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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
    DOI: 10.1016/j.jia.2024.02.019 Online: 15 March 2024
    Abstract4)      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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    Sugarcane/soybean intercropping with reduced nitrogen addition enhances residue-derived labile soil organic carbon and microbial network complexity in the soil during straw decomposition
    Tantan Zhang, Yali Liu, Shiqiang Ge, Peng Peng, Hu Tang, Jianwu Wang
    DOI: 10.1016/j.jia.2024.02.020 Online: 15 March 2024
    Abstract4)      PDF in ScienceDirect      
    Sugarcane/soybean intercropping with reduced nitrogen addition is an important sustainable agricultural pattern that can alter soil ecological functions, thereby affecting straw decomposition in the soil. However, the mechanisms underlying changes in soil organic carbon (SOC) composition and microbial communities during straw decomposition under long-term intercropping with reduced nitrogen addition remain unclear. In this study, we conducted an in-situ microplot incubation experiment with 13C-labeled soybean straw residue addition in a two-factor (cropping pattern: sugarcane monoculture (MS) and sugarcane/soybean intercropping (SB); nitrogen addition levels: reduced nitrogen addition (N1) and conventional nitrogen addition (N2)) long-term experimental field plot. The results showed that the SBN1 treatment significantly increased the residual particulate organic carbon (POC) and residual microbial biomass carbon (MBC) contents during straw decomposition, and the straw carbon in soil was mainly conserved as POC. Straw addition changed the structure and reduced the diversity of the soil microbial community, but microbial diversity gradually recovered with decomposition time. During straw decomposition, the intercropping pattern significantly increased the relative abundances of Firmicutes and Ascomycota. In addition, straw addition reduced microbial network complexity in the sugarcane/soybean intercropping pattern but increased it in the sugarcane monoculture pattern. Nevertheless, microbial network complexity remained higher in the SBN1 treatment than in the MSN1 treatment. In general, the SBN1 treatment significantly increased the diversity of microbial communities and the relative abundance of microorganisms associated with organic matter decomposition, and the changes in microbial communities were mainly driven by the residual labile SOC fractions. These findings suggest that more straw carbon can be sequestered in the soil under sugarcane/soybean intercropping with reduced nitrogen addition to maintain microbial diversity and contribute to the development of sustainable agriculture.
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    Lysobacter enzymogenes: a fully armed biocontrol warrior
    Long Lin, Xiaolong Shao, Yicheng Yang, Aprodisia Kavutu Murero, Limin Wang, Gaoge Xu, Yangyang Zhao, Sen Han, Zhenhe Su, Kangwen Xu, Mingming Yang, Jinxing Liao, Kaihuai Li, Fengquan Liu, Guoliang Qian
    DOI: 10.1016/j.jia.2024.02.021 Online: 15 March 2024
    Abstract3)      PDF in ScienceDirect      
    Lysobacter enzymogenes is less-studied, but emerging as a powerful biocontrol bacterium producing multiple antimicrobial weapons including lytic enzymes, toxins, secondary metabolites and protein secretion systems. The loss of surface-attached flagellum, production of heat-stable antifungal factor (HSAF, also named as Ningrongmycin) as a novel antifungal antibiotic, and the use of the type IV secretion system (T4SS) rather than the common type VI secretion system (T6SS) to kill competitors make this species unique. These distinct features set L. enzymogenes apart from well-studied plant beneficial biocontrol agents, such as Bacillus and Pseudomonas. This review describes what takes L. enzymogenes to be a unique biocontrol warrior by focusing to illustrate how the lack of flagellum governs morphological and functional co-adaptability, what adapted signaling transduction pathways are adopted to coordinate the biosynthesis of HSAF, and how to ecologically adapt plant rhizosphere by cell-to-cell interacting microbiome members via the bacterial-killing T4SS.
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    The P-type pentatricopeptide repeat protein YGS is essential for chloroplast development in rice
    Zhennan Qiu, Dongdong Chen, Peiliang Zhang, Chunmiao Wang, Guihong Liang, Chunyang Jiao, Shuo Han, Cuiping Wen, Xiliang Song, Peiyan Guan, Yan Li, Shiyong Wen, Li Zhu
    DOI: 10.1016/j.jia.2024.02.022 Online: 15 March 2024
    Abstract2)      PDF in ScienceDirect      
    Pentatricopeptide repeat (PPR) proteins play crucial roles in the post-transcriptional regulation of gene expression, specifically RNA editing and RNA splicing, in plant organelles. Despite longstanding research on chloroplast biogenesis and development, the roles of most PPR genes in this process in rice (Oryza sativa) remain unclear. In this study, we identified a novel P-type PPR protein, YELLOW-GREEN LEAF AND SEEDLING LETHAL (YGS), that is targeted to rice chloroplasts.  YGS is preferentially expressed in leaves.  The ygs mutants were obtained by knocking out YGS gene using CRISPR/Cas9-mediated genome editing; these mutants exhibited yellow-green leaves and a seedling-lethal phenotype.  Consistent with these phenotypes, the ygs mutants had lower levels of pigment contents and an abnormal chloroplast ultrastructure compared to the wild type.  Moreover, the expression levels of genes related to chloroplast development and chlorophyll biosynthesis were significantly altered in the ygs mutants.   In addition, loss of function of YGS impaired RNA editing of rpl2 and intron splicing of ycf3-1 in the plastid genome. Finally, YGS interacted with the chloroplast signal recognition particle protein OscpSRP54b in yeast two-hybrid and bimolecular fluorescence complementation assays.  These findings suggest that YGS is involved in RNA editing and RNA splicing in chloroplasts, thereby playing a crucial role in chloroplast development in rice.
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    Mapping QTL for fiber- and seed-related traits in Gossypium tomentosum CSSLs with G. hirsutum background 
    Yongshui Hao, Xueying Liu, Qianqian Wang, Shuxin Wang, Qingqing Li, Yaqing Wang, Zhongni Guo, Tiantian Wu, Qing Yang, Yuting Bai, Yuru Cui, Peng Yang, Wenwen Wang, Zhonghua Teng, Dexin Liu, Kai Guo, Dajun Liu, Jian Zhang, Zhengsheng Zhang
    DOI: 10.1016/j.jia.2024.02.023 Online: 15 March 2024
    Abstract3)      PDF in ScienceDirect      
    Introducing the inherent genetic diversity of wild species into cultivars has become one of the hot spots in crop genetic breeding and genetic resources research.  Fiber- and seed-related traits, which are critical to the global economy and people’s livelihoods, occupy the principal status of cotton breeding.  Here, a wild cotton species Gossypium tomentosum, was used to broaden the genetic basis of G. hirsutum and identify QTL for fiber- and seed-related traits.  A population of 559 chromosome segment substitution lines (CSSLs) was established with various chromosome segments from G. tomentosum in a G. hirsutum cultivar background.  A total of 72, 89, and 76 QTLs were identified for three yield traits, five fiber quality traits, and six cottonseed nutrient quality traits, respectively. Favorable alleles of 104 QTLs were contributed by G. tomentosum.  Sixty-four QTL were identified in two or more environments, and candidate genes for three of them were further identified.  The results of this study contributed to further study on the genetic basis of the morphogenesis of these economic traits, as well as indicating that the great breeding potentials of G. tomentosum in improving the fiber- and seed-related traits in G. hirsutum.
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    circKIF27 inhibits melanogenesis and proliferation by targeting miR-129-5p/TGIF2 pathway in goat melanocytes
    JI Kai-yuan, ZHAO Yi-we, YUAN Xin, LIANG Chun-e, ZHANG Xue-qing, TIAN Wen-li, YU Tong, MA Yang-yang, LING Ying-hui, ZHANG Yun-hai
    DOI: 10.1016/j.jia.2024.02.008 Online: 12 March 2024
    Abstract9)      PDF in ScienceDirect      
    Skin and hair pigmentation in animals involve intricate regulatory processes. Circular RNA-microRNA (circRNA-miRNA) networks play vital roles in various biological processes, although their involvement in pigmentation has been underexplored. This study focused on circKIF27 expression, which differs significantly in melanocytes isolated from white and brown Boer coat-colored skin, yet its function remains unclear. Here, we investigated the roles of circKIF27 in melanocytes. In situ hybridization assays demonstrated that circKIF27 is expressed in the cytoplasm of melanocytes. qRT-PCR results revealed differential expression levels of circKIF27 in various tissues of male and female goats. Functional analysis showed that circKIF27 overexpression in melanocytes significantly reduces melanin production (P<0.01) and inhibits cell proliferation (P<0.0001). Bioinformatics analysis identified a putative miR-129-5p binding site on circKIF27, and luciferase reporter assays confirmed their interaction. Overexpression of miR-129-5p in melanocytes enhances melanin production (P<0.01) and promotes cell proliferation (P<0.05). Further analysis revealed that TGIF2 possesses two potential miR-129-5p binding sites, and miR-129-5p overexpression in melanocytes significantly inhibits TGIF2 expression (P<0.0001), suggesting a targeted regulatory relationship between these two molecules. Silencing TGIF2 expression via siRNA-TGIF2 transfection leads to increased melanocyte proliferation (P<0.0001) and increased melanin production (P<0.01). These findings highlight the involvement of the circRNA-miRNA network in pigmentation, offering new insights into the molecular mechanisms underlying pigmentation and guiding animal hair color breeding strategies.
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    Genetic analysis and candidate gene identification of salt tolerance-related traits in maize
    Hui Fang, Xiuyi Fu, Hanqiu Ge, Mengxue Jia, Jie Ji, Yizhou Zhao, Zijian Qu, Ziqian Cui, Aixia Zhang, Yuandong Wang, Ping Li, Bao-hua Wang
    DOI: 10.1016/j.jia.2024.02.009 Online: 12 March 2024
    Abstract4)      PDF in ScienceDirect      
    Soil salinization poses a threat to maize production worldwide.  The genetic mechanism of salt tolerance in maize is not well understood.  Therefore, identification of the genetic components underlying salt tolerance in maize is of importance.  In the current study, a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related traits.  In total, 125 QTLs were detected by using a high-density genetic bin map, with 1 to 5 QTLs explaining 6.05-32.02% of the phenotypic variation for each trait.  The total phenotypic variation explained (PVE) by all detected QTLs ranged from 6.84 to 63.88% for each trait.  Of all 125 QTLs, only three were major QTLs distributed in 2 genomic regions on chromosome 6, which were involved in 3 salt tolerance-related traits.  In addition, 10 pairs of epistatic QTLs with additive effects were detected for 8 traits, explaining 0.9 to 4.44% of the phenotypic variation.  Furthermore, 18 QTL hotspots affecting 3-7 traits were identified.  In one hotspot (L5), a gene cluster consisting of 4 genes (ZmNSA1, SAG6, ZmCLCg, and ZmHKT1;2) was found, suggesting the involvement of multiple pleiotropic genes.  Finally, two important candidate genes, Zm00001d002090 and Zm00001d002391, were verified to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association analysis.  Zm00001d002090 encodes a calcium-dependent lipid-binding (CaLB domain) family protein, which may function as a Ca2+ sensor for transmitting the salt stress signal downstream, while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related subfamily.  Our findings provide valuable insights into the genetic basis of salt tolerance-related traits and a theoretical foundation for breeders to enhance salt-tolerant maize varieties.
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    Post-anthesis dry matter production and leaf nitrogen distribution are associated with root-derived cytokinins gradient in rice
    Kuanyu Zhu, Yuemei Xu, Zhiwei Sun, Yajun Zhang, Weiyang Zhang, Yunji Xu, Junfei Gu, Hao Zhang, Zhiqin Wang, Lijun Liu, Jianhua Zhang, Jianchang Yang
    DOI: 10.1016/j.jia.2024.02.010 Online: 12 March 2024
    Abstract5)      PDF in ScienceDirect      
    Aligning leaf nitrogen (N) distribution to match the light gradient is crucial for maximizing canopy dry matter production (DMP) and improving N utilization efficiency.  However, the relationship between the gradient of root-derived cytokinins and N distribution in rice leaves, along with its impact on DMP and the underlying mechanisms, remains poorly understood.  A two-year field experiment was conducted using two japonica N-efficient varieties (NEVs) and two japonica N-inefficient varieties (NIVs) under four different N rates (0, 90, 180 and 360 kg N ha1). These selected varieties exhibited similar values in the coefficient of light extinction (KL).  Results showed that, at lower N rates (0-180 kg N ha−1), the NEVs exhibited greater dry matter weight at maturity, higher grain yield and improved internal N use efficiency (IEN), compared to the NIVs, despite possessing comparable total N uptake.  Compared with the NIVs, the NEVs exhibited a more pronounced nitrogen distribution gradient in leaves, as indicated by the coefficient of nitrogen extinction (KN) values during the middle and early grain filling stages.  This enhanced gradient led to improved coordination between light and nitrogen, resulting in greater photosynthetic production, particularly at lower N rates. Furthermore, the NEVs demonstrated a larger gradient of zeatin (Z)+zeatin riboside (ZR) in leaves (i.e., higher ratios of Z+ZR levels between upper and lower leaves), enhanced expression levels of genes related to N export in lower leaves and Z+ZR loading in root, respectively, elevated enzymes activities related to N assimilation in upper leaves, in relative to the NIVs.  Correlation and random forest analyses demonstrated a strong positive correlation between Z+ZR gradient, KN, and DMP, and the gradient facilitated the export of N from lower leaves and its assimilation in upper leaves, contributing significantly to both KN and DMP.  This process was closely linked to root activity, including root oxidation activity, root Z+ZR content, and Z+ZR loading capacity, as confirmed by applying an inhibitor or a promoter of cytokinins biosynthesis to roots.  Interestingly, at the N rate of 360 kg N ha−1, both NEVs and NIVs showed indistinguishable plant traits, achieving a super high-yielding level (over 10.5 t ha−1) but with remarkably low IEN.  The results suggest that increasing Z+ZR gradient can improve KN and DMP, where it needs to maintain higher root activity, thus leading to high yield and high IEN.  Further research is needed to explore and develop cultivation practices with reduced N to unlock the super high-yielding potential of the NEVs.
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    Map-based cloning of qLPA01.1, a favorable allele from G. tomentosum chromosome segment line
    Wenwen Wang, Lei Chen, Yan Wu, Xin Guo, Jinming Yang, Dexin Liu, Xueying Liu, Kai Guo, Dajun Liu, Zhonghua Teng, Yuehua Xiao, Zhengsheng Zhang
    DOI: 10.1016/j.jia.2024.02.011 Online: 12 March 2024
    Abstract2)      PDF in ScienceDirect      
    Cotton is an important natural fiber crop in the world, which play a vital role in our daily life. High yield is a constant goal of cotton breeding. Lint percentage (LP) is one of the important components for cotton fiber yield. A stable QTL qLPA01.1, controlling lint percentage, was identified on chromosome A01 from G. hirsutum introgressed lines with G. tomentosum chromosome segments in the previous study. To fine-map qLPA01.1, a F2 population with 986 individuals was established by crossing G. hirsutum cultivar CCRI35 with a chromosome segment substitution line HT_390. A high-resolution genetic including 47 loci and spanning 56.98-cM was constructed in the QTL region, and qLPA01.1 was finally mapped into an interval corresponding a ~80-kb genome region of chromosome A01 in the reference genome, which contained six annotated genes. Transcriptome data and sequence analysis revealed that S-acyltransferase protein 24 (GoPAT24) might be the target gene of qLPA01.1. This result provides the basis for cotton fiber yield improvement via marker-assisted selection (MAS) and uncovering the mechanism of cotton fiber development.
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    Ovule number a rising star to regulate seed Yield: Hopes or hypes 
    Shahid Ullah Khan, Ahmad Ali, Sumbul Saeed, Yonghai Fan, Ali Shehazd, Hameed Gul, Shah Fahad, Kun Lu
    DOI: 10.1016/j.jia.2024.02.013 Online: 12 March 2024
    Abstract2)      PDF in ScienceDirect      
    Rapeseed (Brassica napus L.) is the second most premium oilseed crop, mainly grown for vegetable oil and protein meal around the globe.  One of the main goals for breeders is to produce high-yield rapeseed cultivars with sustainable production to meet the requirements of the fast-growing population.  Besides the pod number, seeds per silique (SS), and thousand-seed weight (TSW), ovule number (ON) is the decisive yield determining factor of a single plant and final seed yield.  In recent years, tremendous efforts have been made to dissect the genetic and molecular basis of these complex traits.  Still, only relatively few genes or loci controlling these traits have been reported.  This review highlighted the updated hormonal and molecular basis of ON and development in model plants (A. thaliana).  This review also compiled efforts at the hormonal, molecular, and genetic mechanism of ovule development and number and bridge the understanding between the model plant species (A. thaliana) and cultivated species (B. napus).  This report will open a new corridor for primary and applied research in plant biology and benefit rapeseed breeding programs.  This literature will inculcate research interest to understand further ovule number determination, its role in yield improvement, and possible utilization in breeding programs.
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    Studying of the regulatory roles of response regulators GlrR and ArcA in xenocoumacins biosynthesis in Xenorhabdus nematophila CB6
    Xiaohui Li, Xiaobing Zheng, Yijie Dong, Youcai Qin, Fenglian Jia, Baoming Yuan, Jiaqi Duan, Beibei Li, Guangyue Li
    DOI: 10.1016/j.jia.2024.02.014 Online: 12 March 2024
    Abstract2)      PDF in ScienceDirect      
    Xenocoumacins Xcns, the major antimicrobial natural products produced by Xenorhabdus nematophila, have gained widespread attention for their potential application in crop protection. However, the regulatory mechanisms involved in the biosynthesis of Xcns remain poorly understood. In this study, we identified 21 potential two-component systems (TCSs) in X. nematophila CB6 by bioinformatic analysis. Among them, the response regulators (RRs) GlrR and ArcA were proven to positively regulate the production of Xcns based on gene deletion and complementation experiments. In addition, our results showed that GlrR played an important role in cell growth, while ArcA was involved in both cell morphology and growth. Using a variety of molecular biological and biochemical techniques, we found that GlrR controlled the Xcns biosynthesis by indirectly regulating the expression levels of the biosynthetic gene cluster (BGC). ArcA directly binded to the promoter regions of xcnA and xcnB to regulate the transcription of the Xcns BGC, and the binding sites were also identified. This study provides valuable insights into the regulatory network of Xcns biosynthesis, which will contribute to the construction of a high-yielding strain.
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    Effect of nitrogen fertilizer on proso millet starch structure, pasting, and rheological properties
    Honglu Wang, Hui Zhang, Qian Ma, Enguo Wu, Aliaksandr Ivanistau, Baili Feng
    DOI: 10.1016/j.jia.2024.02.015 Online: 12 March 2024
    Abstract1)      PDF in ScienceDirect      
    Nitrogen fertilizer is an important agronomic measure that greatly affects crop yield and grain quality.  This two-year study aimed to explore the effects of four nitrogen levels on the morphology, lamellar and crystalline structure, pasting, and rheological properties of proso millet (PM) starch, and to investigate potential food applications of PM.  The results showed that the starch surface became uneven and the structure of the starch granules shifted towards greater complexity with increasing nitrogen level.  Nitrogen increased the relative crystallinity, ordered structure, and average repeat distance, leading to a stable starch structure and contributing to a higher gelatinization enthalpy.  Furthermore, nitrogen significantly increased peak, breakdown, setback, and final viscosities but decreased apparent amylose content, which caused the shear resistance and storage capacity of PM starch-based foods to deteriorate during processing and transport.  Rheological analysis showed that PM starch exhibited the typical characteristics of a pseudoplastic fluid.  Under nitrogen treatment, PM starch gels showed high potential for application in 3D printing products due to a high resistance to shear thinning, gel strength, and yield stress, presumably owing to the significantly higher G′ than G′′, and the lower amylose content, which in turn promoted the formation of a stable network structure in water to immobilize more water.  Our study provides a reference for the application of PM starch in the food industry and for the development of PM cropping-management programs to improve quality.
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    Establishment of goat infection model of the peste ruminants virus isolated in China for vaccine efficacy evaluation
    Xue Wang, Hefeng Chen, Xianfeng Zhang, Zhengshuang Wu, Shuai Zhang, Lei Shuai, Lulu Wang, Weijie Li, Jinliang Wang, Wenxing Liu, Xijun Wang, Zhiyuan Wen, Jinying Ge, Yuntao Guan, Xijun He, Weiye Chen, Zhigao Bu
    DOI: 10.1016/j.jia.2024.02.016 Online: 12 March 2024
    Abstract3)      PDF in ScienceDirect      
    In 2013, peste des petits ruminants (PPR) re-emerged in China and spread to the majority of provinces across the country. The disease was effectively controlled through a vaccination campaign employing live attenuated vaccines, although sporadic cases still occurred. However, limited information is currently available regarding the peste des petits ruminants virus (PPRV) endemic in China. Here, a PPRV strain (HLJ/13) was isolated from a field sample in China by using Vero cells expressing goat signalling lymphocyte activation molecule. Phylogenetic analysis indicated that HLJ/13 belonged to lineage Ⅳ. Subsequent intranasal and subcutaneous inoculation of goats with a dose of 2×106 TCID50 of HLJ/13 resulted in the development of typical clinical symptoms of PPR, including pyrexia, ocular and nasal discharges, stomatitis, and diarrhea. All infected goats succumbed to the disease by day 8. To gain further insight, viral loading, pathological examination and immunohistochemical analyses were conducted, elucidating the main targets of HLJ/13 as the respiratory system, digestive tract and lymphoid organs. Employing the goat infection model established above, the goat poxvirus-vectored PPR vaccine, which was previously developed and could be used as DIVA (differentiating infected from vaccinated animals) vaccine, provided complete protection against the challenge of HLJ/13. It is important to note that this study represents the first comprehensive report delineating the biology and pathogenicity characterization, and infection model of PPRV isolated in China.
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    Effects of long-term partial substitution of inorganic fertilizer with pig manure and/or straw on nitrogen fractions and microbiological properties in greenhouse vegetable soils
    Shuo Yuan, Ruonan Li, Yinjie Zhang, Haoan Luan, Jiwei Tang, Liying Wang, Hongjie Ji, Shaowen Huang
    DOI: 10.1016/j.jia.2024.02.017 Online: 12 March 2024
    Abstract5)      PDF in ScienceDirect      
    Partial substitution of inorganic fertilizers with organic amendments is an important agricultural management practice. An 11-year field experiment (22 cropping periods) was carried out to analyze the impacts of different partial substitution treatments on crop yields and the transformation of nitrogen fractions in greenhouse vegetable soil. Four treatments with equal N, P2O5, and K2O inputs were selected, including complete inorganic fertilizer N (CN), 50% inorganic fertilizer N plus 50% pig manure-N (CPN), 50% inorganic fertilizer N plus 25% pig manure N and 25% corn straw N (CPSN), and 50% inorganic fertilizer N plus 50% corn straw N (CSN). Organic substitution treatments tended to increase crop yields since the 6th cropping period compared to the CN treatment. From the 8th to the 22nd cropping periods, the highest yields were observed in the CPSN treatment where yields were 7.5-11.1% greater than in CN treatment. After 11-year fertilization, compared to CN, organic substitution treatments significantly increased the concentrations of NO3--N, NH4+-N, acid hydrolysis ammonium-N (AHAN), amino acid-N (AAN), amino sugar-N (ASN), and acid hydrolysis unknown-N (AHUN) in soil by 45.0-69.4%, 32.8-58.1%, 49.3-66.6%, 62.0-69.5%, 34.5-100.3%, and 109.2-172.9%, respectively. Redundancy analysis indicated that soil C/N and OC concentration significantly affected the distribution of N fractions. The highest concentrations of NO3--N, AHAN, AAN, AHUN were found in the CPSN treatment. Organic substitution treatments increased the activities of β-glucosidase, β-cellobiosidase, N-acetyl-glucosamidase, L-aminopeptidase, and phosphatase in the soil. Organic substitution treatments reduced vector length and increased vector angle, indicating alleviation of constraints of C and N on soil microorganisms. Organic substitution treatments increased the total concentrations of PLFAs in the soil by 109.9-205.3%, and increased the relative abundance of G+ bacteria and fungi taxa, but decreased the relative abundance of G- bacteria, total bacteria, and actinomycetes. Overall, long-term organic substitution management increased soil OC concentration, C/N, and the microbial population, the latter in turn positively influenced soil enzyme activity. Enhanced microorganism numbers and enzyme activity enhanced soil N sequestration by transforming inorganic N to acid hydrolysis-N (AHN), and enhanced soil N supply capacity by activating non-acid hydrolysis-N (NAHN) to AHN, thus improving vegetable yield. Application of inorganic fertilizer, manure, and straw was a more effective fertilization model for achieving sustainable greenhouse vegetable production than application of inorganic fertilizer alone.
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    Identification of Fusarium cugenangense as a causal agent of wilt disease on Pyrus pyrifolia in China
    Chaohui Li, Xiaogang Li, Weibo Sun, Yanan Zhao, Yifan Jia, Chenyang Han, Peijie Gong, Shutian Tao, Yancun Zhao, Fengquan Liu
    DOI: 10.1016/j.jia.2024.02.018 Online: 12 March 2024
    Abstract4)      PDF in ScienceDirect      
    In recent years, an unusual wilt disease affecting Pyrus pyrifolia has been observed in various regions of Jiangsu, China. This disease originates from the roots and progresses with distinctive browning patterns along vascular tissues, even extending over two meters above the ground. These symptoms set it apart from recognized pear diseases and typically lead to the death of affected trees within the same or the following year. Furthermore, this disease exhibits a tendency to spread to neighboring trees even after the removal of affected trees, presenting a substantial threat to pear production. To ascertain the causative agent, the present study encompassed pathogen isolation, morphological and molecular identification, as well as validation experiments adhering to Koch's postulates. The fungal isolates obtained were identified as Fusarium cugenangense based on characteristics of the colonies and conidia, in addition to a phylogenetic analysis using DNA sequences of the translation elongation factor 1-alpha (tef1), calmodulin (CaM), and RNA polymerase second largest subunit (rpb2) genes. Pathogenicity of the isolated F. cugenangense on pear was confirmed by artificial inoculation. By introducing GFP-labeled pathogens into the roots, colonization in stem and leaf tissues was observed via fluorescence microscopy and transmission electron microscopy. Furthermore, these pathogens were successfully reisolated from stems and foliage, conclusively providing evidence of systemic infection within the pear plants. To the best of our knowledge, this is the first report of F. cugenangense causing pear wilt disease in China.
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    Trichoderma gamsii strain TC959 with comprehensive functions to effectively reduce seedling damping-off and promote growth of pepper by direct and indirect action mechanisms
    WANG Heng-xu, HU Hao, ZHAO Tian-you ZENG Zhao-qing, ZHUANG Wen-ying
    DOI: 10.1016/j.jia.2024.02.003 Online: 07 March 2024
    Abstract8)      PDF in ScienceDirect      
    A few Trichoderma species have been utilized as biocontrol agents in agriculture due to their ability to inhibit growth of phytopathogens. However, the antagonistic mechanism of some strains is mainly performed by direct action. The objective of our study is to explore an effective strain that has comprehensive abilities, and preliminarily clarify its practical viability and action mechanism. Trichoderma gamsii strain TC959 possessing abilities of strong antagonism and plant growth promotion was singled out. It released secondary metabolites, siderophores and chitinase/xylanase to directly inhibit the growth of plant pathogens, or released indole-3-acetic acid/gibberellin to promote plant growth. The strain also activated induced systemic resistance by increasing chlorophyll a/b ratio and jasmonic acid content of pepper seedlings through root colonization, which resulted in the improvements of defense-related gene expression levels, antioxidant enzyme activity, and indole-3-acetic acid/gibberellin production. Thereby disease resistance and plant growth were enhanced and promoted, respectively. Furthermore, TC959 had a resistance advantage to oxidation and chemical fungicides, which helped viability of the strain to be maintained, and healthy pepper seedlings were effectively ensured. In conclusion, strain TC959 has biocontrol potential and comprehensive functions against pepper damping-off disease, which is valuable for further practical applications.
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    MiR-21-5p ameliorates Busulfan-induced testicular dysfunction and maintains spermatogenesis
    ZHANG Meng-fei, WAN Shi-cheng, CHEN Wen-bo, YANG Dong-hui, WANG Cong-liang, LI Ba-lun, Aili Aierken, DU Xiao-min, LI Yun-xiang, WU Wen-ping, WANG Yu-qi, XIE Fang-de, LUO Xuan, LI Na, LI Xue-ling, YANG Lei, Ahmed Hamed Arisha, HUA Jin-lian
    DOI: 10.1016/j.jia.2024.02.004 Online: 07 March 2024
    Abstract6)      PDF in ScienceDirect      
    Spermatogonial stem cells (SSCs) are the key to maintaining production of the sperms and healthy offsprings, and also treating breeding livestock’s reproductive damage and infertility. MicroRNAs act a decisive role in regulating gene expression in many cells and tissues, including in processes such as proliferation, self-renewal, differentiation, and apoptosis of stem cells. However, the miRNA mechanism in regulation of SSCs is still unclear. Here, high-throughput sequencing was used to identify specific miRNAs. We confirmed that miR-21-5p was concentrated in both goat and mouse SSCs, and enhanced the proliferation and antiapoptotic ability of SSCs. In vivo experiments have shown that miR-21-5p resisted the damage of the chemotherapy drug Busulfan to germ cells, ameliorated Busulfan-induced testicular dysfunction, and maintained spermatogenesis. Further RNA-seq and target gene prediction revealed that SPRY1 and FASLG are targets of miR-21-5p, thereby activating downstream signaling pathways such as MAPK/ERK, PI3K-AKT, and apoptosis. In summary, miR-21-5p is crucial for the self-renewal and maintenance of SSCs. This study provides new avenues for treating breeding livestock’s reproductive damages, infertility, oligospermia, and other conditions.
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    Identification of genomic region and candidate genes underlying carotenoid accumulation in soybeans using next generation sequencing-based bulk segregant analysis
    Berhane S. Gebregziabher, Shengrui Zhang, Jing Li, Bin Li, Junming Sun
    DOI: 10.1016/j.jia.2024.02.005 Online: 07 March 2024
    Abstract2)      PDF in ScienceDirect      
    The improvement of soybean seed carotenoid contents is indispensably important owing to its beneficial role to human health and nutrition.  However, the genetic architecture underlying soybean carotenoid biosynthesis remains largely unknown.  In the present study, we employed the next generation sequencing-based bulked-segregant analysis for identifying new genomic regions governing seed carotenoids in 1551 natural soybean accessions.  The genomic DNA samples of individual plants with extreme phenotype were pooled to form two bulks with high (50 accessions) and low (50 accessions) carotenoid contents for Illumina sequencing.  A total of 125.09 Gbp of clean bases and 89.82% of Q30 were obtained and the average alignment efficiency was 99.45% with average coverage depth of 62.20× and 99.75% genome coverage.  Based on the G' method analysis, a total of 16 candidate genomic loci with a total length 20.41 Mb were found to be related to the trait.  Of these loci, the most significant region displaying the highest elevated G'-value was found in chromosome 06 at a position of 18.53-22.67 Mb, and chromosome 19 at a genomic region intervals of 8.36-10.94, 12.06-13.79 and 18.45-20.26 Mbs, and were preferably taken to identify the key candidate genes.  In these regions, 250 predicted genes were found and analyzed to get 90 significantly enriched (P<0.05) gene ontology (GO)-terms.  Based on ANNOVAR analysis, 50 genes with non-synonymous and stopgained mutations were preferentially selected as potential candidate genes.  Of which, following their gene annotation function and high significant haplotype variation in various environments, five genes were identified as the most promising candidate genes regulating soybean seed carotenoid accumulation, and suggested for further functional validation studies.  Collectively, understanding the genetic bases of carotenoid pigments and identifying genes underpinning carotenoid accumulation via bulked-segregant analysis sequencing (BSA-seq) approach provide new insight for exploring future molecular breeding of high carotenoid content in soybean cultivars.
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    Prediction of the potential distribution and analysis of the freezing injury risk of winter wheat on the Loess Plateau under climate change 
    Qing Liang, Xujing Yang, Yuheng Huang, Zhenwei Yang, Meichen Feng, Mingxing Qing, Chao Wang, Wude Yang, Zhigang Wang, Meijun Zhang, Lujie Xiao, Xiaoyan Song
    DOI: 10.1016/j.jia.2024.02.006 Online: 07 March 2024
    Abstract3)      PDF in ScienceDirect      
    Understanding the suitable areas of winter wheat under climate change and assessing the risk of freezing injury are crucial for the cultivation of winter wheat.  We utilized an optimized MaxEnt model to predict the potential distribution of winter wheat in the current period (1970-2020) and the future period (2021-2100) under four shared socioeconomic pathway scenarios (SSPs).  We applied statistical downscaling methods to downscale future climate data, established a scientific and practical freezing injury index (FII) by considering the growth period of winter wheat, and analyzed the abrupt change characteristics of winter wheat freezing injury by using the M-K test.  The results showed that the prediction accuracy AUC value of MaxEnt model reached 0.976.  The minimum temperature in the coldest month, precipitation in the wettest season and the annual precipitation were the main factors affecting the spatial distribution range of winter wheat.  The total suitable areas of winter wheat was approximately 4.40×107 hm2 in current.  In 2070s, the moderately suitable areas had the most increase by 9.02×105 hm2 under SSP245 and the least increase by 6.53×105 hm2 under SSP370.  The centroid coordinates of the total suitable areas had a tendency to move northward.  The potential risk of freezing injury in the high-latitude and high-altitude areas of the Loess Plateau increased significantly.  The north areas of Xinzhou in Shanxi suffered the most serious freezing injury, and the southern areas of the Loess Plateau suffered the least.  Environmental factors such as temperature, precipitation and geographical location had important impact on the suitable areas distribution and freezing injury risk of winter wheat.  In the future, more attention should be paid to the northward boundary of winter wheat planting areas and the areas of freezing injury risk to provide the early warning of freezing injury and corresponding management strategies.
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    TBX3 orchestrates H3K4 trimethylation for porcine induced pluripotent stem cells to totipotent-like stem cells
    Qiaoyan Shen, Xiaojie Wu, Ziyu Chen, Jianxiong Guo, Wei Yue, Shuai Yu, Rui Zhang, Xiaolong Wu, Heng Zhao, Qin Pan, Juqing Zhang, Zhenshuo Zhu, Xinchun Yang, Wenjing Xu, Yunxiang Li, Anmin Lei, Sha Peng, Fan Yang, Shiqiang Zhang, Gang Ren, Jun Wu, Na Li, Hongjiang Wei, Mingzhi Liao, Jinlian Hua
    DOI: 10.1016/j.jia.2024.02.007 Online: 07 March 2024
    Abstract8)      PDF in ScienceDirect      
    Pluripotent stem cells (PSCs) are useful for developmental and translational research because they have the potential to differentiate into all cell types of an adult individual. Pigs are one of the most important domestic ungulates, commonly used for food and as bioreactors. Generating stable pluripotent porcine PSC lines remains challenging. So far, the pluripotency gene network of porcine PSCs is poorly understood. Here we found that TBX3-derived induced pluripotent stem cells (iPSCs) closely resemble porcine 4-cell embryos with the capacity of totipotent-like stem cells (TLSCs). Interestingly, our data suggest that TBX3 facilitates the activation of H3K4me3 methyltransferase, specifically MLL1. Subsequent investigations revealed that the porcine 4-cell specific gene, MCL1, is a key downstream effector of the TBX3-MLL1 axis. Together, our study of the TBX3 regulatory network is helpful in the understanding of the totipotency characteristics of pigs.
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