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2024 Vol. 23 No. 3 Previous Issue    Next Issue

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


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We initially identified differentially expressed genes (DEGs) by comparing the transcriptomes of folic acid (FA)-treated and water-treated (CK) berries at different time points, and then analyzed the sequences to detect alternatively spliced (AS) genes associated with postharvest softening. During the postharvest storage of FA-treated berries, the VvPE2 gene, which encodes a cell wall-degrading enzyme, undergoes alternative splicing giving rise to two transcripts: the full-length isoform VvPE2.1 and the alternatively spliced form VvPE2.2. VvPE2.1 possesses the complete structure of the PECTINESTERASE gene, and the encoded protein maintains full enzyme functionality, whereas VvPE2.2 encodes an incomplete protein. The up-regulation of VvPE2.2 in FA-treated berries is expected to reduce the accumulation of VvPE2.1, subsequently leading to reduced enzymatic degradation of pectin by PE, thus delaying berry softening. This study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries. The cover photo was provided by Dr. Maosong Pei, College of Horticulture and Plant Protection, Henan University of Science and Technology. See pages 863–875 for details.




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Review

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Molecular mechanisms of stress resistance in sorghum: Implications for crop improvement strategies Hongxiang Zheng, Yingying Dang, Xianmin Diao, Na Sui 2024, 23(3): 741-768.  DOI: 10.1016/j.jia.2023.12.023 Abstract ( )   PDF in ScienceDirect   Abiotic stresses, such as drought, salt, extreme temperatures, and heavy metal pollution, are the main environmental factors that limit crop growth and yield.  Sorghum, a C4 grass plant with high photosynthetic efficiency, can grow in adverse environmental conditions due to its excellent stress resistance characteristics.  Therefore, unraveling the stress-resistance mechanism of sorghum could provide a theoretical basis for developing and cultivating various stress-resistant crops.  This understanding could also help to create a conducive environment for using marginal soil in agriculture and ensuring food security.  In this review, we discuss the adaptation mechanisms of sorghum under drought, salinity, temperature, and soil heavy metal stresses, the specific response to stress, the screening of sorghum-resistant germplasm, and the identification and functional analysis of the relevant genes and quantitative trait loci (QTL).  In addition, we discuss the application potential of different stress-tolerant sorghum germplasms reported to date and emphasize the feasibility and potential use in developing and promoting highly stress-tolerant sorghum in marginal soil.

Crop Science

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Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding Shuliang Jiao, Qinyan Li, Fan Zhang, Yonghong Tao, Yingzhen Yu, Fan Yao, Qingmao Li, Fengyi Hu, Liyu Huang 2024, 23(3): 769-780.  DOI: 10.1016/j.jia.2023.05.010 Abstract ( )   PDF in ScienceDirect   Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution.  The Green Revolution gene Semidwarf 1 (SD1), which modulates gibberellic acid (GA) biosynthesis, plays a principal role in determining rice plant height.  Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production.  The plant height mediated by SD1 also favors grain yield under certain conditions.  However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production.  In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions.  In response to dryland environments, rice requires a reduction in plant height to cope with water deficits.  Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation.  Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem.  Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields.  In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height.  During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height.  Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production.  All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.

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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize Pengcheng , Shuangyi Yin, Yunyun Wang, Tianze Zhu, Xinjie Zhu, Minggang Ji, Wenye Rui, Houmiao Wang Chenwu Xu, Zefeng Yang 2024, 23(3): 781-794.  DOI: 10.1016/j.jia.2023.11.003 Abstract ( )   PDF in ScienceDirect   Nitrogen (N), phosphorus (P), and potassium (K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality.  The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown.  In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination.  We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations.  Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients.  Unconditional quantitative trait locus (QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively.  Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations.  By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Dof-type zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967 encoding a CBL-interacting protein kinase, which was related to the K concentration.  The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

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The NAC transcription factor LuNAC61 negatively regulates fiber development in flax (Linum usitatissimum L.) Dongwei Xie, Jing Li, Wan Li, Lijun Sun, Zhigang Dai, Wenzhi Zhou, Jianguang Su, Jian Sun 2024, 23(3): 795-805.  DOI: 10.1016/j.jia.2023.12.029 Abstract ( )   PDF in ScienceDirect   Flax is a crucial fiber crop that exhibits excellent textile properties and serves as a model plant for investigating phloem fiber development.  The regulation of multiple genes significantly influences fiber development, notably involving NAC (NAM, ATAF1/2, CUC2) transcription factors in forming the fiber secondary cell wall (SCW).  Overexpression of LuNAC61 in flax resulted in sparse top meristematic zone leaves and significantly reduced stem cellulose content.  Scanning electron microscopy and staining observations revealed a significant reduction in fiber bundles.  β-Glucuronidase (GUS) staining analysis demonstrated high activity of the LuNAC61 promoter in the bast fibers of the flax stem.  Additionally, several members of the LuPLATZ and LuCesA families exhibited significant coexpression with LuNAC61.  Subcellular localization indicated the presence of LuPLATZ24 protein in the nucleus and cytoplasm, LuNAC61 protein exclusively in the nucleus, and LuCesA10 in the nucleus and endoplasmic reticulum.  LuPLATZ24 positively regulates LuNAC61, whereas LuNAC61 negatively affects LuCesA10, suggesting the involvement of a metabolic network in regulating flax fiber development.  In conclusion, this study provides a critical opportunity for a comprehensive and in-depth analysis of the mechanisms governing flax fiber development and the potential use of biotechnology to enhance flax fiber yield.

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The underlying mechanism of variety–water–nitrogen–stubble damage interactions on yield formation in ratoon rice with low stubble height under mechanized harvesting Jingnan Zou, Ziqin Pang, Zhou Li, Chunlin Guo, Hongmei Lin, Zheng Li, Hongfei Chen, Jinwen Huang, Ting Chen, Hailong Xu, Bin Qin, Puleng Letuma, Weiwei Lin, Wenxiong Lin 2024, 23(3): 806-823.  DOI: 10.1016/j.jia.2023.05.038 Abstract ( )   PDF in ScienceDirect   Agronomic measures are the key to promote the sustainable development of ratoon rice by reducing the damage from mechanical crushing to the residual stubble of the main crop, thereby mitigating the impact on axillary bud sprouting and yield formation in ratoon rice.  This study used widely recommended conventional rice Jiafuzhan and hybrid rice Yongyou 2640 as the test materials to conduct a four-factor block design field experiment in a greenhouse of the experimental farm of Fujian Agricultural and Forestry University, China from 2018 to 2019.  The treatments included fertilization and no fertilization, alternate wetting and drying irrigation and continuous water flooding irrigation, and plots with and without artificial crushing damage on the rice stubble.  At the same time, a 13C stable isotope in-situ detection technology was used to fertilize the pot experiment.   The results showed significant interactions among varieties, water management, nitrogen application and stubble status.  Relative to the long-term water flooding treatment, the treatment with sequential application of nitrogen fertilizer coupled with moderate field drought for root-vigor and tiller promotion before and after harvesting of the main crop, significantly improved the effective tillers from low position nodes.  This in turn increased the effective panicles per plant and grains per panicle by reducing the influence of artificial crushing damage on rice stubble and achieving a high yield of the regenerated rice.  Furthermore, the partitioning of 13C assimilates to the residual stubble and its axillary buds were significantly improved at the mature stage of the main crop, while the translocation rate to roots and rhizosphere soil was reduced at the later growth stage of ratooning season rice.  This was triggered by the metabolism of hormones and polyamines at the stem base regulated by the interaction of water and fertilizer at this time.  We therefore suggest that to achieve a high yield of ratoon rice with low stubble height under mechanized harvesting, the timely application of nitrogen fertilizer is fundamental, coupled with moderate field drying for root-vigor preservation and tiller promotion before and after the mechanical harvesting of the main crop.

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Rice canopy temperature is affected by nitrogen fertilizer Min Jiang, Zhang Chen, Yuan Li , Xiaomin Huang, Lifen Huang, Zhongyang Huo 2024, 23(3): 824-835.  DOI: 10.1016/j.jia.2023.05.005 Abstract ( )   PDF in ScienceDirect   Canopy temperature strongly influences crop yield formation and is closely related to plant physiological traits.  However, the effects of nitrogen treatment on canopy temperature and rice growth have yet to be comprehensively examined.  We conducted a two-year field experiment with three rice varieties (HD-5, NJ-9108, and YJ-805) and three nitrogen treatments (zero-N control (CK), 200 kg ha–1 (MN), and 300 kg ha–1 (HN)).  We measured canopy temperature using a drone equipped with a high-precision camera at the six stages of the growth period.  Generally, canopy temperature was significantly higher for CK than for MN and HN during the tillering, jointing, booting, and heading stages.  The temperature was not significantly different among the nitrogen treatments between the milky and waxy stages.  The canopy temperature of different rice varieties was found to follow the order: HD-5>NJ-9108>YJ-805, but the difference was not significant.  The canopy temperature of rice was mainly related to plant traits, such as shoot fresh weight (correlation coefficient r=–0.895), plant water content (–0.912), net photosynthesis (–0.84), stomatal conductance (–0.91), transpiration rate (–0.90), and leaf stomatal area (–0.83).  A structural equation model (SEM) showed that nitrogen fertilizer was an important factor affecting the rice canopy temperature.  Our study revealed: (1) A suite of plant traits was associated with the nitrogen effects on canopy temperature, (2) the heading stage was the best time to observe rice canopy temperature, and (3) at that stage, canopy temperature was negatively correlated with rice yield, panicle number, and grain number per panicle.  This study suggests that canopy temperature can be a convenient and accurate indicator of rice growth and yield prediction.

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The first factor affecting dryland winter wheat grain yield under various mulching measures: Spike number Yingxia Dou, Hubing Zhao, Huimin Yang, Tao Wang, Guanfei Liu, Zhaohui Wang, Sukhdev Malhi 2024, 23(3): 836-848.  DOI: 10.1016/j.jia.2023.05.034 Abstract ( )   PDF in ScienceDirect   Water is the key factor limiting dryland wheat grain yield.  Mulching affects crop yield and yield components by affecting soil moisture.  Further research is needed to determine the relationships between yield components and soil moisture with yield, and to identify the most important factor affecting grain yield under various mulching measures.  A long-term 9-year field experiment in the Loess Plateau of Northwest China was carried out with three treatments: no mulch (CK), plastic mulch (MP) and straw mulch (MS).  Yield factors and soil moisture were measured, and the relationships between them were explored by correlation analysis, structural equation modeling and significance analysis.  The results showed that compared with CK, the average grain yields of MP and MS increased by 13.0 and 10.6%, respectively.  The average annual grain yield of the MP treatment was 134 kg ha–1 higher than the MS treatment.  There were no significant differences in yield components among the three treatments (P<0.05).  Soil water storage of the MS treatment was greater than the MP treatment, although the differences were not statistically significant.  Soil water storage during the summer fallow period (SWSSF) and soil water storage before sowing (SWSS) of MS were significantly higher than in CK, which increased by 38.5 and 13.6%, respectively.  The relationship between MP and CK was not statistically significant for SWSSF, but the SWSS in MP was significantly higher than in CK.  In terms of soil water storage after harvest (SWSH) and water consumption in the growth period (ET), there were no significant differences among the three treatments.  Based on the three analysis methods, we found that spike number and ET were positively correlated with grain yield.  However, the relative importance of spike number to yield was the greatest in the MP and MS treatments, while that of ET was the greatest in CK.  Sufficient SWSSF could indirectly increase spike number and ET in the three treatments.  Based on these results, mulch can improve yield and soil water storage.  The most important factor affecting the grain yield of dryland wheat was spike number under mulching, and ET with CK.  These findings may help us to understand the main factors influencing dryland wheat grain yield under mulching conditions compared to CK.

Horticulture

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A mutation in the promoter of the yellow stripe-like transporter gene in cucumber results in a yellow cotyledon phenotype Jiawei Pan, Jia Song, Rahat Sharif, Xuewen Xu, Shutong Li, Xuehao Chen 2024, 23(3): 849-862.  DOI: 10.1016/j.jia.2023.11.024 Abstract ( )   PDF in ScienceDirect   Leaf color mutants in higher plants are considered to be ideal materials for studying the chlorophyll biosynthesis, photosynthesis mechanism and chloroplast development.  Herein, we identified a spontaneous mutant, yc412, in cultivated cucumber that exhibited yellow cotyledons.  The yellow-lethal mutant was diagnosed with an abnormal chloroplast ultrastructure, and reduced photosynthetic capacity and pigment content.  Through bulked segregant analysis-based whole-genome sequencing and fine genetic mapping, we narrowed the yellow cotyledons (yc) locus to a 96.8 kb interval on chromosome 3.  By resequencing and molecular cloning, we showed that Csyc is a potential candidate gene, which encodes a yellow stripe-like (YSL) transporter.  The T to C mutation in the promoter region of Csyc caused the yellow cotyledon phenotype in yc412.  Compared to YZU027A (WT), the expression of Csyc was significantly downregulated in the cotyledons of yc412.  Silencing of Csyc in cucumber via virus-induced gene silencing resulted in chlorotic leaves, mainly by suppressing the chlorophyll content.  Furthermore, a comparative transcriptome analysis revealed that chloroplast-related genes and chlorophyll biosynthesis genes were significantly downregulated in yc412 cotyledons.  Our results provide new insights into the molecular function of the YSL transporter in plant chloroplast development and chlorophyll synthesis.

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Alternative splicing of the PECTINESTERASE gene encoding a cell wall-degrading enzyme affects postharvest softening in grape Hainan Liu, Maosong Pei, Charles Ampomah-Dwamena, Yaxin Shang, Yihe Yu, Tonglu Wei, Qiaofang Shi, Dalong Guo 2024, 23(3): 863-875.  DOI: 10.1016/j.jia.2023.11.023 Abstract ( )   PDF in ScienceDirect   The firmness of table grape berries is a crucial quality parameter.  Despite extensive research on postharvest fruit softening, its precise molecular mechanisms remain elusive.  To enhance our comprehension of the underlying molecular factors, we initially identified differentially expressed genes (DEGs) by comparing the transcriptomes of folic acid (FA)-treated and water-treated (CK) berries at different time points.  We then analyzed the sequences to detect alternatively spliced (AS) genes associated with postharvest softening.  A total of 2,559 DEGs were identified and categorized into four subclusters based on their expression patterns, with subcluster-4 genes exhibiting higher expression in the CK group compared with the FA treatment group.  There were 1,045 AS-associated genes specific to FA-treated berries and 1,042 in the CK-treated berries, respectively.  Gene Ontology (GO) annotation indicated that the AS-associated genes in CK-treated berries were predominantly enriched in cell wall metabolic processes, particularly cell wall degradation processes.  Through a comparison between treatment-associated AS genes and subcluster-4 DEGs, we identified eight genes, including Pectinesterase 2 (VvPE2, Vitvi15g00704), which encodes a cell wall-degrading enzyme and was predicted to undergo an A3SS event.  The reverse transcription polymerase chain reaction further confirmed the presence of a truncated transcript variant of VvPE2 in the FA-treated berries.  Our study provides a comprehensive analysis of AS events in postharvest grape berries using transcriptome sequencing and underscores the pivotal role of VvPE2 during the postharvest storage of grape berries.

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Identification of key genes regulating the synthesis of quercetin derivatives in Rosa roxburghii through integrated transcriptomics and metabolomics Liyao Su, Min Wu, Tian Zhang, Yan Zhong, Zongming (Max) Cheng 2024, 23(3): 876-887.  DOI: 10.1016/j.jia.2023.11.022 Abstract ( )   PDF in ScienceDirect   Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways.  In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development.  Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified.  We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules.  In addition, we found that RrBEH4, RrLBD1 and RrPIF8 could significantly increase the expression of downstream quercetin derivative biosynthesis genes.  Taken together, these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.

Plant Protection

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Identification, pathogenicity, and fungicide sensitivity of Eutiarosporella dactylidis associated with leaf blight on maize in China Cheng Guo, Xiaojie Zhang, Baobao Wang, Zhihuan Yang, Jiping Li, Shengjun Xu, Chunming Wang, Zhijie Guo, Tianwang Zhou, Liu Hong, Xiaoming Wang, Canxing Duan 2024, 23(3): 888-900.  DOI: 10.1016/j.jia.2023.09.032 Abstract ( )   PDF in ScienceDirect   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.

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Improved multi-scale inverse bottleneck residual network based on triplet parallel attention for apple leaf disease identification Lei Tang, Jizheng Yi, Xiaoyao Li 2024, 23(3): 901-922.  DOI: 10.1016/j.jia.2023.06.023 Abstract ( )   PDF in ScienceDirect   Accurate diagnosis of apple leaf diseases is crucial for improving the quality of apple production and promoting the development of the apple industry.  However, apple leaf diseases do not differ significantly from image texture and structural information.  The difficulties in disease feature extraction in complex backgrounds slow the related research progress.  To address the problems, this paper proposes an improved multi-scale inverse bottleneck residual network model based on a triplet parallel attention mechanism, which is built upon ResNet-50, while improving and combining the inception module and ResNext inverse bottleneck blocks, to recognize seven types of apple leaf (including six diseases of alternaria leaf spot, brown spot, grey spot, mosaic, rust, scab, and one healthy).  First, the 3×3 convolutions in some of the residual modules are replaced by multi-scale residual convolutions, the convolution kernels of different sizes contained in each branch of the multi-scale convolution are applied to extract feature maps of different sizes, and the outputs of these branches are multi-scale fused by summing to enrich the output features of the images.  Second, the global layer-wise dynamic coordinated inverse bottleneck structure is used to reduce the network feature loss.  The inverse bottleneck structure makes the image information less lossy when transforming from different dimensional feature spaces.  The fusion of multi-scale and layer-wise dynamic coordinated inverse bottlenecks makes the model effectively balances computational efficiency and feature representation capability, and more robust with a combination of horizontal and vertical features in the fine identification of apple leaf diseases.  Finally, after each improved module, a triplet parallel attention module is integrated with cross-dimensional interactions among channels through rotations and residual transformations, which improves the parallel search efficiency of important features and the recognition rate of the network with relatively small computational costs while the dimensional dependencies are improved.  To verify the validity of the model in this paper, we uniformly enhance apple leaf disease images screened from the public data sets of Plant Village, Baidu Flying Paddle, and the Internet.  The final processed image count is 14,000.  The ablation study, pre-processing comparison, and method comparison are conducted on the processed datasets.  The experimental results demonstrate that the proposed method reaches 98.73% accuracy on the adopted datasets, which is 1.82% higher than the classical ResNet-50 model, and 0.29% better than the apple leaf disease datasets before preprocessing.  It also achieves competitive results in apple leaf disease identification compared to some state-of-the-art methods.

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A chorismate mutase from Radopholus similis plays an essential role in pathogenicity Sihua Yang, Junyi Li, Shuai Yang, Shiqiao Tang, Huizhong Wang, Chunling Xu, Hui Xie 2024, 23(3): 923-937.  DOI: 10.1016/j.jia.2023.04.040 Abstract ( )   PDF in ScienceDirect   In the process of infecting plants, plant parasitic nematodes release a series of proteins that play an essential role in the successful infection and pathogenesis of plant cells and tissues through stylets or body walls.  In this study, based on transcriptome data, a chorismate mutase gene of Radopholus similis (RsCM) was identified and cloned, which is a single copy gene specifically expressed in the oesophageal gland and highly expressed in juveniles and females.  Transient expression of RsCM in tobacco leaves showed that it was localised in the cytoplasm and nucleus of tobacco leaf cells, which inhibited the pattern-triggered immunity (PTI) induced by flg22, including callose deposition and defence gene expression, and cell death induced by immune elicitors BAX, but could not inhibit cell death induced by immune elicitors Gpa2/RBP-1.  The RNA interference (RNAi) transgenic tomato of RsCM obviously inhibited the infection, pathogenicity, and reproduction of R. similis.  However, the resistance of the overexpression transgenic tomato of RsCM to R. similis infection was significantly reduced, and the expression levels of two salicylic acid (SA) pathway genes (PR1 and PR5) in roots infected by the nematode were significantly down-regulated, which indicated that RsCM might be involved in the inhibition of SA pathway.  The results of this study demonstrate that RsCM suppresses the host immune system and might be a new target for the control of R. similis, which also provides new data for the function and mechanism of CM genes of migratory parasitic plant nematodes.

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Silencing transformer and transformer-2 in Zeugodacus cucurbitae causes defective sex determination with inviability of most pseudomales Qin Ma, Zizhen Fan, Ping Wang, Siya Ma, Jian Wen, Fengqin Cao, Xianwu Lin, Rihui Yan 2024, 23(3): 938-947.  DOI: 10.1016/j.jia.2023.06.019 Abstract ( )   PDF in ScienceDirect   transformer is a switch gene for sex determination in many insects, which cooperates with transformer-2 that is expressed in both sexes to regulate female differentiation, particularly in dipterans.  Zeugodacus cucurbitae (Coquillett) is a very destructive pest worldwide, however, its sex determination pathway remains largely uncharacterized.  Here, we show that the female sex ratio is sharply reduced with knockdown of either transformer or transformer-2 by RNA interference in early embryos of Z. cucurbitae.  Most of the males grown from the embryos with transient transformer and transformer-2 suppression mated with wild-type females and produced mixed sex progeny, with one exception that produced only female progeny, and all of the few remaining males failed to mate with wild-type females and produced no progeny.  The exceptional male and those males with mating failure were XX pseudomales as determined by the detection of Y chromosome-linked Maleness-on-the-Y, indicating that most XX pseudomales are not viable.  The phenotypes of transformer and transformer-2 suggest that they play a key role in regulating sex determination and are required for female sexual development of Z. cucurbitae.  Our results will be beneficial to the understanding of sex determination in Z. cucurbitae and can facilitate the development of genetic sexing strains for its biological control.

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Acaricidal effect of the antimicrobial metabolite xenocoumacin 1 on spider mite control Jiaxing Wei, Hong Yan, Jie Ren, Guangyue Li, Bo Zhang, Xuenong Xu 2024, 23(3): 948-959.  DOI: 10.1016/j.jia.2023.06.008 Abstract ( )   PDF in ScienceDirect   The two-spotted spider mite, Tetranychus urticae Koch, is one of the most harmful pests in many agroecosystems worldwide.  To effectively manage this pest, there is an urgent need to develop novel bio-active acaricides that support integrated pest management strategies targeting T. urticae.  In this study, we explored the acaricidal effects of xenocoumacin 1 (Xcn1) on T. urticae and its predator Neoseiulus californicus using the highly purified compound.  Xcn1 was extracted and purified from the cell-free supernatant of the Xenorhabdus nematophila CB6 mutant constructed by the easy promoter activated compound identification (easyPACId) method.  When the concentration of Xcn1 exceeded 100 μg mL–1, the survival rate of spider mite adults declined to below 40% and the fecundity was decreased by 80% at six days post-application.  At concentrations of 25 and 50 μg mL–1, Xcn1 significantly impeded spider mite development by inhibiting the molt.  However, neither concentration had any adverse effects on the survival or reproduction of the predatory mite N. californicus.  The results from laboratory and semi-field experiments consistently demonstrated the effectiveness of the antimicrobial metabolite Xcn1 in controlling pest mites at both the molecular and physiological levels.  Our study offers a promising possibility that combines the compatible biocontrol agents of Xcn1 and predatory mites for integrated pest mite control.

Animal Science · Veterinary Medicine

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circRNA3669 promotes goat endometrial epithelial cells proliferation via miR-26a/RCN2 to activate PI3K/AKT-mTOR and MAPK pathways Xiaorui Liu, Jiuzeng Cui, Mengyao Wei, Xiaofei Wang, Yuexia Liu, Zhongshi Zhu, Min Zhou, Gui Ba, Langda Suo, Yuxuan Song, Lei Zhang 2024, 23(3): 960-974.  DOI: 10.1016/j.jia.2023.05.029 Abstract ( )   PDF in ScienceDirect   The development of receptive endometrium (RE) from pre-receptive endometrium (PE) for successful embryo implantation is a complex dynamic process in which the morphology and physiological states of the endometrial epithelium undergo a series of significant changes, including cell proliferation and apoptosis.  However, the molecular mechanisms are not yet fully understood.  In this study, a higher circRNA3669 level was observed in PE than in RE of goats.  Functional assays revealed that this overexpression promoted the proliferation of goat endometrial epithelial cells (GEECs) by activating the expression of genes related to the PI3K/AKT-mTOR and MAPK pathways, thereby inhibiting apoptosis in vitro.  Furthermore, circRNA3669 functioned as a competing endogenous RNA (ceRNA) to upregulate Reticulocalbin-2 (RCN2) expression at the post-transcriptional level by interacting with and downregulating miR-26a in GEECs.  In addition, RCN2, which is highly expressed in the PE of goats, was found to be regulated by β-estradiol (E2) and progesterone (P4).  Our results demonstrated that RCN2 also affected the key proteins PI3K, AKT, mTOR, JNK, and P38 in the PI3K/AKT-mTOR and MAPK pathways, thereby facilitating GEECs proliferation and suppressing their apoptosis in vitro.  Collectively, we constructed a new circRNA3669-miR-26a-RCN2 regulatory network in GEECs, which further provides strong evidence that circRNA could potentially play a crucial regulatory role in the development of RE in goats.

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Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs Wenting Li, Chaoqun Gao, Zhao Cai, Sensen Yan, Yanru Lei, Mengya Wei, Guirong Sun, Yadong Tian, Kejun Wang, Xiangtao Kang 2024, 23(3): 975-987.  DOI: 10.1016/j.jia.2023.10.009 Abstract ( )   PDF in ScienceDirect   Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations.  In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure.  The breeds were divided into five conservation populations (GS1, 2010, ex-situ; GS2, 2019, ex-situ; GS3, 2019, in-situ; XB1, 2010, in-situ; and XB2, 2019, in-situ) based on conservation methods and generations.  The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest.  The degree of inbreeding of GS2 was higher than that of GS1 and GS3.  Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2.  In terms of population structure, the GS3 population were stratified relative to GS1 and GS2.  According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar.   We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs (in-situ and ex-situ).  While XB1 and XB2 had similar levels of genetic diversity.  Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

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Porcine enteric alphacoronavirus infection increases lipid droplet accumulation to facilitate the virus replication Qi Gao, Yongzhi Feng, Ting Gong, Dongdong Wu, Xiaoyu Zheng, Yizhuo Luo, Yunlong Yang, Zebu Song, Lang Gong, Guihong Zhang 2024, 23(3): 988-1005.  DOI: 10.1016/j.jia.2023.10.010 Abstract ( )   PDF in ScienceDirect   Coronaviruses are widely transmissible between humans and animals, causing diseases of varying severity.  Porcine enteric alphacoronavirus (PEAV) is a newly-discovered pathogenic porcine enteric coronavirus in recent years, which causes watery diarrhea in newborn piglets.  The host inflammatory responses to PEAV and its metabolic regulation mechanisms remain unclear, and no antiviral studies have been reported.  Therefore, we investigated the pathogenic mechanism and antiviral drugs of PEAV.  The transcriptomic analysis of PEAV-infected host cells revealed that PEAV could upregulate lipid metabolism pathways.  In lipid metabolism, steady-state energy processes, which can be mediated by lipid droplets (LDs), are the main functions of organelles.  LDs are also important in viral infection and inflammation.  In infected cells, PEAV increased LD accumulation, upregulated NF-κB signaling, promoted the production of the inflammatory cytokines IL-1β and IL-8, and induced cell death.  Inhibiting LD accumulation with a DGAT-1 inhibitor significantly inhibited PEAV replication, downregulated the NF-κB signaling pathway, reduced the production of IL-1β and IL-8, and inhibited cell death.  The NF-κB signaling pathway inhibitor BAY11-7082 significantly inhibited LD accumulation and PEAV replication.  Metformin hydrochloride also exerted anti-PEAV effects and significantly inhibited LD accumulation, downregulated the NF-κB signaling pathway, reduced the production of IL-1β and IL-8, and inhibited cell death.  LD accumulation in the lipid metabolism pathway therefore plays an important role in the replication and pathogenesis of PEAV, and metformin hydrochloride inhibits LD accumulation and the inflammatory response to exert anti-PEAV activity and reducing pathological injury.  These findings contribute new targets for developing treatments for PEAV infections.

Agro-ecosystem & Environment

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Combining field data and modeling to better understand maize growth response to phosphorus (P) fertilizer application and soil P dynamics in calcareous soils Weina Zhang, Zhigan Zhao, Di He, Junhe Liu, Haigang Li, Enli Wang 2024, 23(3): 1006-1021.  DOI: 10.1016/j.jia.2023.07.034 Abstract ( )   PDF in ScienceDirect   We used field experimental data to evaluate the ability of the agricultural production system model (APSIM) to simulate soil P availability, maize biomass and grain yield in response to P fertilizer applications on a fluvo-aquic soil in the North China Plain.  Crop and soil data from a 2-year experiment with three P fertilizer application rates (0, 75 and 300 kg P2O5 ha–1) were used to calibrate the model.  Sensitivity analysis was carried out to investigate the influence of APSIM SoilP parameters on the simulated P availability in soil and maize growth.  Crop and soil P parameters were then derived by matching or relating the simulation results to observed crop biomass, yield, P uptake and Olsen-P in soil.  The re-parameterized model was further validated against 2 years of independent data at the same sites.  The re-parameterized model enabled good simulation of the maize leaf area index (LAI), biomass, grain yield, P uptake, and grain P content in response to different levels of P additions against both the calibration and validation datasets.  Our results showed that APSIM needs to be re-parameterized for simulation of maize LAI dynamics through modification of leaf size curve and a reduction in the rate of leaf senescence for modern stay-green maize cultivars in China.  The P concentration limits (maximum and minimum P concentrations in organs) at different stages also need to be adjusted.  Our results further showed a curvilinear relationship between the measured Olsen-P concentration and simulated labile P content, which could facilitate the initialization of APSIM P pools in the NCP with Olsen-P measurements in future studies.  It remains difficult to parameterize the APSIM SoilP module due to the conceptual nature of the pools and simplified conceptualization of key P transformation processes.  A fundamental understanding still needs to be developed for modelling and predicting the fate of applied P fertilizers in soils with contrasting physical and chemical characteristics.

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Irrigation and nitrogen fertiliser optimisation in protected vegetable fields of northern China: Achieving environmental and agronomic sustainability Bingqian Fan, Yitao Zhang, Owen Fenton, Karen Daly, Jungai Li, Hongyuan Wang, Limei Zhai, Xiaosheng Luo, Qiuliang Lei, Shuxia Wu, Hongbin Liu 2024, 23(3): 1022-1033.  DOI: 10.1016/j.jia.2023.12.019 Abstract ( )   PDF in ScienceDirect   Globally, sub-optimal use of nitrogen (N) fertiliser and elevated N irrigation groundwater have led to high leached nitrate (NO3–) losses from protected vegetable field systems.  Optimising fertiliser and irrigation management in different soil types is crucial to reduce future N loads from such systems.  The present 4-year study examined leached N loads from lysimeter monitoring arrays set up across 18 protected vegetable system sites encompassing the dominant soil types of northern China.  The treatments applied at each field site were: 1) a high N and high irrigation input treatment (HNHI); 2) a low N but high irrigation input treatment (LNHI) and 3) a low N with low irrigation input treatment (LNLI).  Results showed that the mean annual leached total nitrogen loads from the HNHI, LNHI and LNLI treatments were 325, 294 and 257 kg N ha–1 in the fluvo-aquic soil, 114, 100 and 78 kg N ha–1 in the cinnamon soil and 79, 68 and 57 kg N ha–1 in the black soil, respectively.  The N dissolved in irrigation water in the fluvo-aquic soil areas was 8.26-fold higher than in the cinnamon areas.  A structural equation model showed that N fertiliser inputs and leaching water amounts explained 14.7 and 81.8% of the variation of leached N loads, respectively.  Correspondingly, reducing irrigation water by 21.5% decreased leached N loads by 20.9%, while reducing manure N and chemical N inputs by 22 and 25% decreased leached N loads by only 9.5%.  This study highlights that protected vegetable fields dominated by fluvo-aquic soil need management to curtail leached N losses in northern China.

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Calcium carbonate promotes the formation and stability of soil macroaggregates in mining areas of China Junyu Xie, Jianyong Gao, Hanbing Cao, Jiahui Li, Xiang Wang, Jie Zhang, Huisheng Meng, Jianping Hong, Tingliang Li, Minggang Xu 2024, 23(3): 1034-1047.  DOI: 10.1016/j.jia.2023.09.015 Abstract ( )   PDF in ScienceDirect   We studied changes in the concentrations of aggregate-cementing agents after different reclamation times and with different fertilization regimes, as well as the formation mechanism of aggregates in reclaimed soil, to provide a theoretical basis for rapid reclamation of soil fertility in the subsidence area of coal mines in Shanxi Province, China.  In this study, soil samples of 0–20 cm depth were collected from four fertilization treatments of a long-term experiment started in 2008: no fertilizer (CK), inorganic fertilizer (NPK), chicken manure compost (M), and 50% inorganic fertilizer plus 50% chicken manure compost (MNPK).  The concentrations of cementing agents and changes in soil aggregate size distribution and stability were analysed.  The results showed that the formation of >2 mm aggregates, the aggregate mean weight diameter (MWD), and the proportion of >0.25 mm water-stable aggregates (WR0.25) increased significantly after 6 and 11 years of reclamation.  The concentration of organic cementing agents tended to increase with reclamation time, whereas free iron oxide (Fed) and free aluminium oxide (Ald) concentrations initially increased but then decreased.  In general, the MNPK treatment significantly increased the concentrations of organic cementing agents and CaCO3, and CaCO3 increased by 60.4% at 11 years after reclamation.  Additionally, CaCO3 had the greatest effect on the stability of aggregates, promoting the formation of >0.25 mm aggregates and accounting for 54.4% of the variance in the proportion and stability of the aggregates.  It was concluded that long-term reclamation is beneficial for improving soil structure.  The MNPK treatment was the most effective measure for increasing maize grain yield and concentration of organic cementing agents and CaCO3.

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Lateral root elongation in maize is related to auxin synthesis and transportation mediated by N metabolism under a mixed NO3– and NH4+ supply Peng Wang, Lan Yang, Xichao Sun, Wenjun Shi, Rui Dong, Yuanhua Wu, Guohua Mi 2024, 23(3): 1048-1060.  DOI: 10.1016/j.jia.2023.07.012 Abstract ( )   PDF in ScienceDirect   A mixed nitrate (NO3–) and ammonium (NH4+) supply can promote root growth in maize (Zea mays), however, the changes in root morphology and the related physiological mechanism under different N forms are still unclear.  Here, maize seedlings were grown hydroponically with three N supplied in three different forms (NO3– only, 75/25 NO3–/NH4+ and NH4+ only).  Compared with sole NO3– or NH4+, the mixed N supply increased the total root length of maize but did not affect the number of axial roots.  The main reason was the increased total lateral root length, while the average lateral root (LR) length in each axle was only slightly increased.  In addition, the average LR density of 2nd whorl crown root under mixed N was also increased.  Compared with sole nitrate, mixed N could improve the N metabolism of roots (such as the N influx rate, nitrate reductase (NR) and glutamine synthase (GS)enzyme activities and total amino content of the roots).  Experiments with exogenously added NR and GS inhibitors suggested that the increase in the average LR length under mixed N was related to the process of N assimilation, and whether the NR mediated NO synthesis participates in this process needs further exploration.  Meanwhile, an investigation of the changes in root-shoot ratio and carbon (C) concentration showed that C transportation from shoots to roots may not be the key factor in mediating lateral root elongation, and the changes in the sugar concentration in roots further proved this conclusion.  Furthermore, the synthesis and transportation of auxin in axial roots may play a key role in lateral root elongation, in which the expression of ZmPIN1B and ZmPIN9 may be involved in this pathway.  This study preliminarily clarified the changes in root morphology and explored the possible physiological mechanism under a mixed N supply in maize, which may provide some theoretical basis for the cultivation of crop varieties with high N efficiency.

Agricultural Economics and Management

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Does Green Food Certification promote agri-food export quality?  Evidence from China Ping Wei, Hongman Liu, Chaokai Xu, Shibin Wen 2024, 23(3): 1061-1074.  DOI: 10.1016/j.jia.2023.11.033 Abstract ( )   PDF in ScienceDirect   The construction of a food certification system plays a vital role in upgrading export quality, which previous studies have largely overlooked.  We match China’s industry-level data of Green Food Certification with its HS6-digit export data of agri-food products to quantify the impact of Green Food Certification on export quality.  We identify the significant and positive effect of Green Food Certification on export quality.  The 2SLS estimation based on instrumental variables and a range of robustness checks confirm the validity and robustness of the benchmark conclusions.  Further analysis discloses that Green Food Certification improves export quality by raising agricultural production efficiency and brand premiums.  Heterogeneity analysis shows that the effect of Green Food Certification varies across regions, notably improving the quality of agri-food products exported to developed regions and regions with high levels of import supervision.  Furthermore, among various product types, Green Food Certification significantly improves the export quality of primary products and products vulnerable to non-tariff measures.  The above findings could guide the future development of agri-food quality certification systems, potentially leading to a transformation and promotion of the agri-food trade.

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Temporal and spatial evolution of global major grain trade patterns Ziqi Yin, Jiaxuan Hu, Jing Zhang, Xiangyang Zhou, Lingling Li, Jianzhai Wu 2024, 23(3): 1075-1086.  DOI: 10.1016/j.jia.2023.10.032 Abstract ( )   PDF in ScienceDirect   The complex and volatile international landscape has significantly impacted global grain supply security.  This study uses a complex network analysis model to examine the evolution and trends of the global major grain trade from 1990 to 2020, focusing on network topology, centrality ranking, and community structure.  There are three major findings.  First, the global major grain trade network has expanded in scale, with a growing emphasis on diversification and balance.  During the study period, the United States, Canada, China, and Brazil were the core nodes of the network.  Grain-exporting countries were mainly situated in Asia, the Americas, and Europe, and importing countries in Asia, Africa, and Europe.  Second, a significant increase in the number of high centrality countries with high export capacity occurred, benefiting from natural advantages such as fertile land and favorable climates.  Third, the main global grain trade network is divided into four communities, with the Americas-Europe community being the largest and most widespread.  The formation of the community pattern was influenced by geographic proximity, driven by the core exporting countries.  Therefore, the world needs to enhance the existing trade model, promote the multi-polarization of the grain trade network, and establish a global vision for the future community.  Countries and regions should participate actively in global grain trade security governance and institutional reform, expand trade links with other countries, and optimize import and export policies to reduce trade risks.