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PEX5-mediated modulation of apoptotic pathways in response to Newcastle disease virus infection
Hui Jiang, Yanfeng Liu, Ying Liao, Xusheng Qiu, Lei Tan, Cuiping Song, Chan Ding, Yingjie Sun
2026, 25 (6): 2523-2533.   DOI: 10.1016/j.jia.2024.08.016
Abstract74)      PDF in ScienceDirect      

Newcastle disease virus (NDV) is a highly lethal and contagious viral pathogen, and it is also a potent oncolytic virus that selectively replicates in tumor cells.  NDV demonstrates high replication efficiency in avian and tumor cells, causing various types of cell death, including ferroptosis, necrosis, apoptosis and autophagic cell death, with apoptosis being the most thoroughly studied.  Organelles play critical and distinctive roles in the regulation and execution of apoptosis.  However, the involvement of peroxisomes, an important organelle that regulates redox balance and lipid biosynthesis, in virus-induced apoptosis remains unclear.  Our findings reveal that NDV infection promotes the downregulation of several peroxisome biogenesis factors (PEXs) at the mRNA level.  Peroxisomal biogenesis factor 5 (PEX5), a critical peroxisomal shuttle protein, was identified to be significantly downregulated at both the mRNA and protein levels.  Further, gain- and loss-of-function experiments demonstrated the negative regulation of NDV-induced apoptosis by PEX5.  In addition, PEX5 inhibits NDV-induced apoptosis by regulating the anti-apoptotic protein B-cell lymphoma-2 (Bcl-2) expression.  These findings reveal a novel mechanism by which NDV-induced apoptosis is modulated through the downregulation of PEXs, particularly PEX5, shedding light on the potential role of peroxisome in apoptosis regulation in response to virus infection.

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Multi-dimensional comprehensive evaluation reveals the quality trait characteristics of wheat cultivars in the Huang-Huai wheat region of China
Min Xiong, Chuxin Wang, Xinrui Liang, Jiawen Yu, Tingting Liu, Bin Peng, Xiaoxuan Du, Tingyu Yang, Gongneng Feng, Qiaoquan Liu, Qianfeng Li
2026, 25 (6): 2299-2313.   DOI: 10.1016/j.jia.2024.12.029
Abstract62)      PDF in ScienceDirect      

Wheat (Triticum aestivum L.) quality is a major focus of wheat breeding, which is influenced by multiple factors. The Huang-Huai wheat region, one of the main wheat-producing areas in China, provides favourable conditions for cultivating wheat cultivars with strong-gluten and medium-strong-gluten. In this study, a systematic assessment of seven crucial quality traits and important genetic loci (Glu-1 and Sec-1) in 436 wheat cultivars in the Huang-Huai wheat region of China by principal component analysis (PCA) and fuzzy comprehensive evaluation (FCE) methods showed that the stability time (ST), stretch area (SA), and maximum resistance (MAXR) were identified as three key factors, which significantly influenced wheat quality. Glu-1 and Sec-1 primarily impacted these three traits and subsequently influenced wheat quality. Compared to Glu-A1 and Glu-B1, Glu-D1 has a more significant impact on the comprehensive evaluation value D, principal components PC1-PC3, and the main traits ST, SA and MAXR of PC1. Wheat cultivars carrying the high-molecular-weight glutenin subunit (HMW-GS) Dx5+Dy10 exhibited a notable improvement in ST, SA, and MAXR traits compared with those carrying HMW-GS Dx2+Dy12, suggesting that Dx5+Dy10 may enhance wheat quality by improving ST, SA, and MAXR. By combining the results of D value, GYT (genotype by yield×trait) index, and HMW-GS score, 20 high-quality and high yield wheat cultivars were identified, which can be used as elite parents for wheat quality breeding.

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Multi-omics approach reveals the contribution of brassinosteroids to salt tolerance for seed germination in rice
Min Xiong, Chuxin Wang, Xinrui Liang, Jiawen Yu, Tingting Liu, Bin Peng, Xiaoxuan Du, Tingyu Yang, Gongneng Feng, Qiaoquan Liu, Qianfeng Li
2026, 25 (6): 2288-2298.   DOI: 10.1016/j.jia.2025.08.008
Abstract107)      PDF in ScienceDirect      

Seed germination, which initiates the plant life cycle, exhibits high sensitivity to salt stress, a significant environmental factor limiting rice production.  Brassinosteroid (BR), a growth-promoting phytohormone, mitigates various stresses including salt, drought, and extreme temperatures in rice.  However, the mechanisms by which BR alleviates salt stress during seed germination remain inadequately characterized.  This study demonstrates that seed-specific overexpression of OsDWF4, a rate-limiting gene in BR biosynthesis, enhances rice germination.  The DWF4-OX lines, which increase endogenous BR content in seeds, promote germination under salt stress, corroborating results obtained through exogenous BR application.  Antioxidant enzyme analyses demonstrate that BR enhances the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT).  Metabolomic analysis reveals that BR mitigates salt stress primarily through the biosynthesis of phenylpropanoids and secondary metabolites.  Transcriptomic analysis indicates that both endogenous and exogenous BR share five co-regulated target genes and utilize a common biosynthetic pathway for stilbenoids, diarylheptanoids, and gingerols.  These findings confirm BR's capacity to enhance seed germination under salt stress and identify several BR-mediated targets for developing salt-tolerant rice varieties suitable for direct seeding cultivation.

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Core germplasm construction of tea plant populations based on genome-wide SNP and catechins in Shaanxi Province, China
Xinyu Wang, Xiufeng Li, Dan Chen, Jingwen Gao, Shuangqian Hao, He Zhang, Ziyan Zhao, Mengwei Shen, Huirui Chen, Fuqiang Qi, Keyi Zhang, Haozhe Zhou, Yanjun Xi, Jie Zhou, Youben Yu, Qingshan Xu
2026, 25 (5): 1927-1938.   DOI: 10.1016/j.jia.2025.03.024
Abstract86)      PDF in ScienceDirect      

Genetic diversity is crucial to genetic research and crop breeding, and core collections are important resources for capturing this diversity.  Recently, the core germplasm of tea plants was constructed mainly based on phenotypic data or molecular markers; however, the effective construction of core germplasm resources for plant breeding programs requires consideration of multiple aspects.  In this study, we collected 320 tea germplasm resources and analyzed their single-nucleotide polymorphisms (SNPs) and metabolite data.  Abundant genetic diversity in tea plants was inferred from the mean values of observed heterozygosity (Ho=0.340), expected heterozygosity (He=0.327), minor allele frequency (MAF=0.229), and polymorphic information content (PIC=0.268), based on the data from 2,118,060 high-quality SNP markers.  A mean genetic diversity index (H´) value of 1.902 suggested significant metabolic variation.  The 320 tea samples were categorized into six groups based on phylogenetic analysis, reflecting the influence of geographical origins on genetic diversity.  Based on the genetic and metabolic data, a preliminary core collection of 106 accessions was developed to effectively represent most of the original panel’s molecular, metabolic, population, and regional diversity.  Genome-wide association studies of the core panel successfully replicated the marker-trait associations found in the original panel.  This study contributes to the conservation and management of tea plant germplasm.

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Identification of a pleiotropic QTL and development of KASP markers for 100-pod weight, 100-seed weight, and shelling percentage in peanut
Xiukun Li, Jing Hao, Hongtao Deng, Shunli Cui, Li Li, Mingyu Hou, Yingru Liu, Lifeng Liu
2026, 25 (3): 893-902.   DOI: 10.1016/j.jia.2024.06.013
Abstract189)      PDF in ScienceDirect      

High yield remains the primary objective of peanut breeding.  Key yield components, 100-pod weight (HPW), 100-seed weight (HSW), and shelling percentage (SP), are critical determinants of overall productivity.  This study aimed to construct a high-density linkage map using resequencing data from recombinant inbred lines (RILs) derived from a cross between ‘Silihong’ (Arachis hypogaea var. fastigiate) and ‘Jinonghei 3’ (Ahypogaea var. hypogaea).  The resulting map comprised 4,499 bins distributed across 20 chromosomes, spanning a total length of 1,712.32 cM with an average inter-marker distance of 0.38 cM.  A total of 46 quantitative trait loci (QTLs) were identified across three environments.  Major QTLs, including qHPW5.2, qHPW18.1, qSP7.1, qSP8.1, qSP8.2, qSP18.1, and qSP18.2, explained phenotypic variation (PVE) of 12.04, 11.41, 16.53, 24.17, 10.49, 10.82, and 29.89%, respectively.  Fourteen QTLs detected across multiple environments were considered stable.  Notably, one QTL region (qHPW7, qHSW7.1, and qSP7) was associated with all three traits, accounting for PVE values of 8.91, 9.04, and 16.53% for HPW, HSW, and SP, respectively.  To validate the accuracy of QTL mapping, a genome-wide association study (GWAS) was conducted using the US mini-core collection.  Across two environments, 115 single-nucleotide polymorphisms (SNPs) were significantly associated with HPW, HSW, and SP in the association panel.  Six SNPs were linked to two traits, explaining an average phenotypic variation of 13.84%.  Integration of both mapping populations revealed that AX-176802178, detected on chromosome 7 in the association panel and associated with SP, was located within the confidence interval of QTL qSP7 defined by the recombined inbred lines (RIL) population.  Furthermore, three KASP markers were developed and validated in peanut landraces and cultivated varieties.  These findings provide valuable insights into the genetic architecture underlying HPW, HSW, and SP, and offer useful molecular tools for marker-assisted selection in peanut breeding programs.

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Unbalanced lipid metabolism in anther, especially the disorder of the alpha-linolenic acid metabolism pathway, leads to cotton male sterility
Lihong Ma, Pengtao Wang, QianHao Zhu, Xinqi Cheng, Tao Zhang, Xinyu Zhang, Huaguo Zhu, Zuoren Yang, Jie Sun, Feng Liu
2026, 25 (2): 610-623.   DOI: 10.1016/j.jia.2024.07.036
Abstract248)      PDF in ScienceDirect      


Recent studies have shown that lipid metabolism is a key factor affecting anther development and male fertility.  However, how plants regulating the metabolic balance of multiple lipids to ensure proper anther development and male fertility remains unclear.  Analyzing lipid molecules related to anther fertility and genes responsible for their biosynthesis is crucial for understanding the physiological significance of lipid metabolism in crop fertility.  In this study, we compared the transcriptome and the composition and content of lipids in anthers of two upland cotton (Gossypium hirsutum) materials, Shida 98 (WT) and its nearly-isogenic male sterile line Shida 98A (MS).  Transcriptomics analysis identified many differentially expressed genes (DEGs) between the two materials, with the genes of the alpha-linolenic acid metabolism pathway being the most significantly associated with the male sterility phenotype.  Investigations on lipids revealed that the MS anthers over-accumulated free fatty acids (FFAs), phosphatidic acid (PA), mono- and di-galactosyldiacylglycerol (MGDG and DGDG), and had a decreased content of triacylglycerol (TAG), which was closely related to the abnormal metabolism of alpha-linolenic acid (C18:3); therefore, the major lipids containing C18:3-acyl chains, such as PA, MGDG, DGDG, and TAG, are proposed to play a major role in cotton anther development.  We also showed that an excessive level of MGDG and DGDG caused jasmonic acid (JA) overaccumulation in MS anthers, which in turn inhibited the expression of GhFAD3 and consequently reduced the C18:3 content, presumably via a feedback regulation mechanism, ultimately affecting plant fertility.  Together, our results revealed the importance of a balanced lipid metabolism in regulating the development of cotton anther and pollen and consequently male fertility.


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Development of a smart device android-based decision support system for controlling non-point source nitrogen and phosphorus pollution in an agricultural catchment
Meihui Wang, Wenqian Jiang, Yuxi Fu, Yi Wang, Xinliang Liu, Jianlin Shen, Feng Liu, Yong Li
2026, 25 (2): 565-576.   DOI: 10.1016/j.jia.2025.03.023
Abstract109)      PDF in ScienceDirect      


Intervention strategies to control non-point source nitrogen (N) and phosphorus (P) pollution in agriculture are expensive and there is a trade-off between engineering cost and treatment effectiveness.  Implementing strategies often result in unsatisfactory outcomes and massive engineering costs when managing diffusive pollution in agricultural catchments.  To address this issue, this paper proposes a robust, handy, catchment N&P decision support system (CNPDSS), an Android-based smartphone system integrated with a web-based geographic information system (GIS).  The CNPDSS aims to provide artificial intelligence-driven decisions that minimize N&P loadings and engineering costs for mitigating pollution in agricultural catchments.  It consists of four components: a general user interface (GUI), GIS, N&P pollution modeling (NPPM), and a DSS.  The CNPDSS simplifies the GUI and integrates GIS modules to create a user-friendly interface, enabling non-professional users to operate the system easily through intuitive actions.  The NPPM uses straightforward empirical models to predict N&P loadings, enhancing efficiency by avoiding excessive parameters.  Taking into account the N&P movement pathway in the catchment, the DSS incorporates three control measures: source reduction in farmland (before migration stage), process retention by ecological ditch (midway transport stage), and down-end purification by constructed wetland (waterbody discharge stage), to formulate a comprehensive ternary controlling strategy.  To optimize the cost-effectiveness of any proposed N&P control strategies for sub-catchments, a differential evolution algorithm (DEA) is employed in CNPDSS to carry out a dual-objective decision-making optimization computation.  In this study, the CNPDSS is applied to a case study in an agricultural catchment in Central China to develop the most cost-effective ternary N&P control strategies that ensure the catchment water quality within Criterion III of the Chinese Surface Water Quality Standard GB3838-2002 is met (total N concentration≤1.0 mg L−1 and total P concentration≤0.2 mg L−1).  Our results demonstrate that the CNPDSS is feasible and also possesses an adaptive design and flexible architecture to enable its generalization and extension to support strong hands-on applications in other catchments.


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Surface soil organic carbon losses in Dongting Lake floodplain as evidenced by field observations from 2013 to 2022
Liyan Wang, Buqing Wang, Zhengmiao Deng, Yonghong Xie, Tao Wang, Feng Li, Shao’an Wu, Cong Hu, Xu Li, Zhiyong Hou, Jing Zeng Ye’ai Zou, Zelin Liu, Changhui Peng, Andrew Macrae
2026, 25 (2): 436-447.   DOI: 10.1016/j.jia.2025.02.007
Abstract204)      PDF in ScienceDirect      
In floodplain wetlands, alterations in hydrological patterns resulting from climate change and human activities could potentially diminish the carbon sequestration capacity of the soils, thereby having a negative impact on global climate change.  However, the magnitude of the influence of hydrological regime change on soil carbon remains inadequately monitored.  To address this research gap, we collected 306 upper layer (0–20 cm) soil samples from the Dongting Lake floodplain between 2013 and 2022.  The random forest (RF) algorithm was used to analyze the spatial distribution of soil organic carbon (SOC) in the upper soil layer of Dongting Lake floodplain and the impact of climate and hydrological changes in the past decade on surface SOC in the East Dongting Lake area was studied.  In 2022, the SOC concentration of the Dongting Lake floodplain upper layer soil ranged from 3.34 to 17.67 g kg–1, averaging 10.43 g kg–1, with a corresponding SOC density of (2.65±0.49) kg m–2 and total SOC stock of 6.82 Tg C (2.87–13.48 Tg C).  From 2013 to 2022, the SOC concentration of the upper soil layer of the East Dongting Lake area decreased from 18.37 to 10.82 g kg–1.  This reduction could be attributed to climate and hydrological changes which reduce SOC input by reducing vegetation growth and accelerating SOC decomposition.  Above 21.4 m elevation, the amount of SOC loss increased with elevation, the loss being related to the decline in Miscanthus community biomass and greater susceptibility of higher altitude areas to climate and hydrological changes.  Our results highlight the need for strengthening wetland SOC management to increase SOC in the soils to help combat climate change.
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SlIDL6–SlHSL1/2/3 ligand-receptor pairs regulate tomato pedicel abscission
Yanyun Tu, Lina Cheng, Xianfeng Liu, Marta Hammerstad, Chunlin Shi, Sida Meng, Mingfang Qi, Tianlai Li, Tao Xu
2026, 25 (1): 118-126.   DOI: 10.1016/j.jia.2025.03.018
Abstract162)      PDF in ScienceDirect      

Flower and fruit abscission reduce crop yield, so decreasing abscission is a significant agricultural issue.  HAESA (HAE) and HAESA-like2 (HSL2) kinases and their ligand, INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide, have been confirmed to be the core elements regulating floral organ abscission in Arabidopsis thaliana.  Our earlier research revealed that SlIDL6, a homolog of IDA in tomato, functions similarly to AtIDA, regulating the abscission of tomato flower organs.  Here, we further isolated three HAESA-like homologs, SlHSL1/2/3, which are involved in tomato flower abscission.  SlHSL1/2/3 are highly expressed in the abscission zone (AZ).  The knockout mutant lines of Slhsl1, Slhsl2, and Slhsl3 showed lower flower pedicel abscission than wild type (WT).  The double mutant of Slhsl1Slhsl2, Slhsl1Slhsl3, and Slhsl2Slhsl3 further depressed abscission than each of the single mutant lines, while triple mutants Slhsl1Slhsl2Slhsl3 exhibited the lowest abscission, indicating that SlHSL1/2/3 mediated abscission is non-redundancy, at least partially.  Treating tomato pedicel explants with SlIDL6 peptide significantly accelerated pedicel abscission in WT.  However, it had little effect on the abscission rate of SlHSL1/2/3 knockout lines, indicating that SlHSL1/2/3 are the receptors of SlIDL6 in pedicel abscission.  Ethylene action inhibitor 1-methylcyclopropene (1-MCP) can significantly depress the expression of SlHSL1/2/3.  Ethylene can significantly accelerate the abscission of WT, while less abscission was found in SlHSL1/2/3 knockout lines.  Our findings indicate that SlHSL1/2/3 can act as receptors for SlIDL6 to positively regulate tomato pedicel abscission, and the abscission regulated by SlHSL1/2/3 was partially dependent on ethylene

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PDL1-dependent trans-acting siRNAs regulate lateral organ polarity development in rice
Yi Zhang, Jing You, Jun Tang, Wenwen Xiao, Mi Wei, Ruhui Wu, Jinyan Liu, Hanying Zong, Shuoyu Zhang, Jie Qiu, Huan Chen, Yinghua Ling, Fangming Zhao, Yunfeng Li, Guanghua He, Ting Zhang
2025, 24 (9): 3297-3310.   DOI: 10.1016/j.jia.2024.01.025
Abstract383)      PDF in ScienceDirect      

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.


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Genome-wide analysis of the CaYABBY family in pepper and functional identification of CaYABBY5 in the regulation of floral determinacy and fruit morphogenesis
Ke Fang, Yi Liu, Zhiquan Wang, Xiang Zhang, Xuexiao Zou, Feng Liu, Zhongyi Wang
2025, 24 (8): 3024-3039.   DOI: 10.1016/j.jia.2025.03.025
Abstract248)      PDF in ScienceDirect      

Pepper fruit is highly favored for its spicy taste, diverse flavors, and significant nutritional benefits.  The proper development of flowers and fruits directly determines the quality of pepper fruit.  The YABBY gene family exhibits diverse functions in growth and development, which is crucial to the identity of flower organs.  However, the specific functions of these genes in pepper remain unclear.  In this study, nine CaYABBY genes were identified and characterized in pepper.  Most CaYABBY genes were highly expressed in reproductive organs, albeit with varying expression patterns.  The CaYABBY5 gene, uniquely expressed in petals and carpels, has been demonstrated to modulate floral organ determinacy and fruit shape through gene silencing in pepper and ectopic expression in tomato.  Protein interaction analysis revealed an interacting protein SEPALLATA3-like protein (SEP3), exhibiting a similar expression profile to CaYABBY5.  These findings suggest that CaYABBY5 may modulate the morphogenesis of floral organs and fruits by interacting with CaSEP3.  This study provided valuable insights into the classification and function of CaYABBY genes in pepper.

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Time-course transcriptomic information reveals the mechanisms of improved drought tolerance by drought priming in wheat
Qing Li, Zhuangzhuang Sun, Zihan Jing, Xiao Wang, Chuan Zhong, Wenliang Wan, Maguje Masa Malko, Linfeng Xu, Zhaofeng Li, Qin Zhou, Jian Cai, Yingxin Zhong, Mei Huang, Dong Jiang
2025, 24 (8): 2902-2919.   DOI: 10.1016/j.jia.2024.03.081
Abstract270)      PDF in ScienceDirect      
Frequent drought events severely restrict global crop productivity, especially those occurring in the reproductive stages.  Moderate drought priming during the earlier growth stages is a promising strategy for allowing plants to resist recurrent severe drought stress.  However, the underlying mechanisms remain unclear.  Here, we subjected wheat plants to drought priming during the vegetative growth stage and to severe drought stress at 10 days after anthesis.  We then collected leaf samples at the ends of the drought priming and recovery periods, and at the end of drought stress for transcriptome sequencing in combination with phenotypic and physiological analyses.  The drought-primed wheat plants maintained a lower plant temperature, with higher stomatal openness and photosynthesis, thereby resulting in much lower 1,000-grain weight and grain yield losses under the later drought stress than the non-primed plants.  Interestingly, 416 genes, including 27 transcription factors (e.g., MYB, NAC, HSF), seemed to be closely related to the improved drought tolerance as indicated by the dynamic transcriptome analysis.  Moreover, the candidate genes showed six temporal expression patterns and were significantly enriched in several stress response related pathways, such as plant hormone signal transduction, starch and sucrose metabolism, arginine and proline metabolism, inositol phosphate metabolism, and wax synthesis.  These findings provide new insights into the physiological and molecular mechanisms of the long-term effects of early drought priming that can effectively improve drought tolerance in wheat, and may provide potential approaches for addressing the challenges of increasing abiotic stresses and securing food safety under global warming scenarios.  
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Inclusion of sorghum grain rich in condensed tannins in the diet of steers did not affect the nitrogen utilization efficiency but increased the urine nitrous oxide emissions
Biao Xie, Changfa Mao, Xu Shen, Yufeng Liu, Qingyue Liang, Guangyong Zhao
2025, 24 (4): 1296-1309.   DOI: 10.1016/j.jia.2023.11.035
Abstract188)      PDF in ScienceDirect      
The objectives of this study which included two experiments were to investigate the effects of dietary inclusion of sorghum grain rich in condensed tannins (CT) (18.9 g kg–1 dry matter (DM)) on nitrogen (N) metabolism and urine nitrous oxide (N2O) emissions of beef steers.  In experiment 1, six Limousin×Luxi crossbreed steers with an initial liveweight of (245.0±18.7) kg were used as experimental animals.  Three levels of sorghum grain, i.e., 0, 167 and 338 g kg–1 DM were included in diets as experimental treatments.  The animals and the treatments were randomly assigned to a replicated 3×3 Latin square design.  In experiment 2, static incubation technique was used to determine the N2O emissions of the urine samples collected in experiment 1.  The results of experiment 1 showed that dietary inclusion of sorghum grain linearly increased the faecal N excretion (P=0.001), the total N excretion (P=0.010) and the faecal N to N intake ratio (P=0.021), but it did not affect the N retention and the N utilization efficiency (P>0.10).  The plasma metabolomic data showed that dietary inclusion of sorghum grain increased the relative concentrations of phenolic acid (N1, N5, N10-tris-trans-p-coumaroylspermine and prenyl cis-caffeate) and carnitine (3-hydroxyisovalerylcarnitine and linoelaidyl carnitine).  The results also showed that dietary inclusion of sorghum grain linearly increased the urinary urea excretion (P=0.010) and decreased the urinary excretion of purine derivatives (P=0.041) as well as the estimated rumen microbial N supply (P=0.012) based on urinary purine derivatives.  The results of experiment 2 showed that including sorghum grain in the diet linearly increased the average concentrations of NH4+-N (P=0.012), NO2-N (P=0.009), NO3-N (P=0.001) and the total inorganic N (P<0.001) in the soil enriched with urine samples.  The urine sample N2O-N flux (P=0.001), the estimated steer urine N2O-N flux (P=0.021) and the N2O-N to urinary N ratio (P=0.038) linearly increased with increasing inclusion of sorghum grain in the diet.  In conclusion, dietary inclusion of sorghum grain containing high CT at 167 and 338 g kg–1 DM did not affect the N utilization efficiency of steers but increased the urine N2O-N emissions by 5.7 and 31.4%, respectively.  For reducing the N2O emissions to the environment, high levels of sorghum grain should not be included in the diet of steers.


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Abscisic acid alleviates photosynthetic damage in the tomato ABA-deficient mutant sitiens and protects photosystem II from damage via the WRKY22–PsbA complex under low-temperature stress
Jiamao Gu, Pengkun Liu, Wenting Nie, Zhijun Wang, Xiaoyu Cui, Hongdan Fu, Feng Wang, Mingfang Qi, Zhouping Sun, Tianlai Li, Yufeng Liu
2025, 24 (2): 546-563.   DOI: 10.1016/j.jia.2024.11.040
Abstract207)      PDF in ScienceDirect      
Abscisic acid (ABA) plays a key role in promoting the growth and development of plants, as well as mediating the responses of plants to adverse environmental conditions.  Here, we measured the photosynthetic capacity of wild-type RR, mutant sitiens (sit), and ABA-pretreated sit tomato seedlings following exposure to low-temperature (LT) stress.  We found that the net photosynthetic rate, intercellular carbon dioxide concentration, transpiration rate, and stomatal conductance of sit seedlings were lower than those of RR seedlings under LT stress.  The chloroplast width, area, and number of osmiophilic granules were significantly larger in sit seedlings than in RR seedlings, while the chloroplast length/width ratio was significantly lower in sit seedlings than in RR seedlings.  The photochemical activity of sit seedlings was lower, and the expression of photosynthesis-related genes in sit seedlings was altered following exposure to LT stress.  ABA pretreatment significantly alleviated the above phenomenon.  We also conducted an RNA sequencing analysis and characterized the expression patterns of genes in tomato seedlings following exposure to LT stress.  We constructed 15 cDNA libraries and identified several differentially expressed genes involved in photosynthesis, plant hormone signaling transduction, and primary and secondary metabolism.  Additional analyses of genes encoding transcription factors and proteins involved in photosynthesis-related processes showed pronounced changes in expression under LT stress.  Luciferase reporter assay and electrophoretic mobility shift assay revealed that WRKY22 regulates the expression of PsbA.  The PSII of WRKY22 and PsbA-silenced plants was inhibited.  Our findings indicate that ABA plays a role in regulating the process of photosynthesis and protecting PSII in tomato under LT stress through the WRKY22–PsbA complex.
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Long-term excessive nitrogen application decreases spring maize nitrogen use efficiency via suppressing root physiological characteristics
Hong Ren, Zheng Liu, Xinbing Wang, Wenbin Zhou, Baoyuan Zhou, Ming Zhao, Congfeng Li
2025, 24 (11): 4195-4210.   DOI: 10.1016/j.jia.2024.05.031
Abstract352)      PDF in ScienceDirect      
Long-term excessive nitrogen (N) application neither increases nor enhances grain yield and N use efficiency (NUE) of maize, yet the mechanisms involving root morphological and physiological characteristics remain unclear.  This study aimed to elucidate the mechanisms underlying stagnant grain yield under excessive N application by examining root morphological and physiological characteristics.  A 10-year N fertilizer trial was conducted in Jilin Province, Northeast China, cultivating maize at three N fertilizer levels (zero N, N0; recommended N, N2; and high N level, N4) from 2019 to 2021.  Two widely cultivated maize genotypes, ‘Xianyu 335’ (XY335) and ‘Zhengdan 958’ (ZD958), were evaluated.  Grain yield, N content, root morphology, and physiological characteristics were analyzed to assess the relationships between N uptake, N utilization, plant growth, and root systems under different N treatments.  Compared to N0, root biomass, post-silking N uptake, and grain yield improved significantly with increased N input, while no significant differences emerged between recommended N and high N.  High N application enhanced root length and root surface area but decreased root activity (measured by TTC (2,3,5-triphenyltetrazolium chloride) method), nitrate reductase activity, and root activity absorbing area across genotypes.  Root length and root to shoot ratio negatively affected N uptake (by –1.2 and –24.6%), while root surface area, root activity, nitrate reductase activity, and root activity absorbing area contributed positively.  The interaction between cultivar and N application significantly influenced NUE.  XY335 achieved the highest NUE (11.6%) and N recovery efficiency (18.4%) through superior root surface area (23.6%), root activity (12.5%), nitrate reductase activity (8.3%), and root activity absorbing area (6.9%) compared to other treatments.  Recommended N application enhanced Post N uptake, NUE, and grain yield through improved root characteristics, while high N application failed to increase or decreased NUE by reducing these parameters.  This study demonstrates that root surface area, root activity, nitrate reductase activity, and root activity absorbing area limit NUE increase under high N application.
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Rapid improvement of rice appearance quality by targeted knockout of the GS9 gene
Tao Zhang, Jiaqi Tang, Qianfeng Li, Lin Zhang, Changquan Zhang, Qiaoquan Liu, Dongsheng Zhao
2025, 24 (10): 4100-4104.   DOI: 10.1016/j.jia.2025.04.002
Abstract146)      PDF in ScienceDirect      
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Genome-wide analysis of AhCN genes reveals that AhCN34 is involved in bacterial wilt resistance in peanut
Kai Zhao, Yanzhe Li, Zhan Li, Zenghui Cao, Xingli Ma, Rui Ren, Kuopeng Wang, Lin Meng, Yang Yang, Miaomiao Yao, Yang Yang, Xiaoxuan Wang, Jinzhi Wang, Sasa Hu, Yaoyao Li, Qian Ma, Di Cao, Kunkun Zhao, Ding Qiu, Fangping Gong, Zhongfeng Li, Xingguo Zhang, Dongmei Yin
2025, 24 (10): 3757-3771.   DOI: 10.1016/j.jia.2024.03.006
Abstract295)      PDF in ScienceDirect      

Peanut (Arachis hypogaea L.) bacterial wilt (BW) is a devastating soil-borne disease caused by Ralstonia solanacearum (RS) that poses a significant threat to peanut yield and quality.  Nucleotide-binding leucine-rich repeat (NBS-LRR) proteins are a class of plant-specific immune receptors that recognize pathogen-secreted effector molecules and activate immune responses to resist pathogen infections.  However, the precise functions of AhCN genes (where CN is a class of nucleotide-binding site, leucine-rich repeat receptor (NLR) genes that lack LRR structural domains) in peanut plants are not fully understood.  In this study, a total of 150 AhCN genes were identified and classified into nine subfamilies based on a systematic phylogenetic analysis.  The AhCN genes showed highly conserved structural features, and the promoter cis-elements indicated involvement in plant hormone signaling and defense responses.  After inoculation with RS, the highly resistant peanut variety ‘H108’ significantly outperformed the susceptible variety ‘H107’ based on physiological indicators such as plant height, main stem diameter, and fresh weight, likely due to the inhibition of bacterial proliferation and diffusion in the stem vascular bundle.  AhCN34 was found to be significantly upregulated in ‘H108’ compared to ‘H107’ during plant infection and in response to treatments with each of three plant hormones.  Importantly, AhCN34 overexpression in peanut leaves enhanced their resistance to BW.  These findings demonstrate the great potential of AhCN34 for applications in peanut resistance breeding.  Our identification and characterization of the AhCN genes provide insights into the mechanisms underlying BW resistance in peanut and can inform future research into genetic methods of improving BW resistance in peanut.

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Emergence of a novel multi-resistance-mediating integrative and conjugative element ICEPmu3 in Pasteurella multocida
Jiao He, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Juan Huang, Xumin Ou, Di Sun, Bin Tian, Yu He, Zhen Wu, Anchun Cheng, Dekang Zhu
2024, 23 (11): 3938-3942.   DOI: 10.1016/j.jia.2024.07.008
Abstract233)      PDF in ScienceDirect      
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Identification of key genes and metabolites involved in meat quality performance in Qinchuan cattle by WGCNA
Hengwei Yu, Zhimei Yang, Jianfang Wang, Huaxuan Li, Xuefeng Li, Entang Liang, Chugang Mei, Linsen Zan
2024, 23 (11): 3923-3937.   DOI: 10.1016/j.jia.2024.07.044
Abstract281)      PDF in ScienceDirect      
Understanding the genetic and metabolic elements that impact meat quality is crucial to improving production and meeting consumer demands in the beef sector.  Differences in meat quality among various muscle areas in beef cattle can impact pricing in the market.  Despite progress in genomics, the specific genes and metabolites that affect meat quality characteristics in Qinchuan cattle remain inadequately understood.  Therefore, this study aims to evaluate the meat quality characteristics of four specific muscle locations (tenderloin, striploin, high rib, and ribeye muscles) in Qinchuan bulls, including 10 traits (total protein content (TPC), intramuscular fat (IMF), non-esterified fatty acid (NEFA), meat color (L*, a*, and b*), shear force (SF), cooking loss (CL), pH0, and pH24).  This experiment uses transcriptome, metabolome sequencing, and sophisticated analytical methodologies such as weighted gene co-expression network analysis (WGCNA) and protein–protein interaction networks (PPI) to identify the key genes and metabolites associated with specific traits.  The findings highlight three notable genes (NDUFAB1, NDUFA12, and NDUFB7) linked to intramuscular fat (IMF), three key genes (CSRP3, ACAA3, and ACADVL) correlated with non-esterified fatty acids (NEFA), and one crucial gene (CREBBP) influencing meat color.  In conclusion, this investigation offers a new perspective on the differences in bovine muscle locations and contributes to the molecular understanding of bovine meat quality.  Future research endeavors could delve deeper into the identified genes and pathways to enhance beef cattle’s quality and yield.


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Subsoil tillage enhances wheat productivity, soil organic carbon and available nutrient status in dryland fields

Qiuyan Yan, Linjia Wu, Fei Dong, Shuangdui Yan, Feng Li, Yaqin Jia, Jiancheng Zhang, Ruifu Zhang, Xiao Huang
2024, 23 (1): 251-266.   DOI: 10.1016/j.jia.2023.06.011
Abstract389)      PDF in ScienceDirect      

Tillage practices during the fallow period benefit water storage and yield in dryland wheat crops.  However, there is currently no clarity on the responses of soil organic carbon (SOC), total nitrogen (TN), and available nutrients to tillage practices within the growing season.  This study evaluated the effects of three tillage practices (NT, no tillage; SS, subsoil tillage; DT, deep tillage) over five years on soil physicochemical properties.  Soil samples at harvest stage from the fifth year were analyzed to determine the soil aggregate and aggregate-associated C and N fractions.  The results indicated that SS and DT improved grain yield, straw biomass and straw carbon return of wheat compared with NT.  In contrast to DT and NT, SS favored SOC and TN concentrations and stocks by increasing the soil organic carbon sequestration rate (SOCSR) and soil nitrogen sequestration rate (TNSR) in the 0–40 cm layer.  Higher SOC levels under SS and NT were associated with greater aggregate-associated C fractions, while TN was positively associated with soluble organic nitrogen (SON).  Compared with DT, the NT and SS treatments improved soil available nutrients in the 0–20 cm layer.  These findings suggest that SS is an excellent practice for increasing soil carbon, nitrogen and nutrient availability in dryland wheat fields in North China.

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A mite parasitoid, Pyemotes zhonghuajia, negatively impacts the fitness traits and immune response of the fall armyworm, Spodoptera frugiperda
Yanfei Song, Tai’an Tian, Yichai Chen, Keshi Zhang, Maofa Yang, Jianfeng Liu
2024, 23 (1): 205-216.   DOI: 10.1016/j.jia.2023.05.022
Abstract435)      PDF in ScienceDirect      

Parasitoids are key regulators in ecological communities and widely used as agents in biocontrol programmes.  The fall armyworm, Spodoptera frugiperda, recently invaded multiple continents and caused substantial economic losses in agriculture.  Pyemotes zhonghuajia, a newly identified mite parasitoid, has shown potential for controlling various agricultural insect pests.  Therefore, this study tested the performance of Pzhonghuajia in parasitising S. frugiperda.  We also investigated the sublethal effects of parasitism by Pzhonghuajia on host fitness traits, transgenerational impacts, and cellular and humoral immunity.  Our result showed that the fifth-instar larvae of Sfrugiperda parasitised by 40 Pzhonghuajia were all dead (i.e., a lethal effect), while parasitism by 5 or 10 Pzhonghuajia was considered sublethal since many Sfrugiperda survived to adulthood and produced offspring after mating.  The sublethal influences from parasitism by Pzhonghuajia resulted in reduced pupal weight, adult emergence rate and fecundity, but increased developmental time and longevity.  Parasitism at both lethal (40 mites) and sublethal (10 mites) levels impaired the cellular and humoral immunity of Sfrugiperda.  This study presents the first empirical evidence that mite parasitoids can negatively influence host immunity.  Moreover, it provides insights into the biocontrol potential of mite parasitoids and their interactions with hosts.

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Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat (Triticum aestivum L.)

Simin Liao, Zhibin Xu, Xiaoli Fan, Qiang Zhou, Xiaofeng Liu, Cheng Jiang, Liangen Chen, Dian Lin, Bo Feng, Tao Wang
2024, 23 (1): 77-92.   DOI: 10.1016/j.jia.2023.04.023
Abstract421)      PDF in ScienceDirect      

Grain weight is one of the key components of wheat (Triticum aestivum L.) yield.  Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.  A recombinant inbred line (RIL) population derived from a cross between W7268 and Chuanyu 12 (CY12) was employed to detect quantitative trait loci (QTLs) for thousand-grain weight (TGW), grain length (GL), grain width (GW), and the ratio of grain length to width (GLW) in six environments.  Seven major QTLs, QGl.cib-2D, QGw.cib-2D, QGw.cib-3B, QGw.cib-4B.1, QGlw.cib-2D.1, QTgw.cib-2D.1 and QTgw.cib-3B.1, were consistently identified in at least four environments and the best linear unbiased estimation (BLUE) datasets, and they explained 2.61 to 34.85% of the phenotypic variance.  Significant interactions were detected between the two major TGW QTLs and three major GW loci.  In addition, QTgw.cib-3B.1 and QGw.cib-3B were co-located, and the improved TGW at this locus was contributed by GW.  Unlike other loci, QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike (GNS).  They were further validated in advanced lines using Kompetitive Allele Specific PCR (KASP) markers, and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.  Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.  According to gene annotation, spatial expression patterns, ortholog analysis and sequence variation, the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.  Collectively, the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

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Significant reduction of ammonia emissions while increasing crop yields using the 4R nutrient stewardship in an intensive cropping system
ZHANG Chong, WANG Dan-dan, ZHAO Yong-jian, XIAO Yu-lin, CHEN Huan-xuan, LIU He-pu, FENG Li-yuan, YU Chang-hao, JU Xiao-tang
2023, 22 (6): 1883-1895.   DOI: 10.1016/j.jia.2022.12.008
Abstract397)      PDF in ScienceDirect      

Ammonia (NH3) emissions should be mitigated to improve environmental quality.  Croplands are one of the largest NH3 sources, they must be managed properly to reduce their emissions while achieving the target yields.  Herein, we report the NH3 emissions, crop yield and changes in soil fertility in a long-term trial with various fertilization regimes, to explore whether NH3 emissions can be significantly reduced using the 4R nutrient stewardship (4Rs), and its interaction with the organic amendments (i.e., manure and straw) in a wheat–maize rotation.  Implementing the 4Rs significantly reduced NH3 emissions to 6 kg N ha–1 yr–1 and the emission factor to 1.72%, without compromising grain yield (12.37 Mg ha–1 yr–1) and soil fertility (soil organic carbon of 7.58 g kg–1) compared to the conventional chemical N management.  When using the 4R plus manure, NH3 emissions (7 kg N ha–1 yr–1) and the emission factor (1.74%) were as low as 4Rs, and grain yield and soil organic carbon increased to 14.79 Mg ha–1 yr–1 and 10.09 g kg–1, respectively.  Partial manure substitution not only significantly reduced NH3 emissions but also increased crop yields and improved soil fertility, compared to conventional chemical N management.  Straw return exerted a minor effect on NH3 emissions.  These results highlight that 4R plus manure, which couples nitrogen and carbon management can help achieve both high yields and low environmental costs.

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Screening and characterization of a novel ruminal cellulase gene (Umcel-1) from a metagenomic library of gayal (Bos frontalis)
LI Bi-feng, ZHU Ya-xin, GU Zhao-bing, CHEN Yuan, LENG Jing, GOU Xiao, FENG Li, LI Qing, XI Dong-mei, MAO Hua-ming, YANG Shu-Li
2016, 15 (4): 855-861.   DOI: 10.1016/S2095-3119(15)61144-3
Abstract1862)      PDF in ScienceDirect      
Gayal is a rare semi-wild bovine species found in the Indo-China. They can graze grasses, including bamboo leaves, as well as reeds and other plant species, and grow to higher mature live weights than Yunnan Yellow cattle maintained in similar harsh environments. The aim of this study was to identify specific cellulase in the gayal rumen. A metagenomic fosmid library was constructed using genomic DNA isolated from the ruminal contents of four adult gayals. This library contained 38 400 clones with an average insert size of 35.5 kb. The Umcel-1 gene was isolated from this library. Investigation of the cellulase activity of 24 random clones led to the identification of the Umcel-1 gene, which exhibited the most potent cellulase activity. Sequencing the Umcel-1 gene revealed that it contained an open reading frame of 942 base pairs that encoded a product of 313 amino acids. The putative gene Umcel-1 product belonged to the glycosyl hydrolase family 5 and showed the highest homology to the cellulase (GenBank accession no. YP_004310852.1) from Clostridium lentocellum DSM 5427, with 44% identity and 62% similarity. The Umcel-1 gene was heterologously expressed in Escherichia coli BL21, and recombinant Umcel-1 was purified. The activity of purified recombinant Umcel-1 was assessed, and the results revealed that it hydrolyzed carboxymethyl cellulose with optimal activity at pH 5.5 and 45°C. To our knowledge, this study provides the first evidence for a cellulase produced by bacteria in gayal rumen.
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Investigating the mechanisms of glyphosate resistance in goosegrass (Eleusine indica) population from South China
ZHANG Chun, FENG Li, HE Ting-ting, YANG Cai-hong, CHEN Guo-qi, TIAN Xing-shan
2015, 14 (5): 909-918.   DOI: 10.1016/S2095-3119(14)60890-X
Abstract2113)      PDF in ScienceDirect      
Glyphosate has been used worldwide for nearly 40 years, and 30 types of resistant weeds have been reported. Glyphosate is mass-produced and widely used in China, but few studies and reports on glyphosate-resistant weeds and resistance mechanisms exist. Previous studies found a goosegrass species with high glyphosate resistance from orchards in South China and its glyphosate resistant mechanism was described in this study. The cDNA of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS, EC 2.5.1.19), the target enzyme of glyphosate, was cloned from the glyphosate-resistant and -susceptible goosegrass, respectively, and referred as EPSPS-R and EPSPS-S. The Pro106 residue was known to be involved in the glyphosate resistance in most goosegrass populations. However, sequence analysis did not find the mutation at the Pro106 residue in the R biotype EPSPS amino acid sequence. The residue 133 and 382 was mutated in the R biotype EPSPS amino acid sequence instead, but it did not affect the EPSPS-S and EPSPS-R genes sensitivities to glyphosate. RT-PCR and Western blot analyses suggested that EPSPS mRNA and protein are mainly present in the shoot tissues both in the R and S goosegrass biotypes. The EPSPS-R rapidly responds to the glyphosate in R-biotype goosegrass and the induced expression was detected at 12 h post glyphosate treatment. The mRNA and protein expression of EPSPS-R increased constantly as the increasing concentration of glyphosate. However, the expression of the EPSPS-S was not induced significantly by glyphosate in the S goosegrass biotype. Quantification of real-time PCR results showed that the copy number of the EPSPS in R-biotype goosegrass was 4.7 times higher than that in the S goosegrass biotype. All the results implied that EPSPS gene amplification might mainly caused the glyphosate resistance of a goosegrass population collected from orchards in South China.
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Use of chlorophyll fluorescence and P700 absorbance to rapidly detect glyphosate resistance in goosegrass (Eleusine indica)
ZHANG Tai-jie, FENG Li, TIAN Xing-shan, YANG Cai-hong, GAO Jia-dong
2015, 14 (4): 714-723.   DOI: 10.1016/S2095-3119(14)60869-8
Abstract1916)      PDF in ScienceDirect      
The rapid detection of glyphosate resistance in goosegrass (Eleusine indica) will enhance our ability to respond to new resistant populations of this major weed. Chlorophyll fluorescence (Fluo) and P700 (reaction center chlorophyll of photosystem I) absorbance were analyzed in one biotype of goosegrass that is resistant to glyphosate and in another that remains sensitive to the herbicide. Both biotypes were treated with a foliar spray of glyphosate. Differences in photosystem II maximum quantum yield (Fv/Fm), effective photochemical quantum yield (Y(II)), and non-photochemical quenching (NPQ) between the biotypes increased over time. Values for Fv/Fm and Y(II) differed between the two biotypes 24 h after treatment (HAT). Differentiated activities and energy dissipation processes of photosystem II (PSII) and energy dissipation processes of photosystem I (PSI) were manifested in the two biotypes 24 HAT with 20 mmol L–1 glyphosate. Differentiated energy dissipation processes of PSI were still apparent 24 HAT with 200 mmol L–1 glyphosate. These results indicate that the Fluo parameters related to PSII activity and energy dissipation and the P700 parameters related to energy dissipation are suitable indicators that enable rapid detection of glyphosate resistance in goosegrass.
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Geographic Variation of Rice Yield Response to Past Climate Change in China
YANG Jie, XIONG Wei, YANG Xiao-guang, CAO Yang , FENG Ling-zhi
2014, 13 (7): 1586-1598.   DOI: 10.1016/S2095-3119(14)60803-0
Abstract1830)      PDF in ScienceDirect      
Previous studies demonstrated climate change had reduced rice yield in China, but the magnitude of the reduction and the spatial variations of the impact have remained in controversy to date. Based on a gridded daily weather dataset, we found there were obvious changes in temperatures, diurnal temperature range, and radiation during the rice-growing season from 1961 to 2010 in China. These changes resulted in a significant decline of simulated national rice yield (simulated with CERES-Rice), with a magnitude of 11.5%. However, changes in growing-season radiation and diurnal temperature range, not growing-season temperatures, contributed most to the simulated yield reduction, which confirmed previous estimates by empirical studies. Yield responses to changes of the climatic variables varied across different rice production areas. In rice production areas with the mean growing-season temperature at 12-14°C and above 20°C, a 1°C growing-season warming decreased rice yield by roughly 4%. This decrease was partly attributed to increased heat stresses and shorter growth period under the warmer climate. In some rice areas of the southern China and the Yangtze River Basin where the rice growing-season temperature was greater than 20°C, decrease in the growing-season radiation partly interpreted the widespread yield decline of the simulation, suggesting the significant negative contribution of recent global dimming on rice production in China’s main rice areas. Whereas in the northern rice production areas with relatively low growing-season temperature, decrease of the diurnal temperature range was identified as the main climatic contributor for the decline of simulated rice yield, with larger decreasing magnitude under cooler areas.
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Genetic dissection and validation of a stable QTL for grain roundness on chromosome 5A in bread wheat (Triticum aestivum L.)
Jiajie He, Zhibin Xu, Bo Feng, Qiang Zhou, Xiaofeng Liu, Guangsi Ji, Shaodan Guo, Xiaoli Fan, Tao Wang
DOI: 10.1016/j.jia.2024.11.030 Online: 14 November 2024
Abstract33)      PDF in ScienceDirect      

Wheat grain morphology is an important breeding target considering its impact on yield and end-use properties.  However, the genetic basis of grain roundness, a major determinant of grain morphology, remains largely unexplored.  In this study, an F2 and a recombinant inbred line (RIL) populations from Zhongkemai 138 (ZKM138)×Chinese Spring (CS) cross were employed to analyze the genetic basis of grain shape variation.  Kompetitive Allele Specific PCR (KASP) markers were developed according to single nucleotide polymorphism (SNP) from bulked segregant exome sequencing (BSE-Seq) of F2 and Wheat 55K SNP array data online, and then were used to construct two genetic maps of F2 and RIL populations, spanning 148.89 cM (30 KASP markers) and 129.82 cM (25 KASP markers), respectively.  By the traditional QTL mapping method based on these two maps, a stable quantitative trait locus (QTL) for grain roundness (GR), QGr.cib-5A, could be repeatedly highlighted in the interval of 444.8-455.5 Mb on chromosome 5A.  Further conditional QTL mapping analysis revealed that grain width was the major contributor to GR at this locus.  Besides, the utilization of two tightly linked markers 5A4-15 and 55k-31 showed a 96.27% transmissibility of ZKM138-derived alleles in 134 ZKM138 derivatives alongside a 7.38% increase in GR, and a 65.19% distribution of worldwide varieties.  Finally, TraesCS5A02G236400, possibly encoding a hydroxyproline-rich glycoprotein family protein, was deduced to be the candidate gene.  Collectively, these results provided the possibility of facilitating wheat grain shape improvement and enhancing wheat market value.

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TaRLK-1B: A novel wheat gene conferring resistance to leaf rust revealed by a genome-wide association study
Shujuan Liu, Li Zhao, Chenyang Hao, Yuxue Pan, Mengjiao Guo, Yilin Huang, Haixia Liu, Jian Hou, Zaifeng Li, Tian Li, Xinhong Chen, Xueyong Zhang
DOI: 10.1016/j.jia.2025.02.028 Online: 19 February 2025
Abstract40)      PDF in ScienceDirect      

Leaf rust is a highly destructive foliar disease in wheat, causing major constraints in wheat production worldwide.  In this study, we conducted a comprehensive assessment of adult plant resistance to leaf rust in 590 accessions from the advanced backcross-nested association mapping plus inter-crossed (AB-NAMIC) population. We used 660K genotype data to perform a genome-wide association study (GWAS), identifying significant quantitative trait loci (QTLs) on chromosomes 1B, 2A, 2B, and 7D, with particular emphasis on the candidate gene TaRLK-1B on chromosome 1B.  A cleaved amplified polymorphic sequence (CAPS) marker was developed based on TaRLK-1B haplotypes and effectively differentiated between resistant and susceptible varieties.  This gene encodes a membrane-localized leucine-rich repeat receptor-like kinase (LRR-RLK) that is upregulated in response to the fungal infection that causes leaf rust.  Targeted knockout of TaRLK-1B in wheat led to reduced resistance to leaf rust, underscoring its essential role as a positive regulator in defense against this disease.  Additionally, we propose that TaRLK-1B interacts with the receptor-like cytoplasmic kinase TaRLCK1B, potentially facilitating immune signal transduction.  Our findings also demonstrate that pyramiding minor effect QTLs significantly increases resistance to leaf rust.  This study provides novel insights into resistance genes and valuable QTL information, which could improve marker-assisted wheat breeding efforts.

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Genotypic advantages of root-shoot growth alleviate grain yield reduction of maize (Zea mays L.) under various soil compactions
Lu Liang, Zhuohan Gao, Zaisong Ding, Wenchao Zhen, Zheng Liu, Congfeng Li, Ming Zhao, Xinbing Wang, Baoyuan Zhou
DOI: 10.1016/j.jia.2025.02.040 Online: 21 February 2025
Abstract40)      PDF in ScienceDirect      

Soil compaction has become a seriously limitation for further increasing grain yield of maize (Zea mays L.) in the North China Plain (NCP).  However, considerable variability exists among maize hybrids in their grain yield response to soil compaction.  To understand the physiological processes relate to the variation of responses to various soil compactions among maize hybrids, a two-year field experiment was conducted with 17 maize hybrids and three soil compaction treatments (NC, no compaction, SBD, soil bulk density=1.0-1.3 g cm-3; MC, moderate compaction, SBD=1.4-1.5 g cm-3, and HC, heavy compaction, SBD>1.6 g cm-3) to examine the root and shoot morphological traits, dry matter accumulation, and grain yield.  Compared to NC, MC and HC significantly decreased maize yield by 0.9-26.7% and 5.9-41.1% across hybrids and years, respectively.  High compaction tolerance (H) had greater grain yield than hybrids of middle compaction tolerance (M) and low compaction tolerance (L), particularly under HC.  Yield benefits obtained from H hybrid were enhanced due to better root and shoot growth under HC condition.  Greater root length, root surface area, and root weight, as well as root activity, absorption capacity, and antioxidant capacity for H hybrid were found under HC condition, and then maintained increased leaf area index and dry matter accumulation.  Moreover, the increases of root growth indices for H hybrid were greater than that of shoot growth, particularly under HC condition, leading to an increased root/shoot ratio.  We conclude that soil compaction impacts maize root and shoot growth differently depending on genotype, and root growth advantages of H hybrid were more obviously than shoot growth, which enhanced the yield benefits from H hybrid under heavy compaction condition.

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