Papers by Journal of Integrative Agriculture (JIA)
Journal of Integrative Agriculture, 2025
Leaves and glumes act as lateral organs and have essential effects on photosynthesis and seed mor... more Leaves and glumes act as lateral organs and have essential effects on photosynthesis and seed morphology, thus affecting yield. However, the molecular mechanisms controlling their polarity development in rice still need further study. Here, we isolated a polarity defect of lateral organs 1 (pdl1) mutant in rice, which exhibits twisted/filamentous-shaped leaves and cracked/filamentous-shaped lemmas caused by defects in polarity development. PDL1 encodes a SUPPRESSOR OF GENE SILENCING 3 protein localized in the cytoplasmic granules. PDL1 is expressed in the shoot apical meristem, inflorescence meristem, floral meristem, and lateral organs including leaves and floral organs. PDL1 is involved in the synthesis of tasiR-ARF, which may subsequently modulate the expression of OsARFs. Meanwhile, the expression levels of abaxial miR165/166 and the adaxial identity genes OSHBs were respectively increased and reduced significantly. The results of this study clarify the molecular mechanism by which PDL1-mediated tasiR-ARF synthesis regulates the lateral organ polarity development in rice.
Journal of Integrative Agriculture, 2025
Southern corn leaf blight (SCLB) caused by Cochliobolus heterostrophus, is a widespread foliar di... more Southern corn leaf blight (SCLB) caused by Cochliobolus heterostrophus, is a widespread foliar disease that has a substantial impact on maize yield in the Huang-Huai-Hai Region of China. Pydiflumetofen (Pyd), a new succinate dehydrogenase inhibitor (SDHI), has been found as a promising fungicide for the efficient control of SCLB, however, resistance of C. heterostrophus to Pyd has not been studied well. Here, five Pyd-resistant mutants were generated through fungicide adaptation. Sequence alignment analysis revealed that these mutants primarily mutated in ChSdhB and ChSdhD, with three genotypes: ChSdhBH277Y, ChSdhBI279T and ChSdhDH133Y, exhibiting two distinct categories of resistance: high resistance (HR) and moderate resistance (MR), among which the resistance factors were 214.22 and 44.33–53.67, respectively. These mutants were more pathogenic than the wild-type parental strains, but there was a significant reduction in mycelial growth rate and sporulation in the resistant mutants, indicating a significant fitness cost associated with resistance to Pyd. In addition, this study revealed a positive cross-resistance between Pyd and another SDHI fungicide cyclobutrifluram. However, no cross-resistance was found between Pyd and other classes of fungicides, including prochloraz, fludioxonil, iprodione or pyraclostrobin. Homology modeling and molecular docking further confirmed that point mutations of ChSdhBH277Y, ChSdhBI279T, and ChSdhDH133Y could reduce binding affinity between Pyd and its target subunits from –74.07, –74.07, –152.52 kcal mol–1 to –3.90, –4.95, –9.93 kcal mol–1, respectively. These findings not only provided valuable insights for managing SCLB caused by C. heterostrophus, but also enhanced our understanding of molecular mechanism underlying plant pathogen resistance to Pyd.
Journal of Integrative Agriculture, 2025
Chestnuts are important economic forest tree species with enormous application value in the wood,... more Chestnuts are important economic forest tree species with enormous application value in the wood, medicine, and chemical industries. Currently, the limited genome-wide SSR molecular marker information on chestnut resources significantly limits research on genetic diversity and identification of chestnut resources. To address this issue, we used GMATA to screen simple sequence repeat (SSR) markers throughout the Chinese chestnut genome. A total of 312,302 molecular markers were obtained with a density of 434.38/Mb. Subsequently, all SSR markers were examined for polymorphism using the HipSTR program and 138,208 polymorphic loci were finally obtained. To verify the identification ability of the developed SSR, we randomly selected 36 markers on 12 chromosomes to construct fingerprint maps of 96 ancient chestnut resources from the Yanshan Mountains. The results showed that only 6 pairs of primers were required to create a unique DNA fingerprint of the tested ancient trees, showing that the developed markers have high identification potential. We then evaluated the inter-specific universality and polymorphism of these markers using three species, including 91 chestnut plants. The molecular markers amplified 94% of the interspecies with a PIC value of 0.859. Cluster analysis revealed that testing resources using these developed markers can be well differentiated and these markers have been widely used to identify interspecific boundaries. These results proved that the developed molecular markers have the potential for genotypic diversity, which can provide references for genetic diversity research, variety identification, kinship analysis, selection of good products, and construction of core germplasm resources of chestnut and even chestnut plants. They lay a solid foundation for the molecular design of hybrids to improve breeding and develop germplasm resources.
Journal of Integrative Agriculture, 2025
Southern corn leaf blight (SCLB) caused by Cochliobolus heterostrophus, is a widespread foliar di... more Southern corn leaf blight (SCLB) caused by Cochliobolus heterostrophus, is a widespread foliar disease that has a substantial impact on maize yield in the Huang-Huai-Hai Region of China. Pydiflumetofen (Pyd), a new succinate dehydrogenase inhibitor (SDHI), has been found as a promising fungicide for the efficient control of SCLB, however, resistance of C. heterostrophus to Pyd has not been studied well. Here, five Pyd-resistant mutants were generated through fungicide adaptation. Sequence alignment analysis revealed that these mutants primarily mutated in ChSdhB and ChSdhD, with three genotypes: ChSdhBH277Y, ChSdhBI279T and ChSdhDH133Y, exhibiting two distinct categories of resistance: high resistance (HR) and moderate resistance (MR), among which the resistance factors were 214.22 and 44.33–53.67, respectively. These mutants were more pathogenic than the wild-type parental strains, but there was a significant reduction in mycelial growth rate and sporulation in the resistant mutants, indicating a significant fitness cost associated with resistance to Pyd. In addition, this study revealed a positive cross-resistance between Pyd and another SDHI fungicide cyclobutrifluram. However, no cross-resistance was found between Pyd and other classes of fungicides, including prochloraz, fludioxonil, iprodione or pyraclostrobin. Homology modeling and molecular docking further confirmed that point mutations of ChSdhBH277Y, ChSdhBI279T, and ChSdhDH133Y could reduce binding affinity between Pyd and its target subunits from –74.07, –74.07, –152.52 kcal mol–1 to –3.90, –4.95, –9.93 kcal mol–1, respectively. These findings not only provided valuable insights for managing SCLB caused by C. heterostrophus, but also enhanced our understanding of molecular mechanism underlying plant pathogen resistance to Pyd.
Journal of Integrative Agriculture, 2025
Malate dehydrogenase (MDH) is a widely expressed enzyme that plays a key role in plant growth, de... more Malate dehydrogenase (MDH) is a widely expressed enzyme that plays a key role in plant growth, development, and stress responses. However, information on MDH genes in the soybean genome is limited. Seventeen members of the soybean MDH family were identified by genome-wide analysis, and the genes were analyzed for the presence of conserved protein motifs. The genes were divided into five clusters according to their phylogenetic relationships. The intracellular localizations of six GmMDHs were determined by confocal microscopy of Arabidopsis mesophyll protoplasts. Transcripts of GmMDHs were significantly increased by abiotic stress (drought, salt, and alkalinity) and hormone treatments, as shown by an analysis of cis-regulatory elements and quantitative real-time polymerase chain reaction (qRT-PCR). The GmMDHs displayed unique expression patterns in various soybean tissues. Notably, the expression levels of a chloroplast isoform (GmMDH2) were unusually high under salt stress, presumably indicating a critical role in soybean responses to salinity. Expression of GmMDH2 in Escherichia coli showed that the recombinant enzyme has nicotinamide adenine dinucleotide phosphate (NADP)-dependent MDH activity. The redox states of the NADP (reduced form) (NADPH) pool and antioxidant activities were shown to be modulated by GmMDH2 gene overexpression, which in turn reduced reactive oxygen species (ROS) formation in transgenic soybean, significantly enhancing the salt stress resistance. Gene-based association analysis showed that variations in GmMDH2 were strongly linked to seedling salt tolerance. A polymorphism potentially associated with salt tolerance was discovered in the promoter region of GmMDH2. These findings not only improve our understanding of the stress response mechanism by identifying and characterizing the MDH gene family throughout the soybean genome but they also identified a potential candidate gene for the future enhancement of salt tolerance in soybean.
Journal of Integrative Agriculture, 2025
Large grain is a favorable trait for appearance quality and a large sink potential in wheat breed... more Large grain is a favorable trait for appearance quality and a large sink potential in wheat breeding. The stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895). Here, a BC1F6 residual heterozygous line was selected from the cross of a ZM871/ZM895//ZM871 population, and six heterozygous recombinant plants were identified in the BC1F7 population from self-pollination of the heterozygous line. QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2 (25.3–27.5 Mb) by phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants. Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses. Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS. The gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed, and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population of 166 cultivars using this marker. These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.
Journal of Integrative Agriculture, 2025
Here we explore the disruption of gut health by DON, considering aspects such as intestinal histo... more Here we explore the disruption of gut health by DON, considering aspects such as intestinal histomorphology, epithelial barrier functions, immune system, microflora, and short-chain fatty acid production in the intestines. Numerous additives have been documented for their potential in the detoxification of DON. These additives can alleviate the toxic effects of DON on pigs by modulating the Nrf2-Keap1, mitogen-activated protein kinases (MAPKs) and Nuclear factor kappa-B (NF-κB) signaling pathways. Additionally, there are additives capable of mitigating the toxicity of DON through adsorption or biotransformation. This update has novel potential for advancing our comprehension of the mechanisms linked to DON intestinal toxicity and facilitating the formulation of innovative strategies to mitigate the impact of DON.
Journal of Integrative Agriculture, 2025
The “Greater Food” approach has replaced the older “taking grain production as a top priority” ap... more 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.
Journal of Integrative Agriculture, 2025
Grain soybean (Glycine max (L.) Merr.) shows potential as a forage crop following its introductio... more Grain soybean (Glycine max (L.) Merr.) shows potential as a forage crop following its introduction from low to high latitudes due to in its growth phenotype. However, the application of this approach is impeded by the diverse ecological types of soybean, their adaptability to the introduction, and the uncertainty surrounding the growth phenotype post-introduction. This study introduced 24 grain soybean varieties from low-latitude regions (22–31°N) to the high-latitude northwestern Loess Plateau (39°N) between 2018 and 2019. The growth phenotypes were observed, and their forage productivity potential was assessed. All varieties displayed delayed flowering following cross-latitude introduction, with the vegetative growth phase of some varieties even exceeding their entire growth duration at their origin. Rapid dry matter accumulation rates indicated growth adaptation performance and formed the basis for soybean forage yield. Varieties from the tropical South China region exhibited significant yield advantages, with dry matter yields of 8.97–14.68 t ha–1 and crude protein yields of 1.44–2.51 t ha–1. Varieties HX3 and GX7 from this region demonstrated optimal growth adaptability and productivity in the cross-latitude environment, achieving the highest dry matter yields of 14.68 and 13.86 t ha–1, respectively. As a result, HX3 and GX7 are recommended for local farming systems to provide high-quality forage. The cross-latitude introduction of soybean is proposed as a viable and efficient strategy for forage improvement and application.
Journal of Integrative Agriculture, 2025
Highlights • • Developed a novel biomass estimation model, AUR-50, with an average R² exceeding 0... more Highlights • • Developed a novel biomass estimation model, AUR-50, with an average R² exceeding 0.77. • • Enhanced model accuracy by integrating convolutional features into traditional image features. • • Reduced the impact of vegetation saturation on estimation accuracy using convolutional features.
Journal of Integrative Agriculture, 2025
In our previous study, a stable quantitative trait locus (QTL) qIF05-1 controlling the seed isofl... more In our previous study, a stable quantitative trait locus (QTL) qIF05-1 controlling the seed isoflavone content in soybean was detected on chromosome (Chr.) 05 in a recombinant inbred line (RIL) population from a cross of Huachun 2×Wayao. In this study, the parental lines were re-sequenced using the Illumina Solexa System with deep coverage. A total of 63,099 polymorphic long insertions and deletions (InDels) (≥15 bp) were identified between the parents Huachun 2 and Wayao. The InDels were unevenly distributed on 20 chromosomes of soybean, varying from 1,826 in Chr. 12 to 4,544 in Chr. 18. A total of 10,002 long InDels (15.85% of total) were located in genic regions, including 1,139 large-effect long InDels which resulted in truncated or elongated protein sequences. In the qIF05-1 region, 68 long InDels were detected between the two parents. Using a progeny recombination experiment and genotype analysis, the qIF05-1 locus was mapped into a 102.2 kb genomic region, and this region contained 12 genes. By RNA-seq data analysis, genome sequence comparison and functional validation through ectopic expression in Arabidopsis thaliana, Glyma.05G208300 (described as GmEGL3), which is a basic helix-loop-helix (bHLH) transcription factor in plants, emerged as the most likely confirmed gene in qIF05-1. These long InDels can be used as a type of complementary genetic method for QTL fine mapping, and they can facilitate genetic studies and molecular-assisted selection breeding in soybean.
Journal of Integrative Agriculture, 2025
• • This method ensures the precise content of flavonoids in the phenylpropanoid pathway.
• • ... more • • This method ensures the precise content of flavonoids in the phenylpropanoid pathway.
• • For flavonoid-rich plants, the approach is very reliable.
• • This method clarifies flavonoid dynamics, aiding gene function understanding.
Journal of Integrative Agriculture , 2025
Based on the RCEP agreement, this study employed the global trade analysis project (GTAP) model t... more Based on the RCEP agreement, this study employed the global trade analysis project (GTAP) model to evaluate the impact of RCEP on AVC of member countries in terms of time, tariff reduction, and reduction of non-tariff barriers (NTB). The results indicate that (1) the implementation of RCEP boosts the value-added to agricultural exports for most member countries, particularly in competitive industries; (2) the increase in domestic production and processing capacity, reflected in domestic value-added (DVA), is the primary factor driving the rise in the value-added of agricultural exports across various industries of member countries; (3) RCEP enhances the participation of most regional countries in AVC, with varying impacts on AVC positioning, thereby fostering regional AVC development; and (4) RCEP has a positive effect on AVC indicators both in the short and long term, with the effect becoming more pronounced over time. Additionally, reducing NTB enhances the positive effects of tariff reductions on AVC indicators. Based on the analyses, the following recommendations are proposed: (1) Leverage the development opportunities arising from RCEP implementation to enhance the agricultural DVA; (2) capitalize on cooperative opportunities created by RCEP to build cohesive regional AVC; and (3) prioritize the effective implementation of RCEP’s high-quality rules.
Journal of Integrative Agriculture, 2025
Nitrogen (N) serves as an essential nutrient for yield formation across diverse crop types. Howe... more Nitrogen (N) serves as an essential nutrient for yield formation across diverse crop types. However, agricultural production encounters numerous challenges, notably high N fertilizer rates coupled with low N use efficiency and serious environmental pollution. Deep placement of nitrogen fertilizer (DPNF) is an agronomic measure that shows promise in addressing these issues. This review aims to offer a comprehensive understanding of DPNF, beginning with a succinct overview of its development and methodologies for implementation. Subsequently, the optimal fertilization depth and influencing factors for different crops are analyzed and discussed. Additionally, it investigates the regulation and mechanism underlying the DPNF on crop development, yield, N use efficiency and greenhouse gas emissions. Finally, the review delineates the limitations and challenges of this technology and provides suggestions for its improvement and application. This review provides valuable insight and reference for the promotion and adoption of DPNF in agricultural practice.
Journal of Integrative Agriculture, 2025
This study focused on grassland ecological compensation policy (GECP), quantifying herders’ WTA c... more This study focused on grassland ecological compensation policy (GECP), quantifying herders’ WTA compensation for grassland grazing bans. Through face-to-face surveys and employing the contingent valuation method, we estimated households’ WTA for participating in a grassland conservation program to bolster ecosystem service provision. Our findings indicated that herders required an average compensation of 237 CNY mu–1 yr–1 to engage in the grazing ban program. Notably, herders’ environmental awareness positively influenced their willingness to participate, whereas larger family sizes were negatively correlated with WTA. Additionally, herders in better health, with higher livestock incomes or categorized as semi-herders, tended to accept lower compensation levels. These insights are crucial for improving the effectiveness of GECP and provide valuable reference points for similar analyses in economically disadvantaged and ecologically fragile regions.
Journal of Integrative Agriculture, 2025
• The addition of raspberry extract reduced ethyl carbamate level in Chinese rice wine. • Raspber... more • The addition of raspberry extract reduced ethyl carbamate level in Chinese rice wine. • Raspberry extract addition was speculated to promote the catabolism of urea and citrulline. • Raspberry extract addition affected the arginine metabolism of Saccharomyces cerevisiae.
Journal of Integrative Agriculture, 2025
Highlights • • Wheat-straw biochar improves maize growth and water-use efficiency under partial r... more Highlights • • Wheat-straw biochar improves maize growth and water-use efficiency under partial root-zone drying irrigation. • • Biochar modulates the xylem sap constituent and ABA-based chemical signaling. • • Reduced irrigation refines stomatal morphology: smaller but denser distribution.
Journal of Integrative Agriculture, 2025
In this study, SPF chicks at the age of 3 d began to drink water with the FLO at a dose of 100 m... more In this study, SPF chicks at the age of 3 d began to drink water with the FLO at a dose of 100 mg L–1 for 6 consecutive days, and the growth performance of chicks was monitored, the effect of FLO on immune organs was detected by pathological examination and TdT-mediated dUTP nick-end labeling (TUNEL) apoptosis staining. In order to evaluate the level of organism immunity, the level of Newcastle disease virus antibody in serum was detected by hemagglutination inhibition test, the content of cytokines (IL-1, IL-2, IL-6, TNF-α, IFN-γ) in serum was detected by enzyme linked immunosorbent assay (ELISA), and the transcription of interferon-related genes (IRF-7, 2´-5´OAS, Mx1) and cytokine genes (IL-6, TNF-α, IFN-γ) in immune organs were detected by real time fluorescence quantitative PCR. The results showed that the early application of FLO could inhibit the growth and development of chicks, and the body weight and immune organ index of the treatment group were lower than those of the control group. Histopathological examination showed that there was a decrease in the number of lymphocytes in the bursa of Fabricius in the treatment group in the early stage of drug withdrawal, and the results of TUNEL apoptosis staining in the bursa of Fabricius showed that obvious lymphocyte apoptosis occurred in the FLO treatment group. Compared with the control group, the transcription levels of interferon-related genes IRF-7, 2´-5´OAS, and cytokine genes IL-6, TNF-α and IFN-γ in FLO treatment group decreased to a certain extent, while the transcription level of Mx1 gene had no significant difference at all time points. The level of serum Newcastle disease virus (NDV) antibody and the contents of cytokines IL-1, IL-2 and IFN-γ in the FLO treatment group were significantly lower than those in the control group in the early stage of drug withdrawal, but recovered gradually in the later stage. This study showed that FLO has a certain degree of effect on the immune function of chicks, and the results of the study laid the foundation for further research on the mechanism of FLO-induced immunotoxicity.
Journal of Integrative Agriculture, 2025
The main goal of this study was to explore the biological functions of VGLL2 in the development ... more The main goal of this study was to explore the biological functions of VGLL2 in the development of chicken skeletal muscle and the proliferation and differentiation of skeletal muscle cells in vitro. In this study, we detected the effect of VGLL2 on the proliferation of myoblasts by CCK8, EdU and flow cytometry analyses after overexpressing and interfering with VGLL2. Indirect immunofluorescence was used to detect the effect of VGLL2 on the differentiation of myoblasts. qRT-PCR and hematoxylin and eosin (H&E) staining were used to evaluate the effects of VGLL2 overexpression on the growth rate and muscle fiber structure of chicken skeletal muscle. The results showed that VGLL2 inhibited the proliferation of primary cultured chicken myoblasts and promoted the differentiation of these cells. Interestingly, food intake and muscle fiber development were significantly enhanced by the overexpression of VGLL2 in chickens. Taken together, these data demonstrate that the VGLL2 gene may be a useful marker for improving muscle mass in poultry.
Journal of Integrative Agriculture, 2025
The plant growth process is accompanied by dynamic changes in the microtubules, and the rearrange... more The plant growth process is accompanied by dynamic changes in the microtubules, and the rearrangement of microtubules is regulated by diverse microtubule-associated proteins (MAPs). Plant MAP65s have been exhaustively characterized in some species, but the information about MAP65 family members in tomato (Solanum lycopersicum) is limited. In this study, nine SlMAP65 family genes were identified in the tomato genome. Then a systematic analysis that considered the physio-chemical properties, evolution, conserved motifs, domains, gene structure, and cis-regulatory elements of SlMAP65 family members was conducted. The family member SlMAP65-1, which had the highest expression, was knocked out by CRISPR/Cas9. The tomato fruit of slmap65-1 loss of function lines showed an elongated morphology, and the data indicated that SlMAP65-1 is involved in fruit morphogenesis at the early fruit development stage. These results provide new insights for fruit morphogenesis-related research and future functional studies of the SlMAP65 family members in tomato.
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Papers by Journal of Integrative Agriculture (JIA)
• • For flavonoid-rich plants, the approach is very reliable.
• • This method clarifies flavonoid dynamics, aiding gene function understanding.