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Manure substitution improves maize yield by promoting soil fertility and mediating the microbial community in lime concretion black soil

Minghui Cao, Yan Duan, Minghao Li, Caiguo Tang, Wenjie Kan, Jiangye Li, Huilan Zhang, Wenling Zhong, Lifang Wu
2024, 23 (2): 698-710.   DOI: 10.1016/j.jia.2023.05.040
Abstract178)      PDF in ScienceDirect      

Synthetic nitrogen (N) fertilizer has made a great contribution to the improvement of soil fertility and productivity, but excessive application of synthetic N fertilizer may cause agroecosystem risks, such as soil acidification, groundwater contamination and biodiversity reduction.  Meanwhile, organic substitution has received increasing attention for its ecologically and environmentally friendly and productivity benefits.  However, the linkages between manure substitution, crop yield and the underlying microbial mechanisms remain uncertain.  To bridge this gap, a three-year field experiment was conducted with five fertilization regimes: i) Control, non-fertilization; CF, conventional synthetic fertilizer application; CF1/2M1/2, 1/2 N input via synthetic fertilizer and 1/2 N input via manure; CF1/4M3/4, 1/4 N input synthetic fertilizer and 3/4 N input via manure; M, manure application.  All fertilization treatments were designed to have equal N input.  Our results showed that all manure substituted treatments achieved high soil fertility indexes (SFI) and productivities by increasing the soil organic carbon (SOC), total N (TN) and available phosphorus (AP) concentrations, and by altering the bacterial community diversity and composition compared with CF.  SOC, AP, and the soil C:N ratio were mainly responsible for microbial community variations.  The co-occurrence network revealed that SOC and AP had strong positive associations with Rhodospirillales and Burkholderiales, while TN and C:N ratio had positive and negative associations with Micromonosporaceae, respectively.  These specific taxa are implicated in soil macroelement turnover.  Random Forest analysis predicted that both biotic (bacterial composition and Micromonosporaceae) and abiotic (AP, SOC, SFI, and TN) factors had significant effects on crop yield.  The present work strengthens our understanding of the effects of manure substitution on crop yield and provides theoretical support for optimizing fertilization strategies.

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Whole-genome characterization of CKX genes in Prunus persica and their role in bud dormancy and regrowth 
Xuehui Zhao, Jianting Liu, Xiling Fu, Long Xiao, Qingjie Wang, Chaoran Wang, Zhizhang Chen, Jiakui Li, Changkun Lu, Hui Cao, Ling Li
2024, 23 (12): 4058-4073.   DOI: 10.1016/j.jia.2024.09.002
Abstract158)      PDF in ScienceDirect      
Bud dormancy is a complex physiological process of perennial woody plants living in temperate regions, and it can be affected by various phytohormones.  Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes essential for maintaining cytokinin homeostasis, yet a comprehensive analysis of these enzymes in peach remains lacking.  Here, a total of 51 CKX members from different species, including six from peach, eleven from apple, nine from poplar, seven from Arabidopsis, eight from strawberry, and ten from rice, were identified using the Simple HMM Search tool of TBtools and a BLASTP program and classified into four groups using phylogenetic analysis.  Conserved motif and gene structure analysis of these 51 CKX members showed that 10 conserved motifs were identified, and each CKX gene contained at least two introns.  Cis-element analysis of PpCKXs showed that all PpCKX genes have light-responsive elements and at least one hormone-responsive element.  The changed relative expression levels of six PpCKX genes in peach buds from endodormancy to bud-break were observed by qRT-PCR.  Among them, the expression trend of PpCKX6 was almost opposite that of PpEBB1, a positive bud-break regulator in woody plants, around the bud-break stage.  Y1H, EMSA, and dual-luciferase assays indicated that PpEBB1 negatively regulated PpCKX6 through direct binding to a GCC box-like element located in the promoter region of PpCKX6.  In addition, a transient assay showed that overexpression of PpCKX6 delayed the bud-break of peach.  These results indicate that the PpCKX genes play an essential role in the dormancy-regrowth process, and PpCKX6 may act downstream of PpEBB1 directly to regulate the bud-break process, which further improves the hormone-regulatory network of dormancy-regrowth of woody plants, and provides new insights for molecular breeding and genetic engineering of peach.
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Effects of water and nitrogen rate on grain-filling characteristics under high-low seedbed cultivation in winter wheat
Junming Liu, Zhuanyun Si, Shuang Li, Lifeng Wu, Yingying Zhang, Xiaolei Wu, Hui Cao, Yang Gao, Aiwang Duan
2024, 23 (12): 4018-4031.   DOI: 10.1016/j.jia.2023.12.002
Abstract223)      PDF in ScienceDirect      
A high-efficiency mode of high-low seedbed cultivation (HLSC) has been listed as the main agricultural technology to increase land utilization ratio and grain yield in Shandong Province, China.  However, limited information is available on the optimized water and nitrogen management for yield formation, especially the grain-filling process, under HLSC mode.  A three-year field experiment with four nitrogen rates and three irrigation rates of HLSC was conducted to reveal the response of grain-filling parameters, grain weight percentage of spike weight (GPS), spike moisture content (SMC), and winter wheat yield to water and nitrogen rates.  The four nitrogen rates were N1 (360 kg ha–1 pure N), N2 (300 kg ha–1 pure N), N3 (240 kg ha–1 pure N), and N4 (180 kg ha–1 pure N), respectively, and the three irrigation quotas were W1 (120 mm), W2 (90 mm), and W3 (60 mm), respectively.  Results showed that the determinate growth function generally performed well in simulating the temporal dynamics of grain weight (0.989<R2<0.999, where R2 is the determination coefficient).  The occurrence time of maximum filling rate (Tmax) and active grain-filling period (AGP) increased with the increase in the water or nitrogen rate, whereas the average grain-filling rate (Gmean) had a decreasing trend.  The final 1,000-grain weight (FTGW) increased and then decreased with the increase in the nitrogen rates and increased with the increase in the irrigation rates.  The GPS and SMC had a highly significant quadratic polynomial relationship with grain weight and days after anthesis.  Nitrogen, irrigation, and year significantly affected the Tmax, AGP, Gmean, and FTGW.  Particularly, the AGP and FTGW were insignificantly different between high seedbed (HLSC-H) and low seedbed (HLSC-L) across the water and nitrogen levels.  Moreover, the moderate water and nitrogen supply was more beneficial for grain yield, as well as for spike number and grain number per hectare.  The principal component analysis indicated that combining 240–300 kg N ha–1 and 90–120 mm irrigation quota could improve grain-filling efficiency and yield for the HLSC-cultivated winter wheat.  


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Genome-wide analysis of AhCN genes reveals the AhCN34 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
DOI: 10.1016/j.jia.2024.03.006 Online: 22 March 2024
Abstract70)      PDF in ScienceDirect      
Peanut (Arachis hypogaea L.) bacterial wilt (BW), caused by Ralstonia solanacearum (RS), is a devastating soil-borne disease 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 (CN is a class of NLR genes lacking 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; promoter cis-elements indicated involvement in plant hormone signaling and defense responses.  Following inoculation with RS, the highly resistant peanut variety ‘H108’ significantly outperformed the susceptible variety ‘H107’ in physiological indicators such as plant height, main stem diameter, and fresh weight, likely due to 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 treatment 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 AhCN genes provide insights into the mechanisms underlying peanut BW resistance and inform future research into genetic methods of improving peanut BW resistance.
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Differences in N6-methyladenosine (m6A) methylation among the three major clonal lineages of Toxoplasma gondii tachyzoites
Changning Wei, Hui Cao, Chenxu Li, Hongyu Song, Qing Liu, Xingquan Zhu, Wenbin Zheng
DOI: 10.1016/j.jia.2024.03.072 Online: 24 April 2024
Abstract25)      PDF in ScienceDirect      
Toxoplasma gondii is an important zoonotic parasite which has over 200 genotypes worldwide. N6-methyladenosine (m6A) methylation is a common epigenetic modification in messenger RNAs (mRNAs), and has been implicated in many aspects of mRNA biology. However, little is known about the difference in m6A methylation among different genotypes of T. gondii. In the present study, we employed methylated RNA immunoprecipitation sequencing (MeRIP-seq) technology to identify key genes exhibiting m6A methylation in the three major clonal lineages (Types I, II and III) of T. gondii tachyzoites. A total of 7650, 8359 and 7264 m6A peaks were identified in 5211, 5607 and 4974 genes in tachyzoites of RH strain (Type I), ME49 strain (Type II) and VEG strain (Type III), respectively. By comparing RH vs. ME49, RH vs. VEG, and ME49 vs. VEG, 735, 192 and 615 differentially methylated peaks (DMPs) were identified in 676, 168 and 553 genes, respectively. A combined MeRIP-seq and RNA-seq analysis revealed 172, 41 and 153 differentially methylated genes (DMGs) at both the m6A methylation and transcriptional level. Gene ontology term enrichment analysis of the DMPs identified differences related to Golgi apparatus, plasma membrane, signal transduction, RNA processing and catalytic step 2 spliceosome. KEGG pathway enrichment analysis showed that the DMGs are mainly involved in endocytosis, systemic lupus erythematosus and mTOR signaling pathway. These findings reveal genotype-specific differences in m6A methylation, which provide new resources for further investigations of the role of m6A in the pathobiology of T. gondii.
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