泌物和排泄物中存在大量病毒,是BVDV的主要传染源之一。因此,快速准确的诊断对于BVD预防控制,尤其是持续感染牛的净化剔除至关重要。基于此,本研究开发了一种基于CRISPR/Cas12a的BVDV检测方法,用于BVDV的快速现场诊断。首先,通过序列比对和筛选,获得6个BVDV特异crRNA,且通过组合筛选获得可检测当前所有BVDV流行毒株的crRNA混合物;同时,优化设计了RT-ERA特异性扩增反应体系,而后将其与CRISPR-Cas12a系统相结合,建立了一种BVDV结果可视的检测方法。该方法具有高灵敏度和特异性,能在45分钟内检测低至20个拷贝的病毒量,且不与其它共感染的病原体发生交叉反应。此外,该检测方法可识别在中国流行的所有已知的BVDV-1和BVDV-2亚型毒株。在临床样品检测中发现,该检测方法与RNA试剂盒提取样本的荧光定量PCR(qPCR)结果一致,对释放剂释放RNA样本的检测敏感性更高。总之,本研究建立的基于Cas12a的快速、灵敏度高、特异强,不依赖实验室精密仪器,且可得到可视化检测结果的BVDV现地检测方法,该方法的应用对于BVDV精准防控具有重要实践意义。
  • Crop Science
    CAO Peng-hui, WANG Di, GAO Su, LIU Xi, QIAO Zhong-ying, XIE Yu-lin, DONG Ming-hui, DU Tan-xiao, ZHANG Xian, ZHANG Rui, JI Jian-hui
    Journal of Integrative Agriculture. 2023, 22(3): 669-678. https://doi.org/10.1016/j.jia.2022.08.005

    Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors.  In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice.  OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process.  OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein.  Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.  Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines.  Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay.  Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes.

  • Letter
    Kaikai Jin, Junjie Zhao, Huanxin Chen, Zimo Zhang, Zengguo Cao, Zanheng Huang, Hao Li, Yongsai Liu, Lisi Ai, Yufei Liu, Changqi Fan, Yuanyuan Li, Pei Huang, Hualei Wang, Haili Zhang
    Journal of Integrative Agriculture. 2025, 24(2): 790-794. https://doi.org/10.1016/j.jia.2024.11.018

    Nipah virus (NiV) is a member of the genus Henipavirus of the family Paramyxoviridae, and is an emerging zoonotic virus (Singh et al. 2019). NiV was first observed in 1998 and this outbreak triggered an uncontrollable epidemic lasting until 1999, during which more than a million pigs were destroyed (Ang et al. 2018). Since then, several South and Southeast Asian countries have experienced relatively small sporadic outbreaks almost every year, with mortality rates of up to 40-75 % in humans infected with NiV (Raj Kumar et al. 2019). Therefore, NiV not only does terrible damage to the farming industry but is also a serious threat to human public health and safety. Fruit bats are recognized as natural reservoir hosts for NiV, and other species of bats, as well as pigs, horses, dogs, and humans can also be infected (Soman Pillai et al. 2020). Bats act as asymptomatic carriers of the virus, but they excrete the virus through their saliva, urine, semen, and feces (Soman Pillai et al. 2020). NiV infection in humans and animals primarily occurs through the consumption of date palm juice and fruits that have been contaminated by fruit bats (Bruno et al. 2022). Human-to-human transmission is also possible (Garbuglia et al. 2023). NiV infection in humans and pigs can result in fatal encephalitis and severe respiratory disease (Ma et al. 2019, Ming-Yen et al. 2020). Because of its high pathogenicity and mortality, as well as the lack of effective treatments or vaccines for humans or animals (Gómez Román et al. 2022), NiV is included in the list of epidemiological threats requiring urgent R&D action in the World Health Organization (WHO) R&D Blueprint as one of the pathogens. WHO has therefore prepared a technical brief aimed at guiding countries in their preparedness planning for a NiV event, particularly in countries that have not yet reported a NiV event. The technical brief suggests that early diagnosis of NiV can enhance the survival chances of an infected individual and can also prevent transmission to others.

    Currently, the detection methods for NiV are mainly based on traditional serological methods and molecular diagnostic methods. Of the serological detection methods, ELISA, phage plaque assay, and immunofluorescence staining do not require special instruments or equipment, but the NiV-infected samples need to be processed in a Biosafety-Level-4 (BSL-4) laboratory, which is risky for operators and is not available in all regions (Diwakar D et al. 2015, Fischer et al. 2018, Gary et al. 2001). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) tests are the preferred method for viral detection due to their high sensitivity and ability to detect the virus in patients at the earliest stages of infection. However, Real-time RT-PCR requires sophisticated instruments and equipment, as well as specialized operator personnel, and cannot fully satisfy the need for early diagnosis of NiV infection in situ or in poor areas lacking these conditions (Wu et al. 2022). Therefore, the development of a rapid, specific, and sensitive assay that does not require complex instrumentation is critical for the early detection of NiV.

    Nucleic acid isothermal amplification technology, characterized by its rapidity, sensitivity, and specificity, is capable of meeting the demands for speed and simplicity detection, and has significant practical application value (Zhao et al. 2015). Of these methods, recombinase-aided amplification (RAA) technology, with its simplicity and ease of use, is ideal for early diagnosis in resource-limited settings (James et al. 2018). Recombinant enzyme-based isothermal amplification tests have been used to develop three rapid assays for NiV that can detect 1,000 copies μL-1 for synthetic NiV RNA in less than 30 min (Pollak et al. 2023). However, these assays require the transfer of the RPA amplification products, exposing the nucleic acid-rich samples to the environment, and leading to potential aerosol contamination. In the present study, a fully enclosed device was employed, combining reverse transcription recombinase-aided amplification technology with lateral flow immunochromatography (RT-RAA-VF), to establish a rapid and sensitive assay for the detection of NiV. This assay avoids false positives caused by aerosols, does not require sophisticated instruments and equipment, does not require specialized personnel to operate, and holds the potential to fulfill the requirements for early diagnosis during the initial stages of a NiV infection outbreak even in poor and remote areas.

    To detect all known NiV strains, 55 P gene sequences of different NiV strains, including NiV-B (transmitted in Bangladesh and India), NiV-M (transmitted in Malaysia), and NiV-T (transmitted in Thailand) were retrieved from GenBank (https: //www.ncbi.nlm.nih.gov/) and compared using MAFFT version 7. The highly conserved region of the P gene was selected as the target and was used to design the specific RAA primers and probe by the Prime Primer 5.0 software. The probe contained 55 nucleotides with the tetrahydrofuran (THF) residue replacing the adenine at position 37. The 5' end of the probe was labeled with the fluorescent marker FAM, while the 3' end was labeled with a blocking group comprising a C3 spacer. The 5' end of the reverse primer was labeled with biotin (Table 1). The primers and probe were synthesized by Sangon Biotech Co., Ltd. (Shanghai, China). The RNA transcript of NiV P (Genebank: NC_002728) and the positive plasmid pcDNA3.1-NiV-P were also synthesized by Sangon Biotech. In the presence of NiV RNA, the reverse transcriptase is activated to reverse transcribe the NiV RNA to cDNA, and the RAA amplification reaction is followed activated by two priming oligonucleotides to produce targets for probe annealing hybridization. The THF site of the probe can then be cleaved by the nfo enzyme to create a new 3'-hydroxyl group, which is used as a start site for polymerase extension, thus converting the probe into a primer that, together with a reverse primer with biotin, produces double-stranded amplification products labeled with two antigens (FAM and biotin). Subsequently, the reaction tube, which contains the amplified products, is positioned within a sealed and disposable nucleic acid visualization paper device. The amplified DNA products are capable of adhering to streptavidin-coated gold nanoparticles, thereby forming a conjugate that is subsequently immobilized by the anti-FAM antibody present on the test line (T line), which manifests as a red stripe. Meanwhile, any streptavidin-labeled gold nanoparticles that are not associated with the amplified DNA are trapped by the anti-streptavidin antibody at the control line (C line) (Fig. 1-A).

    To find the optimal RT-RAA reaction time, 10-fold gradient dilutions of the plasmid pcDNA3.1-NiV-P (5×1010 copies μL-1) were used as targets for RT-RAA-VF assay. The reaction was performed at three distinct temperatures—42 °C, 39 °C, and 37 °C—for a consistent period of 20 min. The outcomes indicated that at 42 °C, the emergence of discernible bands on both the C and T lines, indicating of a positive result, was observed at plasmid concentrations of 5 copies μL-1 or greater. At 39 °C and 37 °C, the positive results were only observed at plasmid concentrations of 500 copies μL-1 or more. These results suggested that 42 °C was the optimal reaction temperature for the NiV RT-RAA assay (Fig. 1-B). To determine the most efficient amplification time, the assay was executed for time intervals of 15, 20, 25, and 30 min. Analysis of the data provided in Appendix A confirmed that the optimal amplification duration for the assay was 20 min.

    Next, we assessed the sensitivity of the assay using 10-fold gradient dilutions of NiV P RNA transcripts, reacting at 42 °C for 20 min. The results showed that this assay could detect as few as 5 copies μL-1 of RNA transcripts (Fig. 1-C). We further compared the sensitivity of this assay with that of the real-time RT-PCR method currently recommended by the World Organisation for Animal Health (WOAH), using 10-fold serial dilutions of RNA extracted from NiV-infected Vero E6 cells as templates.  The results showed that the two methods shared an identical detection limit, and both were capable of detecting NiV RNA from infected cells diluted 10,000 times (Appendix B). To evaluate the specificity of this assay, the nucleic acids of pathogens that can cause neurological symptoms similar to NiV were also tested, including Hendra virus (HeV), herpes simplex virus type 1 (HSV-1), rabies virus (RABV) and Streptococcus suis. The results showed that our established assay only recognized the nucleic acids of NiV, with no cross-reactivity observed with other pathogens (Fig. 1-D).

    It has been reported that NiV can be transmitted by droplets, or by contact with throat or nasal secretions, from the respiratory tract of patients or sick pigs. To validate the clinical applicability of this assay, we mixed NiV RNA with RNA extracted from human saliva samples to simulate NiV-infected clinical samples. The simulated NiV clinical samples were evaluated using the RT-RAA-VF assay as well as real-time RT-PCR. Of all 47 samples tested, 25 samples were prepared by 3-, 4-, and 5-fold gradient dilutions of NiV RNA using healthy human RNA as the diluent, and 22 samples were healthy human RNA samples without NiV RNA. The RT-RAA-VF assay was able to distinguish between the 25 positive and 22 negative samples, and the real-time RT-PCR assay also detected 25 positive and 22 negative samples, with Ct values ranging from 25 to 40 for positive samples (Fig. 1-E to G). We also simulated the clinical NiV infected swine samples. Among all 28 samples, 15 samples were obtained by 3-, 4- and 5-fold gradient dilutions of NiV RNA with healthy swine RNA as the diluent, and 13 samples were healthy swine RNA samples without NiV RNA. The results demonstrated that the RT-RAA-VF assay was in accordance with the real-time RT-PCR and was capable of effectively differentiating between 15 positive samples and 13 negative samples (Fig 1-H to J). The assay is therefore expected to be an alternative assay for the clinical detection of NiV, being faster, more specific, and more sensitive than real-time RT-PCR and without the need for complex instrumentation.

    As human societies evolve, the combination of urbanization and climate change has resulted in the destruction of bat habitats, leading to increased contact between bats and humans. This has further elevated the risk of NiV infection for both humans and animals (Jonathan A et al. 2004, Kessler et al. 2018). NiV outbreaks have been reported in four countries - Bangladesh, India, Malaysia, and Singapore. However, fruit bats (the natural reservoir host of NiV) have been found in several Southeast Asian countries, suggesting the potential for NiV outbreaks in previously unaffected areas (Mangesh et al. 2022). Given the incubation period associated with NiV, the potential for cross-regional spread due to the movement of infected individuals cannot be dismissed. Consequently, it is imperative to focus on the rapid detection of NiV infections to enhance the survival prospects for those affected and to mitigate the risk of further transmission of the virus to others. In the present study, we developed an RT-RAA-VF assay for the detection of NiV using a sealed disposable nucleic acid visualization test paper device which effectively eliminates false positives caused by aerosol contamination. The assay demonstrated a sensitivity of 5 copies μL-1 for detecting NiV RNA at 42 °C for 20 minutes. The assay exhibits high specificity, with no cross-reactivity observed against other paramyxoviruses or neurological pathogens. Moreover, when evaluated on simulated clinical samples, it demonstrated 100% concordance with the results obtained from the real-time RT-PCR method. With its rapidity, specificity, and sensitivity features, this assay holds promise as an effective tool for early diagnosis of NiV infection.

     

  • Animal Science · Veterinary Medicine
    Chong Li, Yangguang Ren, Yudian Zhao, Zihao Zhang, Bin Zhai, Jing Li, Qi Li, Guoxi Li, Zhuanjian Li, Xiaojun Liu, Xiangtao Kang, Ruirui Jiang, Yadong Tian, Donghua Li
    Journal of Integrative Agriculture. 2025, 24(2): 680-696. https://doi.org/10.1016/j.jia.2023.06.038
    Tissue factor pathway inhibitor 2 (TFPI2) plays a key role in female reproduction.  However, its expression and function in chickens are still unclear.  In this study, RNA-seq was performed on ovarian tissues from chickens aged 30 and 15 weeks to identify the differentially expressed gene TFPI2.  The full-length cDNA of TFPI2 was obtained from adult chicken ovaries by rapid-amplification of cDNA ends (RACE), and the putative TFPI2 protein was found to share a highly conserved amino acid sequence with known bird homologs.  In addition, TFPI2 was widely expressed in the tissues of adult chicken follicles according to quantitative real-time PCR (qRT-PCR) and Western blotting.  Immunohistochemistry suggested that the TFPI2 protein existed in chicken ovary follicles at different developmental states, such as primordial follicles, the ovarian stroma, and the granulosa and theca layers of prehierarchical follicles (6–8 mm) and preovulatory follicles (F1).  In vitro, follicle stimulating hormone or luteinizing hormone (FSH/LH) stimulated the expression of TFPI2 in chicken granulosa cells.  FSH-/LH-induced TFPI2 mRNA expression was mediated by signaling pathways such as the PKA, PKC, PI3K, and mTOR pathways.  Functionally, TFPI2 promoted the proliferation and viability of cultured granulosa cells and decreased the secretion of Progesterone (P4) and Estrogen (E2) and the mRNA abundance of key steroidogenic enzymes (STAR, Cyp17a1, Cyp19a1 and 3B-HSD) as well as MMPs (MMP2, 7, 9 and 11).  Mechanistically, TFPI2 inhibited the expression of MMP7 via the Wnt signaling pathway.  These findings indicate that TFPI2 may play an important role in regulating chicken follicular development and ovulation and suggest the molecular regulation mechanisms.
  • Animal Science · Veterinary Medicine
    ZHAO Ruo-nan, CHEN Si-yuan, TONG Cui-hong, HAO Jie, LI Pei-si, XIE Long-fei, XIAO Dan-yu, ZENG Zhen-ling, XIONG Wen-guang
    Journal of Integrative Agriculture. 2023, 22(6): 1857-1869. https://doi.org/10.1016/j.jia.2022.11.006

    Antimicrobial resistance has become a global problem that poses great threats to human health.  Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome.  To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes (ARGs) and ARG bacterial hosts in the feces of broiler chickens.  Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol.  The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump (marA, soxS, sdiA, rob, evgS and phoP).  These three antimicrobials all led to an increase in Proteobacteria.  The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments.  These results indicated that pulsed antimicrobial administration with amoxicillin, chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs.  The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups.  The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.

  • Crop Science
    LU Yan-li, SONG Gui-pei, WANG Yu-hong, WANG Luo-bin, XU Meng-ze, ZHOU Li-ping, WANG Lei
    Journal of Integrative Agriculture. 2023, 22(9): 2660-2672. https://doi.org/10.1016/j.jia.2023.03.002

    The physiological and metabolic differences in maize under different nitrogen (N) levels are the basis of reasonable N management, which is vital in improving fertilizer utilization and reducing environmental pollution.  In this paper, on the premise of defining the N fertilizer efficiency and yield under different long-term N fertilization treatments, the corresponding differential metabolites and their metabolic pathways were analyzed by untargeted metabolomics in maize.  N stress, including deficiency and excess, affects the balance of carbon (C) metabolism and N metabolism by regulating C metabolites (sugar alcohols and tricarboxylic acid (TCA) cycle intermediates) and N metabolites (various amino acids and their derivatives).  L-alanine, L-phenylalanine, L-histidine, and L-glutamine decreased under N deficiency, and L-valine, proline, and L-histidine increased under N excess.  In addition to sugar alcohols and the above amino acids in C and N metabolism, differential secondary metabolites, flavonoids (e.g., kaempferol, luteolin, rutin, and diosmetin), and hormones (e.g., indoleacetic acid, trans-zeatin, and jasmonic acid) were initially considered as indicators for N stress diagnosis under this experimental conditions.  This study also indicated that the leaf metabolic levels of N2 (120 kg ha–1 N) and N3 (180 kg ha–1 N) were similar, consistent with the differences in their physiological indexes and yields over 12 years.  This study verified the feasibility of reducing N fertilization from 180 kg ha–1 (locally recommended) to 120 kg ha–1 at the metabolic level, which provided a mechanistic basis for reducing N fertilization without reducing yield, further improving the N utilization rate and protecting the ecological environment.

  • Review
    YANG Ning, YANG Dan-dan, YU Xu-chen, XU Cao
    Journal of Integrative Agriculture. 2023, 22(4): 959-971. https://doi.org/10.1016/j.jia.2023.03.007

    Natural rubber (NR) is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.  The Pará rubber tree (Hevea brasiliensis (Willd. ex A. Juss.) Müll. Arg.) is currently the exclusive commercial source of NR, and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.  However, current Pará rubber production barely meets the sharply increasing global industrial demand for rubber.  Petroleum-based synthetic rubber (SR) has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.  Thus, there is an urgent need to develop new productive rubber crops with broader environmental adaptability.  This review summarizes the current research progress on alternative rubber-producing plants, including horticultural plants (Taraxacum kok-saghyz Rodin and Lactuca L. species), woody plants (Parthenium argentatum A. Gray and Eucommia ulmoides Oliv.), and other plant species with potential for NR production.  With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach, we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope, which may accelerate the breeding and improvement of new rubber crops. 

  • WANG Xing-long, ZHU Yu-peng, YAN Ye, HOU Jia-min, WANG Hai-jiang, LUO Ning, WEI Dan, MENG Qing-feng, WANG Pu
    Journal of Integrative Agriculture. 2023, 22(8): 0. https://doi.org/10.1016/j.jia.2023.02.012

    Elevating soil water content (SWC) through irrigation was one of the simple mitigation measures to improve crop resilience to heat stress.  The response of leaf function such as photosynthetic capacity based on chlorophyll fluorescence during the mitigation has received limited attention, especially in field condition. The 2-yr field experiment with three treatments (control treatment (CK); high temperature treatment (H); high temperature together with elevating SWC treatment (HW)) was carried out during grain filling with two maize hybrids at a typical station in North China Plain.  Averagely, the net photosynthetic rate (Pn) was improved by 20% in HW treatment and a 1-3°C decrease in canopy temperature compared with H treatment in two years. Furthermore, the higher SWC in HW treatment significantly improved actual photosynthetic rate (Phi2), linear electron flow (LEF), variable fluorescence (Fv) and maximal potential quantum efficiency (Fv/Fm) for both hybrids.  Meanwhile, different responses in chlorophyll fluorescence between hybrids were also observed.  The higher SWC in HW treatment significantly improved thylakoid proton conductivity (gH+) and maximal fluorescence (Fm) for the hybrid ZD958.  For the hybrid XY335, the proton conductivity of chloroplast ATP synthase (vH+) and minimal fluorescence (F0) was increased by the SWC.  The SEM model further showed that SWC had significantly positive relationships with Pn, LEF, and Fv/Fm.  The elevating SWC alleviated heat stress with the delayed leaf senescence to prolong the effective period of photosynthesis and enhanced leaf photosynthetic capacity by improving Phi2, LEF, Fv and Fv/Fm.  This research demonstrates that elevating SWC through enhancing leaf photosynthesis during grain filling would be an import mitigation measure to adapt to warming climate in maize production.

  • GUO Cheng, ZHANG Xiao-jie, WANG Bao-bao, YANG Zhi-huan, LI Ji-ping, WANG Xiao-ming, XU Sheng-jun, WANG Chun-ming, GUO Zhi-jie, ZHOU Tian-wang, HONG Liu, DUAN Can-xing
    Journal of Integrative Agriculture. 2024, 23(03): 0. https://doi.org/10.1016/j.jia.2023.09.032

    Maize (Zea mays L.) is an economically vital grain crop that is cultivated worldwide. In 2011, a maize foliar disease was detected in Lingtai and Lintao counties in Gansu Province, China. The characteristic signs and symptoms of this disease include irregular chlorotic lesions on the tips and edges of infected leaves and black punctate fruiting bodies in dead leaf tissues. Given favourable environmental conditions, this disease spread to areas surrounding Gansu. In this study, infected leaves were collected from Gansu and Ningxia Hui Autonomous Region between 2018 and 2020 to identify the disease-causing pathogen. Based on morphological features; pathogenicity tests; and multi-locus phylogenetic analysis involving internal transcribed spacer (ITS), 18S small subunit rDNA (SSU), 28S large subunit rDNA (LSU), translation elongation factor 1-alpha (TEF), and β-tubulin (TUB) sequences, Eutiarosporella dactylidis was identified as the causative pathogen of this newly discovered leaf blight. Furthermore, an in vitro bioassay was conducted on representative strains using six fungicides, and both fludioxonil and carbendazim were found to significantly inhibit the mycelial growth of E. dactylidis. The results of this study provide a reference for the detection and management of Eutiarosporella leaf blight.

  • Crop Science
    YAN Sheng-nan, YU Zhao-yu, GAO Wei, WANG Xu-yang, CAO Jia-jia, LU Jie, MA Chuan-xi, CHANG Cheng, ZHANG Hai-ping
    Journal of Integrative Agriculture. 2023, 22(9): 2617-2631. https://doi.org/10.1016/j.jia.2023.04.017
    Pre-harvest sprouting (PHS) adversely affects wheat quality and yield, and grain color (GC) is associated with PHS resistance.  However, the genetic relationship between GC and PHS resistance remains unclear.  In this study, 168 wheat varieties (lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array.  Genome-wide association study (GWAS) based on a mixed linear model showed that 67 marker-trait associations (MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation.  In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation.  Subsequently, two cleaved amplified polymorphic sequences (CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B, were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4 controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively.  Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments (P<0.05).  Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4.  The new CAPS marker CAPS-356 was then developed based on the SNP (T/C) in the coding sequences (CDS) region of TraesCS5B02G545100.  The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines (RILs) constructed based on specific locus amplified fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4.  These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.
  • Ruixuan Xu, Zheng Pu, Shuangxin Han, Hongqian Yu, Chuan Guo, Qingsheng Huang, Yingjun Zhang
    Journal of Integrative Agriculture. 2025, 24(6): 0. https://doi.org/10.1016/j.jia.2024.11.017

    The "Greater Food" approach has replaced the older "taking grain production as a top priority" approach. The importance of feed and forage as the material basis for guaranteeing high-quality development of the livestock industry has gradually become prominent. However, owing to the tradition of "both human staple food and animal feed relying on grain production" in China and the decoupling of feed crop planting and livestock farming, the risk of feed grain security has increased, especially as it relates to the supply of high-quality protein feed ingredients from abroad, which is facing a bottleneck. To ensure food security, effective domestic agricultural production should be adopted. Nevertheless, guaranteeing the supply of high-quality protein feed through domestic soybean production is difficult because of limited arable land; furthermore, pressure on the staple food supply is still extreme. In this article, the historical and realistic implications for the security risks of feed grain in China are analyzed. Proposals are made to separate staple food grains for humans from the feed grain supply for animals and to develop high-quality forage to reduce feed grain use. High-quality forage can be supplied via intercropping with grain crops in arable land and reseeding perennial legumes or grasses into natural grasslands. However, “managing forage for grain” needs to be supported via technical paths and policies as the forage industry develops to effectively increase the capacity to ensure feed grain security.

  • Mansoor SHEIKH, Farooq IQRA, Hamadani AMBREEN, Kumar A PRAVIN, Manzoor IKRA, Yong Suk CHUNG
    Journal of Integrative Agriculture. 2024, 23(06): 0. https://doi.org/10.1016/j.jia.2023.10.019

    Crop improvement is crucial for addressing the global challenges of food security and sustainable agriculture.  Recent advancements in high-throughput phenotyping technologies and artificial intelligence (AI) have revolutionized the field, enabling rapid and accurate assessment of crop traits on a large scale.  The integration of AI and machine learning algorithms with high-throughput phenotyping data has unlocked new opportunities for crop improvement.  AI algorithms can analyze and interpret large datasets, extracting meaningful patterns and correlations between phenotypic traits and genetic factors.  These technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection, reducing the time and cost required for variety development.  However, further research and collaborations are needed to overcome the challenges and fully unlock the power of high-throughput phenotyping and AI in crop improvement.  By leveraging AI algorithms, researchers can efficiently analyze phenotypic data, uncover complex patterns, and establish predictive models that enable precise trait selection and crop breeding.  The aim of this review is to explore the transformative potential of integrating high-throughput phenotyping and AI in crop improvement.  The review will encompass an in-depth analysis of recent advancements and applications, highlighting the numerous benefits and challenges associated with high-throughput phenotyping and intelligence.

  • Agricultural Economics and Management
    LI Shu-tian, DUAN Yu, GUO Tian-wen, ZHANG Ping-liang, HE Ping, Kaushik Majumdar
    Journal of Integrative Agriculture. 2018, 17(12): 2802-2812. https://doi.org/10.1016/S2095-3119(18)62074-X
    Field experiments were conducted in oil and edible sunflower to study the effects of potassium (K) fertilization on achene yield and quality, and to estimate the nutrient internal efficiency (IE) and nutrient requirement in sunflower production.  All trials in edible sunflower and 75% trials in oil sunflower showed positive yield responses to K fertilization.  Compared with control without K fertilization, the application of K increased achene yield by an average of 406 kg ha–1 for oil sunflower and 294 kg ha–1 for edible sunflower.  K application also increased 1 000-achene weight and kernel rate of both oil and edible sunflower.  K fertilization improved the contents of oil, oleic acid, linoleic acid and linolenic acid in achenes of oil sunflower, and increased contents of oil, total unsaturated fatty acid and protein in achenes of edible sunflower.  The average agronomic efficiency of K fertilizer was 4.0 for oil sunflower and 3.0 kg achene kg–1 K2O for edible sunflower.  The average IE of N, P and K under balanced NPK fertilization was 22.9, 82.8, and 9.9 kg kg–1 for oil sunflower, and 27.3, 138.9, and 14.3 kg kg–1 for edible sunflower.  These values were equivalent to 45.5, 14.1, and 108.1 kg, and 39.0, 8.0, and 71.7 kg of N, P and K, respectively, in above-ground dry matter required for production per ton of achenes.  The average harvest index of N, P and K was 0.47, 0.56 and 0.05 kg kg–1 in oil sunflower, and 0.58, 0.58 and 0.14 kg kg–1 in edible sunflower.   
  • Letter
    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
    Journal of Integrative Agriculture. 2023, 22(11): 3560-3563. https://doi.org/10.1016/j.jia.2023.09.021

    非洲猪瘟在我国爆发,给我国养殖业带来巨大的经济损失,目前无可用的商业化疫苗和药物,其相关研究限定于在高等级生物安全实验室中完成,生物安全防护中消毒剂的合理使用尤为重要。MICRO-CHEM PLUSMCP)作为一种复合型季铵盐类消毒剂在高等级生物安全实验室广泛使用,而针对非洲猪瘟病毒(African swine fever VirusASFV)的灭活效果未见相关报道。本文我们探究不同病毒载量、不同消毒剂浓度、不同作用时间及不同作用温度对于灭活非洲猪瘟病毒效果的影响。研究结果表明高病毒载量需要更高浓度的MCP才能将ASFV完全灭活,较低浓度的MCP需要延长作用时间才能达到完全灭活ASFV的效果,不同的作用温度对于MCP灭活ASFV的效果无影响。应用干雾消毒机将5%MCP进行房间喷雾消毒,当浓度达到0.06L/m3,用ASFV、大肠杆菌和金色葡萄球菌作为生物指示剂,可以达到终末消毒效果,但对于枯草芽孢杆菌作为生物指示剂还有部分活菌残留;当浓度为0.03L/m3时,对于大肠杆菌或金黄色葡萄球菌作为生物指示剂,也可以达到了终末消毒效果。该研究为在特定环境中合理使用 MCP 提供了科学依据,可以用于操作ASFV的高等级生物安全实验室的消毒以及猪场非洲猪瘟感染的预防。

  • Jinlin Bao, Jing Huang, Xiaoqing Yang, Xizhi Li, Shengjie Cheng, Wei Huang, Jun Wang, Jian Jin
    Journal of Integrative Agriculture. 2024, 23(9): 0. https://doi.org/10.1016/j.jia.2024.05.006
    PROSTRATE GROWTH1 (PROG1)是一个与水稻驯化相关的重要转录因子,在水稻株型和穗型的调控中发挥着重要作用。PROG1过度积累会使植株结构松散,无效分蘖增加,穗减小,穗粒数降低,最终导致产量下降。相反,PROG1积累不足导致昼夜节律核心调节因子OsGI下调进而从多方面影响水稻生理和发育。因此,维持水稻PROG1的稳态至关重要。在本研究中我们揭示PROG1的负反馈调节机制,PROG1与其自身的启动子直接结合,并负调节其自身的表达,进而达到维持自身稳态的目的此外,我们的研究结果表明,PROG1的反馈调节机制独立于其互作蛋白LA1运作。这些发现为了解水稻驯化相关转录因子PROG1的调控机制提供了有价值的见解。
  • Animal Science · Veterinary Medicine
    ZHOU Rong, YANG Yalan, LIU Ying, CHEN Jie, YANG Bing, TANG Zhong-lin
    Journal of Integrative Agriculture. 2023, 22(11): 3489-3499. https://doi.org/10.1016/j.jia.2023.05.014
    Increasing prolificacy is an important aim in the pig industry.  Regions associated with litter size have been revealed, but detailed molecular mechanisms are unclear.  The Meishan pig is one of the most prolific breeds, with higher prolificacy than the Yorkshire pig, which exhibits high feeding efficiency and lean meat yield.  The ovary is the key organ determining reproductive traits during pregnancy by synthesizing and secreting reproductive hormones essential for conceptus maintenance.  In this comparative multi-omics study of the ovary transcriptome, proteome, and metabolome on day 49 of pregnancy, we aimed to identify genomic, proteomic, and metabolomic differences between the ovaries of Meishan and Yorkshire pigs to reveal potential molecular mechanisms conferring high prolificacy.  Meishan pigs demonstrated general downregulation of steroid biosynthesis and butanoate metabolism in the ovary during mid-pregnancy at both transcriptome and proteome levels but exhibited higher serum cholesterol, estradiol, and progesterone levels than Yorkshire pigs.  We also identified several single-nucleotide polymorphisms in the genes of the steroid hormone pathway associated with litter number, average birth weight, and total litter weight.  Lower biosynthesis rates but elevated serum levels of reproductive hormones during mid- and late pregnancy are essential for the greater prolificacy of Meishan pigs.
  • Deng Jin-sheng, Huang Wei-qi, Zhou Guo-xiong, Hu Ya-hui, Li Liu-jun, Wang Yan-feng
    Journal of Integrative Agriculture. 2024, 23(10): 0. https://doi.org/10.1016/j.jia.2023.11.037

    Banana is a significant crop, and three banana leaf diseases, including Sigatoka, Cordana and Pestalotiopsis, have the potential to have a serious impact on banana production. Existing studies are insufficient to provide a reliable method for accurately identifying banana leaf diseases. Therefore, this paper proposes a novel method to identify banana leaf diseases. First, a new algorithm called K-scale VisuShrink algorithm (KVA) is proposed to denoise banana leaf images. The proposed algorithm introduces a new decomposition scale k based on the semi-soft and middle course thresholds, the ideal threshold solution is obtained and substituted with the newly established threshold function to obtain a less noisy banana leaf image. Then, this paper proposes a novel network for image identification called Ghost ResNeSt-Attention RReLU-Swish Net (GR-ARNet) based on Resnet50. In this, the Ghost Module is implemented to improve the network's effectiveness in extracting deep feature information on banana leaf diseases and the identification speed; the ResNeSt Module adjusts the weight of each channel, increasing the ability of banana disease feature extraction and effectively reducing the error rate of similar disease identification; the model's computational speed is increased using the hybrid activation function of RReLU and Swish. Our model achieves an average accuracy of 96.98% and a precision of 89.31% applied to 13021 images, demonstrating that the proposed method can effectively identify banana leaf diseases.

  • Animal Science · Veterinary Medicine
    Ambreen LEGHARI, Shakeel Ahmed LAKHO, Faiz Muhammad KHAND, Khaliq ur Rehman BHUTTO, Sameen Qayoom LONE, Muhammad Tahir ALEEM, Iqra BANO, Muhammad Ali CHANDIO, Jan Muhammad SHAH, LIN Hui-xing, FAN Hong-jie
    Journal of Integrative Agriculture. 2023, 22(5): 1514-1528. https://doi.org/10.1016/j.jia.2022.10.004

    Streptococcus agalactiae is one of the most common pathogens that cause bovine mastitis worldwide. Identifying pathogen prevalence and virulence factors is critical for developing prevention and control approaches. Herein, 1161 milk samples from various dairy farms in China (n=558) and Pakistan (n=603) were collected between 2019-2021 and were subjected to S. agalactiae isolation. Prevalence, serotyping, virulence genes, and antibiotic-resistant genes of S. agalactiae were evaluated by PCR assay. All isolates were characterized for haemolysis, biofilm production, cytotoxicity, adhesion, and invasion on bovine mammary epithelial cells. The prevalence of S. agalactiae-induced mastitis in cattle was found to be considerably higher in Pakistan than in China. Jiangsu and Sindh provinces had the highest area-wise prevalence in China and Pakistan, respectively. Serotypes Ia and II were prevalent in both countries, whereas serotype III was found only in Pakistan. Moreover, all isolates tested positive for PI-2b gene but negative for PI-1 and PI-2a genes. All isolates harboured cfb, cylE, hylB, and fbsB virulent genes, whereas many of them lacked bibA, rib and bca. However, the absence of bac and scp genes in Chinese isolates and cspA in Pakistani isolates was noted, while spb1 and lmb were not detected in isolates of both countries. Pakistani isolates, particularly serotype Ia-positive, had a considerably higher ability to produce biofilm, haemolysis, cytotoxicity, adhesion, and invasion than Chinese isolates. Most of the isolates were phenotypically resistant to tetracycline, erythromycin, and clindamycin and genotypic resistance was confirmed by the presence of ermA, ermB, tetM and tetO genes. Our study highlights the antimicrobial resistance profile and virulence-related factors contributing to the epidemiological spread of mastitis-causing S. agalactiae in China and Pakistan. The findings may facilitate future studies designed to develop improved treatment and control strategies against this pathogen. 

  • Crop Science
    WANG Xiao-dong, CAI Ying, PANG Cheng-ke, ZHAO Xiao-zhen, SHI Rui, LIU Hong-fang, CHEN Feng, ZHANG Wei, FU San-xiong, HU Mao-long, HUA Wei, ZHENG Ming, ZHANG Jie-fu
    Journal of Integrative Agriculture. 2023, 22(10): 2981-2992. https://doi.org/10.1016/j.jia.2023.02.017

    Plant height is a key plant architectural trait that affects the seed yield, harvest index and lodging resistance in Brassica napus L., although the genetic mechanisms affecting plant height remain unclear.  Here, a semi-dwarf mutant, df34, was obtained by ethyl methanesulphonate-induced mutagenesis.  Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene, which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing, and this gene was named BnaSD.C3.  Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the “Darmor-bzh” genome, but there was no potential candidate gene for the semi-dwarf trait underlying this interval.  Furthermore, the interval was aligned to the Zhongshuang 11 reference genome.  Finally, combining structural variation analysis, transcriptome sequencing, phytohormone analyses and gene annotation information, BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34.  This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in Bnapus

  • Plant Protection
    REN Cong, ZHANG Jie, YUAN Jin-xi, WU Yun-qi-qi-ge, YAN Shan-chun, LIU Wei, WANG Gui-rong
    Journal of Integrative Agriculture. 2023, 22(9): 2772-2782. https://doi.org/10.1016/j.jia.2023.04.025

    The oriental fruit fly, Bactrocera dorsalis (Hendel), is a devastating pest of citrus fruits.  After successful mating, adult females insert their eggs into the ripened fruit, resulting in moldy and rotten fruit and causing great economic losses for the citrus industry.  In the field, flies initiate copulatory behaviors as twilight approaches, and decreasing light intensity in this period is the normal stimulus for copulation.  In this study, ten light intensities ranging from 0–30 000 lux were set to identify the typical intensity that strongly regulates the copulation behavior of Bdorsalis.  Three light intensities found to regulate the copulation behavior were then selected to verify their effects on adult male wing fanning and female chemotaxis towards 2,3,5-trimethylpyrazine (TMP).  At last, strong light and complete darkness were artificially combined in the lab to verify whether they could prevent copulation to inform behavioral manipulation of oriental flies in the future.  The results indicated that adult flies generally initiated copulatory behaviors at low light intensity (<1 000 lux).  
    Stronger light significantly prevented copulation in proportion to intensity, with nearly no copulation events initiated when light intensity was above 20 000 lux.  Both male wing fanning and female chemotaxis towards TMP were attenuated as light intensity became stronger.  However, at 10 000 lux, males still fanned their wings to a certain extent while TMP completely lost its attractiveness to females.  In the darkness, adults did not initiate any sexual behaviors, e.g., copulation, wing fanning, or chemotaxis to TMP.  One hour of strong light (10 000 lux) combined with continuous darkness completely prevented mating.  These results show that light condition is an essential factor for copulatory behaviors in the oriental fruit fly.  Researchers could thus manipulate light conditions artificially or disrupt the molecular target in flies’ light transduction pathway to develop environmentally-friendly techniques to control this pest.

  • Crop Science
    Lihua Liu, Pingping Qu, Yue Zhou, Hongbo Li, Yangna Liu, Mingming Zhang, Liping Zhang, Changping Zhao, Shengquan Zhang, Binshuang Pang
    Journal of Integrative Agriculture. 2024, 23(11): 3641-3656. https://doi.org/10.1016/j.jia.2023.07.028
    Identifying stable quantitative trait loci (QTLs) for yield-related traits across populations and environments is crucial for wheat breeding and genetic studies.  Consensus maps also play important roles in wheat genetic and genomic research.  In the present study, a wheat consensus map was constructed using a doubled haploid (DH) population derived from Jinghua 1×Xiaobaidongmai (JX), an F2 population derived from L43×Shanxibaimai (LS) and the BAAFS Wheat 90K SNP array single nucleotide polymorphism (SNP) array.  A total of 44,503 SNP markers were mapped on the constructed consensus map, and they covered 5,437.92 cM across 21 chromosomes.  The consensus map showed high collinearity with the individual maps and the wheat reference genome IWGSC RefSeq v2.1.  Phenotypic data on eight yield-related traits were collected in the JX population, as well as the F2:3 and F2:4 populations of LS, in six, two and two environments, respectively, and those data were used for QTL analysis.  Inclusive composite interval mapping (ICIM) identified 32 environmentally stable QTLs for the eight yield-related traits.  Among them, four QTLs (QPH.baafs-4B, QKNS.baafs-4B, QTGW.baafs-4B, and QSL.baafs-5A.3) were detected across mapping populations and environments, and nine stable QTLs (qKL.baafs-1D, QPH.baafs-2B, QKNS.baafs-3D, QSL.baafs-3D, QKW.baafs-4B, QPH.baafs-5D, QPH.baafs-6A.1, QSL.baafs-6A, and QSL.baafs-6D) are likely to be new.  The physical region of 17.25–44.91 Mb on chromosome 4B was associated with six yield-related traits, so it is an important region for wheat yield.  The physical region around the dwarfing gene Rht24 contained QTLs for kernel length (KL), kernel width (KW), spike length (SL), and thousand-grain weight (TGW), which are either from a pleiotropic effect of Rht24 or closely linked loci.  For the stable QTLs, 254 promising candidate genes were identified.  Among them, TraesCS5A03G1264300, TraesCS1B03G0624000 and TraesCS6A03G0697000 are particularly noteworthy since their homologous genes have similar functions for the corresponding traits.  The constructed consensus map and the identified QTLs along with their candidate genes will facilitate the genetic dissection of wheat yield-related traits and accelerate the development of wheat cultivars with desirable plant morphology and high yield.


  • Plant Protection
    ZHANG Hao-yang, YANG Yan-fang, GUO Feng, SHEN Xiao-rui, LU Shan, CHEN Bao-sha
    Journal of Integrative Agriculture. 2023, 22(7): 2126-2137. https://doi.org/10.1016/j.jia.2022.10.006
    Sugarcane smut caused by Sporisorium scitamineum is a destructive disease responsible for significant losses in sugarcane production worldwide. However, the mechanisms underlying the pathogenicity of this fungus remain largely unknown. In this study, we found that the disruption of the SsRSS1 gene, which encodes a salicylic acid (SA) sensing regulator, does not affect phenotypic traits such as the morphology, growth rate, and sexual mating ability of haploid basidiospores, but rather reduces the tolerance of basidiospores to SA stress by blocking the induction of SsSRG1, a gene encoding a SA response protein in S. scitamineum. SsRSS1 deletion resulted in the attenuation of the virulence of the fungus. In addition to a significant reduction in whip formation, a portion of plantlets (18.3%) inoculated with the ΔSsRSS1 strains were found to be infected but failed to produce whips for up to 90 days post-inoculation. However, the development of hyphae and teliospore from the ΔSsRSS1-infected plants that formed whips seemed indistinguishable from that in the wild-type-infected plants. Combined, our findings suggested that SsRss1 is required for maintaining fungal fitness in planta by counteracting SA stress.
  • Crop Science
    TAO Jian-bin, ZHANG Xin-yue, WU Qi-fan, WANG Yun
    Journal of Integrative Agriculture. 2023, 22(6): 1645-1657. https://doi.org/10.1016/j.jia.2022.10.008
    Large-scale crop mapping using remote sensing data is of great significance for agricultural production, food security and the sustainable development of human societies. Winter rapeseed is an important oil crop in China that is mainly distributed in the Yangtze River Valley. Traditional winter rapeseed mapping practices are insufficient since they only use the spectral characteristics during the critical phenological period of winter rapeseed, which are usually limited to a small region and cannot meet the needs of large-scale applications. In this study, a novel phenology-based winter rapeseed index (PWRI) was proposed to map winter rapeseed in the Yangtze River Valley. PWRI expands the date window for distinguishing winter rapeseed and winter wheat, and it has good separability throughout the flowering period of winter rapeseed. PWRI also improves the separability of winter rapeseed and winter wheat, which traditionally have been two easily confused winter crops. A PWRI-based method was applied to the Middle Reaches of the Yangtze River Valley to map winter rapeseed on the Google Earth Engine platform. Time series composited Sentinel-2 data were used to map winter rapeseed with 10 m resolution. The mapping achieved a good result with overall accuracy and kappa coefficients exceeding 92% and 0.85, respectively. The PWRI-based method provides a new solution for high spatial resolution winter rapeseed mapping at a large scale.
  • Yunrui Chen, Dayong Fan, Ziliang Li, Yujie Zhang, Yang He, Minzhi Chen, Wangfeng Zhang, Yali Zhang
    Journal of Integrative Agriculture. https://doi.org/10.1016/j.jia.2024.11.012
    Accepted: 2024-11-12

    Hydraulic theory predicts a positive coupling between leaf hydraulic conductance (Kleaf) and stomatal conductance (gs); however, this theory has not been fully supported by observations, and the underlying mechanisms remain unclear.  Currently, subdividing Kleaf into leaf hydraulic conductance inside xylem (Kx) and outside xylem (Kox) offers a new perspective for elucidating the regulatory mechanism of Kleaf on gs.  Optimal planting density can enhance water use efficiency (WUE) by optimizing gs; however, the changes in leaf hydraulic properties during this process and its regulation of gs and WUE remain unclear.  We examined the relationships between Kx and Kox with gs, photosynthetic rate (AN), and WUE, and investigated the structural basis determining Kox in cotton under eight planting densities of 12, 18, 24, 36, 48, 60, 72, and 84 plant m-⊃2;.  The results showed that as the increase of planting density, Kleaf and AN remained consistent while Kox and gs decreased significantly.  Kox was significantly influenced by leaf thickness and the volume fraction of inter-cellular air space.  Kleaf and Kx showed no correlation with AN or gs, but Kox exhibited a significant positive correlation with gs.  Furthermore, Kox is significantly negatively correlated with WUE.  These findings suggest that Kox modulates gs to reduce water loss while maintaining AN, thereby enhancing WUE in cotton under various planting densities.

  • WANG Kang-xu , ZHANG Ke-rou , CAO Cou-gui, JIANG Yang
    Journal of Integrative Agriculture. 2023, 22(8): 0. https://doi.org/10.1016/j.jia.2023.01.001
    Transgene escape could lead to genetically modified rice establishing wild populations in the natural environment, where they would compete for survival space with weeds. However, whether the expression of Bacillus thuringiensis (Bt) gene in rice will alter the relationship between transgene plants and weeds and induce undesirable environmental consequences are poorly understood. Thus, field experiments were conducted to investigate the weed competitiveness and assess the ecological risk of transgenic Bt rice under herbicide-free and lepidopterous pest controlled environment. Results showed that weed-rice competition in direct seeding field (DS) was earlier and more serious than that in transplanting field (TP), which resulted in the significant decrease of biomass and yield in DS. However, the yield between conventional Bt and non-Bt rice was not significant difference. The weed number, weed coverage ratio and weed diversity of conventional Bt rice were significantly higher than those of non-Bt rice at the early growth stage and mature stage, especially in DS plots, suggesting that Bt traits did not increase the weed competitiveness of transgenic rice and had no negative effect on weed diversity. Grain yield and weed number varied between different hybrid rice lines, but those differences were not significant between Bt and non-Bt rice. The number of insects increased with the increase of weeds in hybrid rice plots, whereas the insect number and diversity did not display a significant difference between Bt and non-Bt rice. Therefore, the ecological risk of transgenic Bt rice is comparable to non-Bt rice.
  • YANG Hong-jun, YE Wen-wu, YU Ze, SHEN Wei-liang, LI Su-zhen, WANG Xing, CHEN Jia-jia, WANG Yuan-chao, ZHENG Xiao-bo
    Journal of Integrative Agriculture. 2023, 22(8): 0. https://doi.org/10.1016/j.jia.2023.01.006
    Plant-associated microbes represent a key determinant of plant fitness through acquiring nutrients, promoting growth, and resisting to abiotic and biotic stresses. However, an extensive characterization of the bacterial and fungal microbiomes present in different plant compartments of soybean in field conditions has remained elusive. In this study,we investigated the effects of four niches (roots, stems, leaves, and pods), four genotypes (Andou203, Hedou12, Sanning16, and Zhonghuang13), and three field locations (Jining, Suzhou, and Xuzhou) on the diversity and composition of bacterial and fungal communities in soybean using 16S and internal transcribed spacer rRNA amplicon sequencing,respectively. The soybean microbiome significantly differed across organs.Host genotypes explained more variation in stem bacterial community composition and leaf fungal community composition.Field location significantly affected the composition of bacterial communities in all compartments and the effects were stronger in the root and stem than in the leaf and pod, whereas field location explained more variation in stem and leaf fungal community composition than in the root and pod. The relative abundances of potential soybean fungal pathogens also differed among host organs and genotypes, reflecting the niches of these microbes in the host and probably their compatibility to the host genotypes. Systematic profiling of the microbiome composition and diversity will aid the development of plant protection technologies to benefit soybean health.
  • Xingqi Liu, Zengguo Cao, Boyi Li, Pei Huang, Yujie Bai, Jingbo Huang, Zanheng Huang, Yuanyuan Zhang, Yuanyuan Li, Haili Zhang, Hualei Wang
    Journal of Integrative Agriculture. 2024, 23(06): 0. https://doi.org/10.1016/j.jia.2024.03.050
    为建立针对克里米亚-刚果出血热病毒(Crimean-Congo hemorrhagic fever virus, CCHFV)的简单、快速、适用于现地使用的核酸检测方法,本研究首先比对了20株来自不同国家不同时间分离的CCHFV毒株基因序列,筛选出保守的S基因作为检测靶标,并以中国分离株(YL16070)的S基因保守序列为模板,设计、合成和筛选出反转录重组聚合酶介导恒温扩增(RT-RAA)特异性引物和探针。为实现检测结果的可视化,将四氢呋喃(THF)取代探针3' 端附近的胸腺嘧啶,在探针3' 端引入了阻断基团三碳间隔(C3 spacer),同时对探针和下游引物的5' 端分别使用FAM和生物素标记,最后结合胶体金免疫层析试纸,建立了一种针对CCHFV S基因的可视化快速检测方法CCHFV RT-RAA-VF。为了提高方法的敏感性,对反应温度、反应时间和引物浓度进行了优化,结果显示该方法以浓度为10μM的引物在42 ℃恒温条件下扩增30 min敏感性最高,最低可检出20 copies μL-1的阳性质粒和2 copies μL-1CCHFV RNA转录本。克里米亚-刚果出血热症状与许多出血热病毒感染症状类似,因此将CCHFV与其他可引起出血热的病毒区分开来非常重要。为了评估所建立方法的特异性,分别检测了登革热病毒(DENV)、日本脑炎病毒JEV)、埃博拉病毒(EBOV)、亨德拉病毒(HeV)、尼帕病毒(NIV)及CCHFV的核酸结果表明,该方法仅能识别 CCHFV的核酸,与其他病原无交叉反应。最后为评估该方法的准确性和临床适用性,本研究将所建立的方法与已有的RT-qPCR方法对模拟样品进行平行检测,结果显示两者检测符合率为100%。综上表明,本研究建立的CCHFV RT-RAA-VF快速检测方法敏感性高、特异性好、准确性高,且操作简单、无需特殊仪器,可应用于野外或基层单位CCHFV快速筛查检测工作,在一定程度上响应了世界卫生组织在2018年提出的CCHF研究路线图草案。