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Genome-wide analysis of RAD23 gene family and a functional characterization of AcRAD23D1 in drought resistance in Actinidia
Xiaoli Zhang, Daolin Ye, Xueling Wen, Xinling Liu, Lijin Lin, Xiulan Lü, Jin Wang, Qunxian Deng, Hui Xia, Dong Liang
2025, 24 (5): 1831-1843.   DOI: 10.1016/j.jia.2025.03.003
Abstract19)      PDF in ScienceDirect      

UBL-UBA protein functions as a shuttle factor in the 26S ubiquitin degradation pathway, playing a critical role in plant growth and development, and responding to various biotic and abiotic stresses.  Although RAD23, a type of UBL-UBA protein, has been extensively studied in several plants, there is currently no comprehensive analysis available for kiwifruit (Actinidia chinensis).  In this study, we identified six AcRAD23 genes in kiwifruit and further analyzed their phylogenetic relationships, gene structure, conserved motif composition and cis-acting element in the promoter.  Subcellular localization experiments revealed that all AcRAD23 were localized in the nucleus and the cell membranes.  Quantitative real-time PCR (qRT-PCR) analysis demonstrated differential expression patterns of these AcRAD23 genes across different tissues and under various stress conditions (drought, waterlogging, salt stress, etc.), with AcRAD23D1 showing the highest responsiveness to abiotic stress.  Additionally, we investigated the biological function of AcRAD23D1 using VIGS-mediated gene silencing methods under drought stress conditions.  Suppression of AcRAD23D1 expression resulted in reduced relative water content (RWC) but increased malondialdehyde (MDA) content and relative electrolyte leakage (REL) levels in D1-VIGS lines compared to control lines.  Furthermore, D1-VIGS lines exhibited a higher accumulation of reactive oxygen species (ROS) along with decreased superoxide dismutase (SOD) and peroxidase (POD) enzyme activities.  These findings suggest that AcRAD23D1 may play a positive role in regulating kiwifruit’s response to drought stress.  Our results provide new insights into the potential involvement of AcRAD23 under abiotic stress conditions while offering a theoretical foundation for understanding the molecular mechanisms underlying kiwifruit’s adaptation to stresses. 

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Reduced tillage coupled with straw return improves the grain yield and 2-acetyl-1-pyrroline content in fragrant rice
Zhaowen Mo, Siren Cheng, Yong Ren, Longxin He, Shenggang Pan, Haidong Liu, Hua Tian, Umair Ashraf, Meiyang Duan, Xiangru Tang
2025, 24 (5): 1718-1737.   DOI: 10.1016/j.jia.2024.03.020
Abstract26)      PDF in ScienceDirect      

The practice of conservation tillage or straw return to the farmland influences the grain yield and quality of rice (Oryza sativa).  The key volatile compound responsible for the fragrance of fragrant rice is 2-acetyl-1-pyrroline (2-AP), which is significantly affected by field management measures.  The purpose of this study was to investigate the impact of tillage management and straw return on the grain yield and biosynthesis of 2-AP in fragrant rice.  This study was conducted over two years in 2016 and 2017 and used two fragrant rice cultivars (Meixiangzhan 2 and Xiangyaxiangzhan) as materials.  The experimental design consisted of different tillage management and straw return treatments, which included three tillage management regimes: rotary tillage (T0), minimum tillage (T1), and no tillage (T2); and two straw return treatments: without straw return (S0) and straw return (S1).  The straw used for the experiment was sourced from the residue of the corresponding fragrant rice cultivar harvested in the early season.  Tillage management and straw return substantially affected the grain yields, grain quality, and 2-AP contents of both fragrant rice cultivars.  Compared with the T0S0 treatment, tillage management and straw return resulted in 2-AP content improvements in 2016 (12.41–116.85%) and 2017 (34.85–103.89%) on average.  Higher 2-AP contents were also detected in both fragrant rice cultivars in the T2S1 and T1S1 treatments.  A structural equation model (SEM) demonstrated that the activities of enzymes related to fragrance metabolism in the leaves and grain jointly regulated the biosynthesis of precursors of fragrance metabolism in the grain, which further promoted the accumulation of 2-AP.  In addition, a principal component analysis indicated that the T1S1 treatment was positively correlated with both 2-AP and grain yield.  The SEM demonstrated that the enzymes related to nitrogen metabolism, parameters related to photosynthesis, and yield components contributed to the grain yield.  The T1S1 treatment resulted in the highest average grain yield of 760.75 g m–2, which could be attributed to increases in various attributes, such as the leaf area index, SPAD value, nitrogen metabolism, panicle number m–2, and grain number per panicle.  In summary, the minimum tillage and straw return (T1S1) treatment is more effective at simultaneously improving both the grain yield and 2-AP content in fragrant rice.

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SiEPFs enhance water use efficiency and drought tolerance by regulating stomatal density in foxtail millet (Setaria italica)
Jianhong Hao, Xueting Kang, Lingqian Zhang, Jiajing Zhang, Huashuang Wu, Zidong Li, Dan Wang, Min Su, Shuqi Dong, Xiaorui Li, Lulu Gao, Guanghui Yang, Xiaoqian Chu, Xiangyang Yuan, Jiagang Wang
2025, 24 (2): 786-789.   DOI: 10.1016/j.jia.2024.09.008
Abstract84)      PDF in ScienceDirect      
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Water deficit affects the nitrogen nutrition index of winter wheat under controlled water conditions
Ben Zhao, Anzhen Qin, Wei Feng, Xinqiang Qiu, Pingyan Wang, Haixia Qin, Yang Gao, Guojie Wang, Zhandong Liu, Syed Tahir Ata-Ul-Karim
2025, 24 (2): 724-738.   DOI: 10.1016/j.jia.2024.08.027
Abstract65)      PDF in ScienceDirect      

Nitrogen (N) uptake is regulated by water availability, and a water deficit can limit crop N responses by reducing N uptake and utilization.  The complex and multifaceted interplay between water availability and the crop N response makes it difficult to predict and quantify the effect of water deficit on crop N status.  The nitrogen nutrition index (NNI) has been widely used to accurately diagnose crop N status and to evaluate the effectiveness of N application.  The decline of NNI under water-limiting conditions has been documented, although the underlying mechanism governing this decline is not fully understood.  This study aimed to elucidate the reason for the decline of NNI under water-limiting conditions and to provide insights into the accurate utilization of NNI for assessing crop N status under different water–N interaction treatments.  Rainout shelter experiments were conducted over three growing seasons from 2018 to 2021 under different N (75 and 225 kg N ha–1, low N and high N) and water (120 to 510 mm, W0 to W3) co-limitation treatments.  Plant N accumulation, shoot biomass (SB), plant N concentration (%N), soil nitrate-N content, actual evapotranspiration (ETa), and yield were recorded at the stem elongation, booting, anthesis and grain filling stages.  Compared to W0, W1 to W3 treatments exhibited NNI values that were greater by 10.2 to 20.5%, 12.6 to 24.8%, 14 to 24.8%, and 16.8 to 24.8% at stem elongation, booting, anthesis, and grain filling, respectively, across the 2018–2021 seasons.  This decline in NNI under water-limiting conditions stemmed from two main factors.  First, reduced ETa and SB led to a greater critical N concentration (%Nc) under water-limiting conditions, which contributed to the decline in NNI primarily under high N conditions.  Second, changes in plant %N played a more significant role under low N conditions.  Plant N accumulation exhibited a positive allometric relationship with SB and a negative relationship with soil nitrate-N content under water-limiting conditions, indicating co-regulation by SB and the soil nitrate-N content.  However, this regulation was influenced by water availability.  Plant N accumulation sourced from the soil nitrate-N content reflects soil N availability.  Greater soil water availability facilitated greater absorption of soil nitrate-N into the plants, leading to a positive correlation between plant N accumulation and ETa across the different water–N interaction treatments.  Therefore, considering the impact of soil water availability is crucial when assessing soil N availability under water-limiting conditions.  The findings of this study provide valuable insights into the factors contributing to the decline in NNI among different water–N interaction treatments and can contribute to the more accurate utilization of NNI for assessing winter wheat N status.


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A genome-wide association study and transcriptome analysis reveal the genetic basis for the Southern corn rust resistance in maize
Yang Wang, Chunhua Mu, Xiangdong Li, Canxing Duan, Jianjun Wang, Xin Lu, Wangshu Li, Zhennan Xu, Shufeng Sun, Ao Zhang, Zhiqiang Zhou, Shenghui Wen, Zhuanfang Hao, Jienan Han, Jianzhou Qu, Wanli Du, Fenghai Li, Jianfeng Weng
2025, 24 (2): 453-466.   DOI: 10.1016/j.jia.2023.10.039
Abstract138)      PDF in ScienceDirect      
Southern corn rust (SCR) is an airborne fungal disease caused by Puccinia polysora Underw. (Ppolysora) that adversely impacts maize quality and yields worldwide.  Screening for new elite SCR-resistant maize loci or genes has the potential to enhance overall resistance to this pathogen.  Using phenotypic SCR resistance-related data collected over two years and three geographical environments, a genome-wide association study was carried out in this work, which eventually identified 91 loci that were substantially correlated with SCR susceptibility.  These included 13 loci that were significant in at least three environments and overlapped with 74 candidate genes (B73_RefGen_v4).  Comparative transcriptomic analyses were then performed to identify the genes related to SCR infection, with 2,586 and 797 differentially expressed genes (DEGs) ultimately being identified in the resistant Qi319 and susceptible 8112 inbred lines following Ppolysora infection, respectively, including 306 genes common to both lines.  Subsequent integrative multi-omics investigations identified four potential candidate SCR response-related genes.  One of these genes is ZmHCT9, which encodes the protein hydroxycinnamoyl transferase 9.  This gene was up-regulated in susceptible inbred lines and linked to greater Ppolysora resistance as confirmed through cucumber mosaic virus (CMV)-based virus induced-gene silencing (VIGS) system-mediated gene silencing.  These data provide important insights into the genetic basis of the maize SCR response.  They will be useful for for future research on potential genes related to SCR resistance in maize.


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Optimizing crop yields while minimizing environmental impact through deep placement of nitrogen fertilizer
Lingxiao Zhu, Hongchun Sun, Liantao Liu, Ke Zhang, Yongjiang Zhang, Anchang Li, Zhiying Bai, Guiyan Wang, Xiaoqing Liu, Hezhong Dong, Cundong Li
2025, 24 (1): 36-60.   DOI: 10.1016/j.jia.2024.05.012
Abstract78)      PDF in ScienceDirect      
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.
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Development of a stable attenuated double-mutant of tobacco mosaic virus for cross-protection
Xiaojie Xu, Shaoyan Jiang, Chunju Liu, Xujie Sun, Qing Zhu, Xiuzhai Chen, Pengchao Jiang, Fenglong Wang, Yanping Tian, Xiangdong Li
2024, 23 (7): 2318-2331.   DOI: 10.1016/j.jia.2024.02.019
Abstract95)      PDF in ScienceDirect      

Tobacco (Nicotiana tabacum) and tomato (Solanum lycopersicum) are two major economic crops in China.  Tobacco mosaic virus (TMV; genus Tobamovirus) is the most prevalent virus infecting both crops.  Currently, some widely cultivated tobacco and tomato cultivars are susceptible to TMV and there is no effective strategy to control this virus.  Cross-protection can be a safe and environmentally friendly strategy to prevent viral diseases.  However, stable attenuated TMV mutants are scarce.  In this study, we found that the substitutions in the replicase p126, arginine at position 196 (R196) with aspartic acid (D), glutamic acid at position 614 (E614) with glycine (G), serine at position 643 (S643) with phenylalanine (F), or D at position 730 (D730) with S, significantly reduced the virulence and replication of TMV.  However, only the mutation of S643 to F reduced the RNA silencing suppression activity of TMV p126.  A double-mutant TMV-E614G-S643F induced no visible symptom and was genetically stable through six successive passages in tobacco plants.  Furthermore, our results showed that TMV-E614G-S643F double-mutant could provide effective protection against the wild-type TMV infection in tobacco and tomato plants.  This study reports a promising mild mutant for cross-protection to control TMV in tobacco and tomato plants.


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Increasing root-lower characteristics improves drought tolerance in cotton cultivars at the seedling stage
Congcong Guo, Hongchun Sun, Xiaoyuan Bao, Lingxiao Zhu, Yongjiang Zhang, Ke Zhang, Anchang Li, Zhiying Bai, Liantao Liu, Cundong Li
2024, 23 (7): 2242-2254.   DOI: 10.1016/j.jia.2023.07.013
Abstract123)      PDF in ScienceDirect      
Drought is an important abiotic stress factor in cotton production.  The root system architecture (RSA) of cotton shows high plasticity which can alleviate drought-related stress under drought stress (DS) conditions; however, this alleviation is cultivar dependent.  Therefore, this study estimated the genetic variability of RSA in cotton under DS.  Using the paper-based growth system, we assessed the RSA variability in 80 cotton cultivars at the seedling stage, with 0 and 10% polyethylene glycol 6000 (PEG6000) as the control (CK) and DS treatment, respectively.  An analysis of 23 above-ground and root traits in the 80 cotton cultivars revealed different responses to DS.  On the 10th day after DS treatment, the degree of variation in the RSA traits under DS (5–55%) was greater than that of CK (5–49%).  The 80 cultivars were divided into drought-tolerant cultivars (group 1), intermediate drought-tolerant cultivars (group 2), and drought-sensitive cultivars (group 3) based on their comprehensive evaluation values of drought resistance.  Under DS, the root length-lower, root area-lower, root volume-lower, and root length density-lower were significantly reduced by 63, 71, 76, and 4% in the drought-sensitive cultivars compared to CK.  Notably, the drought-tolerant cultivars maintained their root length-lower, root area-lower, root volume-lower, and root length density–lower attributes.  Compared to CK, the root diameter (0–2 mm)-lower increased by 21% in group 1 but decreased by 3 and 64% in groups 2 and 3, respectively, under DS.  Additionally, the drought-tolerant cultivars displayed a plastic response under DS that was characterized by an increase in the root-lower characteristics.  Drought resistance was positively correlated with the root area-lower and root length density-lower.  Overall, the RSA of the different cotton cultivars varied greatly under DS.  Therefore, important root traits, such as the root-lower traits, provide great insights for exploring whether drought-tolerant cotton cultivars can effectively withstand adverse environments.
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Dynamic regulation of the irrigation–nitrogen–biochar nexus for the synergy of yield, quality, carbon emission and resource use efficiency in tomato

Ping’an Zhang, Mo Li, Qiang Fu, Vijay P. Singh, Changzheng Du, Dong Liu, Tianxiao Li, Aizheng Yang
2024, 23 (2): 680-697.   DOI: 10.1016/j.jia.2023.06.006
Abstract220)      PDF in ScienceDirect      

Integrated water and fertilizer management is important for promoting sustainable development of facility agriculture, and biochar plays an important role in guaranteeing food production, as well as alleviating water shortages and the overuse of fertilizers.  The field experiment had twelve treatments and a control (CK) trial including two irrigation amounts (I1, 100% ETm; I2, 60% ETm; where ETm is the maximum evapotranspiration), two nitrogen applications (N1, 360 kg ha–1; N2, 120 kg ha–1) and three biochar application levels (B1, 60 t ha–1; B2, 30 t ha–1 and B3, 0 t ha–1).  A multi-objective synergistic irrigation–nitrogen–biochar application system for improving tomato yield, quality, water and nitrogen use efficiency, and greenhouse emissions was developed by integrating the techniques of experimentation and optimization.  First, a coupled irrigation–nitrogen–biochar plot experiment was arranged.  Then, tomato yield and fruit quality parameters were determined experimentally to establish the response relationships between irrigation–nitrogen–biochar dosage and yield, comprehensive quality of tomatoes (TCQ), irrigation water use efficiency (IWUE), partial factor productivity of nitrogen (PFPN), and net greenhouse gas emissions (NGE).  Finally, a multi-objective dynamic optimization regulation model of irrigation–nitrogen–biochar resource allocation at different growth stages of tomato was constructed which was solved by the fuzzy programming method.  The results showed that the application of irrigation and nitrogen to biochar promoted increase in yield, IWUE and PFPN, while it had an inhibitory effect on NGE.  In addition, the optimal allocation amounts of water and fertilizer were different under different scenarios.  The yield of the S1 scenario increased by 8.31% compared to the B1I1N2 treatment; TCQ of the S2 scenario increased by 5.14% compared to the B2I2N1 treatment; IWUE of the S3 scenario increased by 10.01% compared to the B1I2N2 treatment; PFPN of the S4 scenario increased by 9.35% compared to the B1I1N2 treatment; and NGE of the S5 scenario decreased by 11.23% compared to the B2I1N1 treatment.  The optimization model showed that the coordination of multiple objectives considering yield, TCQ, IWUE, PFPN, and NGE increased on average from 4.44 to 69.02% compared to each treatment when the irrigation–nitrogen–biochar dosage was 205.18 mm, 186 kg ha–1 and 43.31 t ha–1, respectively.  This study provides a guiding basis for the sustainable management of water and fertilizer in greenhouse tomato production under drip irrigation fertilization conditions.

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Karyotype establishment and development of specific molecular markers of Aegilops geniculata Roth based on SLAF-seq 
Yongfu Wang, Jianzhong Fan, Hong Zhang, Pingchuan Deng, Tingdong Li, Chunhuan Chen, Wanquan Ji, Yajuan Wang
2024, 23 (12): 3953-3965.   DOI: 10.1016/j.jia.2023.09.014
Abstract256)      PDF in ScienceDirect      

The constant evolution of pathogens poses a threat to wheat resistance against diseases, endangering food security.  Developing resistant wheat varieties is the most practical approach for circumventing this problem.  As a close relative of wheat, Aegilops geniculata, particularly accession SY159, has evolved numerous beneficial traits that could be applied to improve wheat.  In this study, we established the karyotype of SY159 by fluorescence in situ hybridization (FISH) using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae. geniculata accession TA2899 addition lines as a reference.  Using specific-locus amplified fragment sequencing (SLAF-seq) technology, 400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.  The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat–Ae. geniculata addition lines.  We used these specific markers on the 7Mg chromosome after classification, and successfully confirmed their suitability for studying the different chromosomes of SY159.  This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat. 

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Exogenous melatonin improves cotton yield under drought stress by enhancing root development and reducing root damage
Lingxiao Zhu, Hongchun Sun, Ranran Wang, Congcong Guo, Liantao Liu, Yongjiang Zhang, Ke Zhang, Zhiying Bai, Anchang Li, Jiehua Zhu, Cundong Li
2024, 23 (10): 3387-3405.   DOI: 10.1016/j.jia.2024.04.011
Abstract120)      PDF in ScienceDirect      
The exogenous application of melatonin by the root drenching method is an effective way to improve crop drought resistance.  However, the optimal concentration of melatonin by root drenching and the physiological mechanisms underlying melatonin-induced drought tolerance in cotton (Gossypium hirsutum L.) roots remain elusive.  This study determined the optimal concentration of melatonin by root drenching and explored the protective effects of melatonin on cotton roots.  The results showed that 50 μmol L–1 melatonin was optimal and significantly mitigated the inhibitory effect of drought on cotton seedling growth.  Exogenous melatonin promoted root development in drought-stressed cotton plants by remarkably increasing the root length, projected area, surface area, volume, diameter, and biomass.  Melatonin also mitigated the drought-weakened photosynthetic capacity of cotton and regulated the endogenous hormone contents by regulating the relative expression levels of hormone-synthesis genes under drought stress.  Melatonin-treated cotton seedlings maintained optimal enzymatic and non-enzymatic antioxidant capacities, and produced relatively lower levels of reactive oxygen species and malondialdehyde, thus reducing the drought stress damage to cotton roots (such as mitochondrial damage).  Moreover, melatonin alleviated the yield and fiber length declines caused by drought stress.  Taken together, these findings show that root drenching with exogenous melatonin increases the cotton yield by enhancing root development and reducing the root damage induced by drought stress.  In summary, these results provide a foundation for the application of melatonin in the field by the root drenching method.


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Azole selenourea disrupted the midgut and caused malformed development of Plutella xylostella 

GUO Xue-ying, HUANG Zi-hao, XIONG Lan-tu, DONG Li, HUANG Yue-kun, WEI Lin-hao, TANG Ri-yuan, WANG Zhi-lin, XU Han-hong
2023, 22 (4): 1104-1116.   DOI: 10.1016/j.jia.2022.09.001
Abstract214)      PDF in ScienceDirect      

Chemical insecticides targeting the digestive system of diamondback moth (DBM), Plutella xylostella, have not been developed.  The discovery of an insecticide with novel mode of action is a challenge for the control of DBM.  In this study, a class of selenium- and difluoromethyl-modified azoles (fluoroazole selenoureas, FASU) were designed and synthesized for the control of DBM.  Of these azoles, compound B4 showed the highest insecticidal activity against DBM.  The LC50 of third- and second-instar larvae reached 32.3 and 4.6 μg mL–1, respectively.  The midgut tissue of larvae was severely disrupted, and the larval intestinal tissue was dotted with unique red spots after treatment with compound B4.  Compound B4 led to disintegration of the peritrophic matrix, swelling of the midgut epithelium, fracture of the microvilli, and extensive leakage of cellular debris in the midgut lumen.  Surviving larvae grew very slowly, and the larval duration was significantly prolonged after exposure to compound B4 at sublethal doses (LC10, LC25 and LC50).  Furthermore, the pupation rate, emergence rate and pupae weight were significantly decreased.  Compound B4 also induced abnormal pupae, causing adults to be trapped in the cocoon or failure to fly due to twisted wings.  These results demonstrated that FASU could reduce the population of DBM in sublethal doses.  FASU is the first synthetic insecticidal lead compound that has been shown to disrupt the midgut tissue of the larvae of DBM, and its mode of action totally differs from that of commercial chemical insecticides.

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Quantification and prediction of enteric methane emissions from Chinese lactating Holstein dairy cows fed diets with different dietary neutral detergent fiber/non-fibrous carbohydrate (NDF/NFC) ratios
DONG Li-feng, JIA Peng, LI Bin-chang, WANG Bei, YANG Chun-lei, LIU Zhi-hao, DIAO Qi-yu
2022, 21 (3): 797-811.   DOI: 10.1016/S2095-3119(21)63825-X
Abstract317)      PDF in ScienceDirect      
Methane (CH4) emissions from ruminant production are a significant source of anthropogenic greenhouse gas production, but few studies have examined the enteric CH4 emissions of lactating dairy cows under different feeding regimes in China.  This study aimed to investigate the influence of different dietary neutral detergent fiber/non-fibrous carbohydrate (NDF/NFC) ratios on production performance, nutrient digestibility, and CH4 emissions for Holstein dairy cows at various stages of lactation. It evaluated the performance of CH4 prediction equations developed using local dietary and milk production variables compared to previously published prediction equations developed in other production regimes.  For this purpose, 36 lactating cows were assigned to one of three treatments with differing dietary NDF/NFC ratios: low (NDF/NFC=1.19), medium (NDF/NFC=1.54), and high (NDF/NFC=1.68).  A modified acid-insoluble ash method was used to determine nutrient digestibility, while the sulfur hexafluoride technique was used to measure enteric CH4 emissions.  The results showed that the dry matter (DM) intake of cows at the early, middle, and late stages of lactation decreased significantly (P<0.01) from 20.9 to 15.4 kg d–1, 15.3 to 11.6 kg d–1, and 16.4 to 15.0 kg d–1, respectively, as dietary NDF/NFC ratios increased.  Across all three treatments, DM and gross energy (GE) digestibility values were the highest (P<0.05) for cows at the middle and late lactation stages.  Daily CH4 emissions increased linearly (P<0.05), from 325.2 to 391.9 kg d–1, 261.0 to 399.8 kg d–1, and 241.8 to 390.6 kg d–1, respectively, as dietary NDF/NFC ratios increased during the early, middle, and late stages of lactation.  CH4 emissions expressed per unit of metabolic body weight, DM intake, NDF intake, or fat-corrected milk yield increased with increasing dietary NDF/NFC ratios.  In addition, CH4 emissions expressed per unit of GE intake increased significantly (P<0.05), from 4.87 to 8.12%, 5.16 to 9.25%, and 5.06 to 8.17% respectively, as dietary NDF/NFC ratios increased during the early, middle, and late lactation stages.  The modelling results showed that the equation using DM intake as the single variable yielded a greater R2 than equations using other dietary or milk production variables.  When data obtained from each lactation stage were combined, DM intake remained a better predictor of CH4 emissions (R2=0.786, P=0.026) than any other variables tested.  Compared to the prediction equations developed herein, previously published equations had a greater root mean square prediction error, reflecting their inability to predict CH4 emissions for Chinese Holstein dairy cows accurately.  The quantification of CH4 production by lactating dairy cows under Chinese production systems and the development of associated prediction equations will help  establish regional or national CH4 inventories and improve mitigation approaches to dairy production.

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Weaning methods affect ruminal methanogenic archaea composition and diversity in Holstein calves
DONG Li-feng, MA Jun-nan, TU Yan, DIAO Qi-yu
2019, 18 (5): 1080-1092.   DOI: 10.1016/S2095-3119(18)62120-3
Abstract184)      PDF in ScienceDirect      
The objective of the present study was to examine the effect of different weaning methods on the ruminal methanogenic archaea composition and diversity in Holstein calves.  Thirty-six newborn Holstein bull calves were assigned to 1 of 3 treatments: (1) conventional weaning (d 56) and fed a high proportion of solid feed (CWS); (2) conventional weaning (d 56) and fed a high proportion of liquid feed (CWL); (3) early weaning (d 42) and fed with a high proportion of solid feed (EWS).  High-throughput sequencing of the methyl coenzyme M reductase (mcrA) gene, which encodes the α-subunit of methyl coenzyme M reductase - the enzyme that catalyzes the final step in methanogenesis was used to determine the composition and diversity of rumen methanogens.  No significant difference (P>0.05) was observed for operational taxonomic units (OTUs) or richness indices, but diversity indices increased (P<0.05) for calves fed high dietary solids.  Predominant families across the three treatments were Methanobacteriaceae, Thermoplasmataceae and Methanomassiliicoccaceae.  Calves in the EWS treatment had a higher (P<0.05) relative abundance of Methanobrevibacter sp. strain AbM4 and Methanosphaera stadtmanae, while calves in the CWL treatment had a higher (P<0.05) abundance of Methanosphaera sp. strain SM9.  A positive (P<0.05) relationship was identified between butyrate and Methanobrevibacter sp. strain AbM4.  In conclusion, the composition and diversity of methanogens in the rumen of Holstein calves varied under the different weaning methods.  This study identified a positive relationship between butyrate and Methanobrevibacter sp. strain AbM4, potentially reflecting correlations between ruminal fermentation variables and methanogenesis function.  These in-depth analyses provide further understanding of weaning methods for intensified production systems. 
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The PhoR/PhoP two-component system regulates fengycin production in Bacillus subtilis NCD-2 under low-phosphate conditions
GUO Qing-gang, DONG Li-hong, WANG Pei-pei, LI She-zeng, ZHAO Wei-song, LU Xiu-yun, ZHANG Xiao-yun, MA Ping
2018, 17 (01): 149-157.   DOI: 10.1016/S2095-3119(17)61669-1
Abstract717)      PDF in ScienceDirect      
Bacillus subtilis strain NCD-2 is an excellent biocontrol agent for plant soil-borne diseases, and the lipopeptide fengycin is one of the active antifungal compounds in strain NCD-2.  The regulator phoP and its sensor kinase PhoR compose a two-component system in B. subtilis.  In this study, the phoR- and phoP-knockout mutants were constructed by in-frame deletion and the role of PhoR/phoP on the production of fengycin was determined.  Inactivation of phoR or phoP in  B. subtilis decreased its inhibition ability against Botrytis cinerea growth in vitro compared to the strain NCD-2 wild type.  The lipopeptides were extracted from strain NCD-2 wild type and its mutant strains by hydrochloric acid precipitate, and the lipopeptides from phoR-null mutant or phoP-null mutant almost lost the inhibition ability against B. cinerea growth compared to the lipopeptides from strain NCD-2 wild type.  Fast protein liquid chromatography (FPLC) analysis of the lipopeptides showed that inactivation of phoR or phoP genes reduced the production of fengycin by strain NCD-2.  The fengycin production abilities were compared for bacteria under low-phosphate medium (LPM) and high-phosphate medium (HPM), respectively.  Results indicated that the regulation of fengycin production by the PhoR/PhoP two-component system occurred in LPM but not in HPM.  Reverse transcriptional-PCR confirmed that the fengycin synthetase gene fenC was positively regulated by phoP when cultured in LPM.  All of these characteristics could be partially restored by complementation of intact phoR or phoP gene in the mutant.  These data indicated that the PhoR/PhoP two-component system greatly regulated fengycin production and antifungal ability in B. subtilis NCD-2 mainly under low-phosphate conditions.
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Effects of different feeding methods and space allowance on the growth performance, individual and social behaviors of Holstein calves
DONG Li-feng, XU Xian-cha, ZHANG Nai-feng, TU Yan, DIAO Qi-yu
2017, 16 (06): 1375-1382.   DOI: 10.1016/S2095-3119(16)61484-3
Abstract666)      PDF in ScienceDirect      
The importance of nutrient provisions and weaning methods for calves has been well established over the past few years, while as increasing interest has focused on contribution of animal behavior and their overall performance in production regimes.  The present study investigated the effects of feeding methods and space allowance on growth performance, individual and social behaviors in Holstein calves.  Twenty-four Chinese Holstein male and female calves were allocated to either an individual or group of 6 and fed either with a bucket or a teat.  Milk replacer, calf starter, and Chinese wildrye were offered during the experiment.  A fecal index used in the present study was defined as the total fecal scores/total number of calves in each treatment.  The results showed that there was no significant difference among the 4 treatments in terms of feed intake, body weight, average daily gain, and fecal index.  For the feeding behaviors, the ingesting milk time and ingesting milk rate were significantly affected by space allowance, while the feeding methods showed a significant influence on the bunting behavior of the calves.  There was no significant difference among the 4 treatments in terms of licking fixtures, self-grooming, and lying down behaviors, irrespective of the feeding method or space allowance.  However, sucking an empty bucket or the teat was significantly affected by the feeding method.  Several selected group behaviors were examined in the present study, and similar values for sniffing the other calves, social grooming, and cross-sucking behaviors were observed.  Overall, the present study demonstrated that different feeding methods and space allowances had a significant effect on the feeding behavior of calves, while the feed intake, growth performance, health condition, individual and group social behaviors were not significantly influenced.  Furthermore, under intensified production systems, Holstein calves raised in a group may obtain a similar production performance, thus reducing management input and profitability compared with those kept individually.  However, there may be competition during the feeding period.
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Cytogenetic characterization and molecular marker development of a novel wheat-Thinopyrum ponticum 5E (5D) disomic substitution line with resistance to powdery mildew and stripe rust 
Xiaofang Cheng, Yi Xiao, Luhui Wang, Xiaoying Yang, Pingchuan Deng, Jixin Zhao, Changyou Wang, Chunhuan Chen, Tingdong Li, Wanquan Ji
DOI: 10.1016/j.jia.2024.04.012 Online: 10 May 2024
Abstract30)      PDF in ScienceDirect      
Thinopyrum ponticum (2n=10x=70), a wild relative of common wheat (Triticum aestivum L.), is considered an invaluable genetic resource for wheat improvement due to its abundance of genes that confer resistance to biotic and abiotic stresses.  This study focused on the CH97 line, derived from the BC1F7 progeny of a cross between wheat cv. 7182 and Th. ponticum.  Cytological evidence showed that CH97 has 42 chromosomes, forming 21 bivalents at meiotic metaphase I, with the bivalents subsequently separating and moving to opposite poles during meiotic anaphase I.  Through a combination of FISH (fluorescence in situ hybridization), GISH (genomic in situ hybridization), mc-GISH (multicolor genomic in situ hybridization), and liquid array analysis, it was determined that CH97 comprises 40 wheat chromosomes and two alien chromosomes from the Ee genome of Th. ponticum, featuring the absence of a pair of 5D chromosomes and variations in 1B, 6B, and 7B chromosomes.  These findings confirm that CH97 is a stable wheat-Th. ponticum 5E (5D) alien disomic substitution line.  Inoculation experiments revealed that CH97 exhibits high resistance to wheat powdery mildew and stripe rust throughout the growth period, in contrast to the highly susceptible common wheat parent 7182.  Compared to 7182, CH97 displayed improvements in spikelets per spike, thousand-kernel weight, and kernel length.  Additionally, utilizing SLAF-seq technology, chromosome 5E-specific molecular markers were developed and validated, achieving a 33.3% success rate, which facilitates marker-assisted selection to enhance disease resistance in wheat.  Overall, the CH97 substitution line, with its resistance to diseases and improved agronomic traits represents valuable new germplasm for wheat chromosome engineering and breeding.
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Alleviating vanadium-induced stress on rice growth using phosphorus-loaded biochar
Jianan Li, Weidong Li, Wenjie Ou, Waqas Ahmed, Mohsin Mahmood, Ahmed S.M. Elnahal, Haider Sultan, Zhan Xin, Sajid Mehmood
DOI: 10.1016/j.jia.2023.12.022 Online: 03 January 2024
Abstract41)      PDF in ScienceDirect      
The current investigation aimed at evaluating the impact of as-is biochar (BC) and phosphorous (P)-loaded biochar (PBC) (3%) on the growth and biochemical characteristics of rice under exposure to vanadium (V) (60 mg L-1).  The results indicate that rice plants exposed to V-only treatment experienced a decline in growth parameters.  Conversely, the inclusion of BC and PBC caused a noteworthy increase in physiological traits.  PBC performed well in stress environments, specifically, shoot and root fresh weight increased by 82.86 and 53.33%, respectively, when compared to V-only treatment.  Additionally, the SPAD chlorophyll of the shoot increased by 13.05% than V-amended plants.  Moreover, the antioxidant enzyme traits of plant shoot and root, such as superoxide dismutase (SOD by 56.11&117.35%), catalase (CAT by 34.19&35.77%), and peroxidase (POD 25.90&18.74%), exhibited significant increases when compared to V-only amended plants, respectively.  These findings strongly suggest that the application of BC and PBC can trigger biochemical pathways that facilitate biomass accumulation in meristematic cells.  However, further investigations are required to elucidate the underlying mechanisms responsible for this growth promotion.
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Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22
Tiantian Chen, Lei Li, Dan Liu, Yubing Tian, Lingli Li, Jianqi Zeng, Awais Rasheed, Shuanghe Cao, Xianchun Xia, Zhonghu He, Jindong Liu, Yong Zhang
DOI: 10.1016/j.jia.2023.12.039 Online: 19 January 2024
Abstract42)      PDF in ScienceDirect      
Black point, a black discoloration of the grain embryo, downgrades the grain quality and commodity grade.  Identification of the underlying genetic loci can facilitate the improvement of black point resistance in wheat.  Here, 262 recombinant inbred lines (RILs) from the cross of Zhongmai 578/Jimai 22 were evaluated for black point reaction in five environments.  A high-density genetic linkage map of the RIL population was constructed with the wheat 50K single nucleotide polymorphism (SNP) array.  Six stable QTLs for black point resistance, QBp.caas-2A, QBp.caas-2B1, QBp.caas-2B2QBp.caas-2D, QBp.caas-3A and QBp.caas-5B were detected, explaining 2.1-28.8% of the phenotypic variances.  The resistance alleles of QBp.caas-2B1 and QBp.caas-2B2 were contributed by Zhongmai 578 while the others were from Jimai 22.  QBp.caas-2B2, QBp.caas-2D and QBp.caas-3A are overlapped with previously reported loci, whereas QBp.caas-2AQBp.caas-2B1 and QBp.caas-5B are likely to be new.  Five KASP markers, Kasp_2A_BP, Kasp_2B1_BP, Kasp_2B2_BP, Kasp_3A_BP and Kasp_5B_BP were validated in a natural population of 165 cultivars.  The findings provide useful QTL and molecular markers for improvement of black point in wheat resistance in marker-assisted breeding.
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A rescued virus from the infectious clone of a PRRSV NADC34-like strain exhibits high pathogenicity for nursery pigs
Zhenbang Zhu, Zhengqin Ye, Wenqiang Wang, Yanhua Li, Zhe Sun, Xiuling Yu, Kegong Tian, Xiangdong Li
DOI: 10.1016/j.jia.2024.08.015 Online: 23 August 2024
Abstract45)      PDF in ScienceDirect      

NADC34-like porcine reproductive and respiratory syndrome virus (PRRSV) has been circulating in China for several years and became the dominant field strain in some provinces. Current commercial vaccines could not provide complete cross-protection to NADC34-like PRRSV infection, which led to huge economic losses on pig farms. Co-infections of NADC34-like PRRSV with some other PRRSV strains are commonly found in many clinical cases, and successful isolation of NADC34-like PRRSV strain from the clinical samples has been a challenge to study its biological characters and perform animal experiments to evaluate its pathogenicity. In this study, we constructed a NADC34-like PRRSV infectious clone derived from the isolated JS2021NADC34 PRRSV strain using the reverse genetics technique and investigated its virulence and pathogenicity for nursery pigs. The rescued (rNADC34) strain could proliferate well in porcine alveolar macrophages (PAMs), and the viral copy number and titers were comparable to parental strain. For pathogenicity, the rNADC34 strain-infected pigs showed high body temperature and body weight loss. The histopathological results presented interstitial pneumonia and severe hemorrhage, infiltration of neutrophils and lymphocyte in lungs, lymph nodes, and tonsils. The viral proteins were also detectable in rNADC34 strain-infected pigs using immunohistochemistry staining. Moreover, the trends of PRRSV-specific antibody and viremia in PRRSV rNADC34-infected pigs were similar with the parental strain-infected pigs. These data indicated that rNADC34 strain manifested strong virulence and high pathogenicity for nursery pigs. 

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QTL mapping of maize plant height based on a population of doubled haploid lines using UAV LiDAR high-throughput phenotyping data
Xin Zhang, Jidong Zhang, Yunling Peng, Xun Yu, Lirong Lu, Yadong Liu, Yang Song, Dameng Yin, Shaogeng Zhao, Hongwu Wang, Xiuliang Jin, Jun Zheng
DOI: 10.1016/j.jia.2024.09.004 Online: 12 September 2024
Abstract37)      PDF in ScienceDirect      

Maize (Zea mays L.) is a globally significant crop that plays a crucial role in feeding the growing global population.  Among its various traits, plant height is particularly important as it affects yield, lodging resistance, ecological adaptability, and other important factors.  Traditional methods for measuring plant height often lack cost-efficiency and accuracy.  In this study, we employed a light detection and ranging (LiDAR) sensor mounted on an unmanned aerial vehicle (UAV) to collect point cloud data from 270 doubled haploid (DH) lines.  This innovative application of UAV-based LiDAR technology was explored for high-throughput phenotyping in maize breeding.  We constructed high-density genetic maps and assessed plant height at both single-plant and row scales across multiple developmental stages and genetic backgrounds.  Our findings revealed that for many varieties and small areas, single-plant-scale estimation accuracy was superior to row-scale estimation, with an R² of 0.67 versus 0.56 and an RMSE of 0.12 m vs. 0.17 m, respectively.  Two high-density genetic maps were constructed based on SNP markers.  In Sanya and Xinxiang, the F1DH and F2DH populations identified 12 and 20 QTLs (quantitative trait loci) for plant height, respectively.  The study successfully identified and validated QTLs associated with plant height, revealing novel genetic loci and candidate genes.  This research highlights the potential of UAV-based remote sensing to advance precision agriculture by enabling efficient, large-scale phenotyping and gene discovery in maize breeding programs.

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Magnesium supply is vital for improving fruit yield, fruit quality and magnesium balance in citrus orchards with increasingly acidic soil
Yuheng Wang, Furong Kang, Bo Yu, Quan Long, Huaye Xiong, Jiawei Xie, Dong Li, Xiaojun Shi, Prakash Lakshmanan, Yueqiang Zhang, Fusuo Zhang
DOI: 10.1016/j.jia.2024.12.025 Online: 25 December 2024
Abstract25)      PDF in ScienceDirect      

Magnesium (Mg) deficiency is becoming a limiting factor for citrus production in acid soils of subtropical and tropical zones. It is speculated that soil Mg leaching and thereby its imbalance may be a major cause of yield decline, yet Mg deficiency in citrus receives little attention. A two-year field experiment was therefore conducted to quantify soil Mg leaching in a typical citrus orchard in China fertilized with varying levels of Mg (0 (Mg0), 45 (Mg45), 90 (Mg90) and 180 (Mg180) kg MgO ha-1 yr-1). Results showed that Mg application significantly increased citrus fruit yield by 4.1-16.4% compared with where MgO was not added. The average amount of soil Mg leaching was 65.7 kg ha-1 yr-1 where no Mg fertilizer was added, while it reached up to 91.3 kg Mg ha-1 yr-1 where MgO was added at the rate of 180 kg ha-1. Over the 4 treatments, Mg leaching accounted for 12.1-42.4% of the applied Mg fertilizer. Mg leaching and its removal through harvested fruits resulted in an orchard soil Mg balance of -69.9, -51.1, -27.4 and 10.9 kg ha-1 in the Mg0, Mg45, Mg90 and Mg180, treatments, respectively. The pH values of leachate from the acid soil were alkaline and it contained higher amounts of calcium and potassium than that of Mg. Considering the high leaching of Mg from the acid soils of citrus orchards, applications of Mg fertilizer or Mg-fortified soil conditioner are vital to sustain soil Mg balance, high fruit yield and fruit quality in citrus production systems in humid subtropical regions.

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Development and application of a double-antigen Sandwich ELISA using capsid protein to detect multispecies antibodies against porcine circovirus type 3
Dexin Li, Junhua Deng, Yufang Li, Liying Hao, Wenqiang Pang, Zhendong Zhang, Yi Yang, Xiangdong Li, Kegong Tian
DOI: 10.1016/j.jia.2025.03.016 Online: 22 March 2025
Abstract7)      PDF in ScienceDirect      
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