Journal of Integrative Agriculture最新文献

{"title":"3D genomic alterations during development of skeletal muscle in chicken1","authors":"Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He, Yan Li, Hua Kui, Xue Bai, Bo Zeng, Yao Zhang, Qing Zhu, Xiaoling Zhao, Mingzhou Li, Diyan Li","doi":"10.1016/j.jia.2024.03.052","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.052","url":null,"abstract":"The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build a chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140200588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Straw interlayer improves sunflower root growth: Evidence from moisture and salt migration and the microbial community in saline-alkali soil","authors":"Mengmeng Chen, Guoli Wang, Yupeng Jing, Jie Zhou, Jiashen Song, Fangdi Chang, Ru Yu, Jing Wang, Weini Wang, Xia Sun, Hongyuan Zhang, Yuyi Li","doi":"10.1016/j.jia.2024.03.048","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.048","url":null,"abstract":"A straw interlayer added to soil can effectively reduce soil salinity effects on plant growth, however, the effects of soil moisture, salt and microbial community composition on plant growth under a straw interlayer are unclear. A rhizobox study was conducted to investigate the role of straw interlayer thickness on soil moisture, salt migration, microbial community composition, as well as root growth in sunflower. The study included four treatments: Control (no straw interlayer); S3 (straw interlayer of 3.0 cm); S5 (straw interlayer of 5.0 cm); S7 (straw interlayer of 7.0 cm). Straw interlayer treatments increased soil moisture by 8.2%-11.0% after irrigation and decreased soil salt content after the bud stage in 0-40 cm soil. Total root length, total root surface area, average root diameter, total root volume and the number of root tips of sunflower plants were higher under straw interlayer treatments than in the control, and were highest under the S5 treatment. This stimulated root growth was ascribed to the higher abundance of Chloroflexi and Verrucomicrobia bacteria in soil with a straw interlayer, which was increased by 55.7 and 54.7%, respectively, in the S5 treatment. Addition of a straw interlayer of 5 cm thickness is a practical and environmentally feasible approach for improving sunflower root growth in saline-alkali soil.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140146468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitigation of N2O emissions in water-saving paddy fields: Evaluating organic fertilizer substitution and microbial mechanisms","authors":"Delei Kong, Xianduo Zhang, Qidong Yu, Yaguo Jin, Peikun Jiang, Shuang Wu, Shuwei Liu, Jianwen Zou","doi":"10.1016/j.jia.2024.03.047","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.047","url":null,"abstract":"Water-saving irrigation strategies can successfully alleviate methane emissions from rice fields, but significantly stimulate nitrous oxide (NO) emissions because of variations in soil oxygen level and redox potential. However, the relationship linking soil NO emissions to nitrogen (N) functional genes during various fertilization treatments in water-saving paddy fields has rarely been investigated. Furthermore, the mitigation potential of organic fertilizer substitution on NO emissions and the microbial mechanism in rice fields must be further elucidated. Our study examined how soil NO emissions were affected by related functional microorganisms [ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and ] to various fertilization treatments in a rice field in southeast China over two years. In this study, three fertilization regimes were applied to rice cultivation: a no nitrogen (N) (Control), an inorganic N (N), and an inorganic N with partial N substitution with organic manure (N+N). Over two rice-growing seasons, cumulative NO emissions averaged 0.47, 4.62 and 4.08 kg ha for the Control, N and N+N treatments, respectively. In comparison to the N treatment, the N+N fertilization regime considerably reduced soil NO emissions by 11.6% while maintaining rice yield, with a lower NO emission factor from fertilizer N (EF) of 0.95%. Nitrogen fertilization considerably raised the AOB, and gene abundances, in comparison to the Control treatment. Moreover, the substitution of organic manure for inorganic N fertilizer significantly decreased AOB and gene abundances and increased gene abundance. The AOB responded to N fertilization more sensitively than the AOA. Total NO emissions significantly correlated positively with AOB and gene abundances while having a negative correlation with gene abundance and the / ratio across N-fertilized plots. In summary, we conclude that organic manure substitution for inorganic N fertilizer decreased soil NO emissions primarily by changing the soil NO-N, pH and DOC levels, thus inhibiting the activities of ammonia oxidation in nitrification and nitrite reduction in denitrification, and strengthening NO reduction in denitrification from water-saving rice paddies.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140146318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fhb9, a major QTL for Fusarium head blight resistance improvement in wheat","authors":"Fuping Zhang, Hongjun Zhang, Jilu Liu, Xiaomeng Ren, Yanpeng Ding, Fangyao Sun, Zhenzhen Zhu, Xi He, Yang Zhou, Guihua Bai, Zhongfu Ni, Qixin Sun, Zhenqi Su","doi":"10.1016/j.jia.2024.03.045","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.045","url":null,"abstract":"head blight (FHB), mainly caused by , is one of the most devastating diseases of wheat worldwide. Identification and validation of major quantitative trait loci (QTLs) for FHB resistance without negative effects on agronomic traits is critical to success in breeding FHB-resistant cultivars. In this study, a stable major QTL on chromosome arm 2DL was identified by evaluating a recombinant inbred line (RIL) population derived from Shi4185×Shijiazhuang 8 in both field and greenhouse experiments. QTL mapping and pedigree analyses indicated that the 2DL QTL is the same QTL as previously identified in Ji5265, therefore, designated . Four kompetitive amplicon sequence polymorphism (KASP) markers were developed based on exome capture sequencing data to enhance marker density in the region, and it was delimited to an interval between single nucleotide polymorphism (SNP) markers (533.8) and (525.9 Mb) explained 26.0-30.1% of the phenotypic variation. Analysis of the geographic distribution of the resistance allele suggested that it originated from Huang-Huai winter wheat region in China, and very low frequency of in modern Chinese cultivars reveals that it has not been widely deployed in breeding programs. Field and greenhouse evaluation of yield-related traits of near-isogenic lines (NILs) contrasting in alleles indicated that resistance allele did not show any adverse effects on those traits. showed an additive effect on enhancing FHB resistance with . Therefore, is a valuable major QTL for improving FHB resistance in wheat and the near-diagnostic markers developed in this study will facilitate its deployment in wheat breeding programs.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140146316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shading and waterlogging interactions exacerbate summer maize yield losses by reducing assimilate accumulation and remobilization processes","authors":"Qinghao Wang, Juan Hu, Weizhen Yu, Limin Gu, Peng Liu, Bin Zhao, Wenchao Zhen, Jiwang Zhang, Baizhao Ren","doi":"10.1016/j.jia.2024.03.046","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.046","url":null,"abstract":"Persistent overcast rain was an essential limiting factor for summer maize production, of which immediate impact was the dual pressure of waterlogging and shading. However, the mechanism of independent and combined effects of waterlogging and shading induced maize yield losses are rarely studied, especially at different growth stages. Denghai 605 (DH605) was selected to be subjected shading, waterlogging, and their combined stress at the 3rd leaf stage (V3), the 6th leaf stage (V6), and tasseling stage (VT). Results showed that shading, waterlogging and their combination significantly limited the expansion of leaf area, and decreased leaf net photosynthetic rate () and net assimilation rate (NAR), thus reducing the crop growth rate (CGR) and biomass accumulation. At the same time, compared to control, the process of lignin synthesis was inhibited under stressed treatment, resulting in reduced stem mechanical strength and a poor development of the vascular system, of which change significantly reduced efficiency of assimilate remobilization to the ear and ultimately grain yield. The most significant effects of waterlogging and combined stresses on yield were occurred at V3 stage, followed by the V6 and VT stages. The most significant effects of shading were occurred at VT stage, followed by the V6 and V3 stages. Moreover, the compound stress exacerbated the damage brought about by a single stress. It is predicted that climate change will increase the frequency of abiotic stress assemblages, and the results of these findings provide some direction for further research on maize breeding in summer maize under continuous rainy conditions in the future.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140156240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated transcriptomics and metabolomics analysis provide insights into the alleviation of waterlogging stress in maize by exogenous spermidine application","authors":"Xiuling Wang, Li Niu, Huaipan Liu, Xucun Jia, Yulong Zhao, Qun Wang, Yali Zhao, Pengfei Dong, Moubiao Zhang, Hongping Li, Panpan An, Zhi Li, Xiaohuan Mu, Yongen Zhang, Chaohai Li","doi":"10.1016/j.jia.2024.03.041","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.041","url":null,"abstract":"Waterlogging stress has been found to have adverse impacts on plant growth, subsequently reducing crop yields. Spermidine (Spd), a second messenger, positively affects the growth of plants under waterlogging stress. However, the molecular mechanisms of exogenous Spd application alleviating waterlogging stress remained unclear. In this study, we performed physiological analysis and multi-omics to underlying the effect of Spd application on waterlogging stress. Spd application increased genes expression level of light-harvesting complex (LHC) and photosynthesis-related and starch-related pathway, inhibited chlorophyll degradation and maintained higher photosynthetic rate, thus increased biomass accumulation under waterlogging stress. The activation of genes related trehalose and Spd biosynthesis would result in high accumulation of trehalose and endogenous Spd. Inhibiting 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase (ACO,) expression contributed to reduced ethylene emission. All those changes increased maize resistance to waterlogging. After Spd sparying, auxin-related genes up-regulated and IAA content was increased, those favor cell elongation in maize and thus keep normal growth after Spd application under waterlogging stress. Most of genes involved in lipids were up-regulated and thus increased lipids content and protected cell membranes in maize after Spd application under waterlogging conditions. All those changes contributed to increasing the resistance to waterlogging stress. These findings broaden our understanding of the regulatory roles of Spd in alleviating waterlogging damage and will provide evidence for breeding waterlogging-tolerant maize varieties.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated assessment of yield, nitrogen use efficiency and ecosystem economic benefits of use of controlled-release and common urea in ratoon rice production","authors":"Zijuan Ding, Ren Hu, Yuxian Cao, Jintao Li, Dakang Xiao, Jun Hou, Xuexia Wang","doi":"10.1016/j.jia.2024.03.038","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.038","url":null,"abstract":"Controlled-release urea (CRU) is commonly used to improve the crop yield and nitrogen use efficiency (NUE). However, few studies have investigated the effects of CRU in the ratoon rice system. Ratoon rice is the practice of obtaining a second harvest from tillers originating from the stubble of the previously harvested main crop. In this study, a 2-year field experiment using a randomized complete block design was conducted to determine the effects of CRU on the yield, NUE, and economic benefits of ratoon rice, including the main crop, to provide a theoretical basis for fertilization of ratoon rice. The experiment included four treatments: (i) no N fertilizer (CK); (ii) traditional practice with 5 applications of urea applied at different crop growth stages by surface broadcasting (FFP); (iii) one-time basal application of CRU (BF1); and (iv) one-time basal application of CRU combined with common urea (BF2). The BF1 and BF2 treatments significantly increased the main crop yield by 17.47 and 15.99% in 2019, and by 17.91 and 16.44% in 2020, respectively, compared with FFP treatment. The BF2 treatment achieved similar yield of the ratoon crop to the FFP treatment, whereas the BF1 treatment significantly increased the yield of the ratoon crop by 14.81% in 2019 and 12.21% in 2020 compared with the FFP treatment. The BF1 and BF2 treatments significantly improved the 2-year apparent N recovery efficiency, agronomic NUE, and partial factor productivity of applied N by 11.47–16.66, 27.31–44.49, and 9.23–15.60%, respectively, compared with FFP treatment. The BF1 and BF2 treatments reduced the chalky rice rate and chalkiness of main and ratoon crops relative to the FFP treatment. Furthermore, emergy analysis showed that the production efficiency of the BF treatments was higher than that of the FFP treatment. The BF treatments reduced labor input due to reduced fertilization times and improved the economic benefits of ratoon rice. Compared with the FFP treatment, the BF1 and BF2 treatments increased the net income by 14.21–16.87 and 23.76–25.96%, respectively. Overall, the one-time blending use of CRU and common urea should be encouraged to achieve high yield, high nitrogen use efficiency, and good quality of ratoon rice, which has low labor input and low apparent N loss.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140128173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Control of highly pathogenic avian influenza through vaccination1","authors":"Xianying Zeng, Jianzhong Shi, Hualan Chen","doi":"10.1016/j.jia.2024.03.044","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.044","url":null,"abstract":"The stamping-out strategy has been used to control highly pathogenic avian influenza viruses in many countries, driven by the belief that vaccination would not be successful against such viruses and fears that avian influenza virus in vaccinated birds would evolve more rapidly and pose a greater risk to humans. In this article, we summarize the successes in controlling highly pathogenic avian influenza in China and make suggestions regarding the requirements for vaccine selection and effectiveness. In addition, we present evidence that vaccination of poultry not only eliminates human infection with avian influenza virus, but also significantly reduces and abolishes some harmful characteristics of avian influenza virus.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a novel multi-drug resistant plasmid co-harbouring Extended-Spectrum β-Lactamase resistance genes blaPER-4 and blaOXA-10 in Moellerella wisconsensis of sheep","authors":"Xueliang Zhao, Yongqiang Miao, Hongmei Chen, Honghu Shan, Juan Wang, Yang Wang, Jianzhong Shen, Zengqi Yang","doi":"10.1016/j.jia.2024.03.040","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.040","url":null,"abstract":"","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional characterization of sensory neuron membrane protein 1a involved in sex pheromone detection of Apolygus lucorum (Hemiptera: Miridae)","authors":"Yan Li, Xingkui An, Shuang Shan, Xiaoqian Pang, Xiaohe Liu, Yang Sun, Adel Khashaveh, Yong-jun Zhang","doi":"10.1016/j.jia.2024.03.043","DOIUrl":"https://doi.org/10.1016/j.jia.2024.03.043","url":null,"abstract":"The mirid bug (Hemiptera: Miridae) is a polyphagous pest that affects a wide range of host plants. Its control remains challenging mainly due to its rapid reproduction, necessitating an understanding of sex pheromone communication. The recognition of sex pheromones is vital for courtship and mating behaviors, and is mediated by various chemosensory-associated proteins. Among these, sensory neuron membrane protein (SNMP), a CD36-related protein, is suggested to play crucial roles in detecting sex pheromones. In this study, we employed transcriptomic and genomic data from . and phylogenetic approaches, and identified four putative genes (, and ) with full open reading frames. Expression analysis revealed the ubiquitous presence of transcripts in multiple tissues, with only exhibiting male-biased expression in the antennae, suggesting its potential role in male chemosensation. Functional analysis using the oocyte expression system, coupled with two-electrode voltage clamp recording, demonstrated that the co-expression of AlucSNMP1a with specific pheromone receptors (PRs) and the co-receptor (Orco) significantly enhanced electrophysiological responses to sex pheromones compared to the co-expression of PRs and Orco alone. Moreover, the results indicated that the presence of AlucSNMP1a not only affected the responsiveness to sex pheromones but also influenced the kinetics (activation and inactivation) of the induced signals. In contrast, the co-expression of AlucSNMP1b with AlucPR/Orco complexes had no impact on the inward currents induced by two pheromone compounds. An examination of the selective pressures on genes across 20 species indicated strong purifying selection, implying potential functional conservation in various insects. These findings highlight the crucial role of AlucSNMP1a in the response to sex pheromones.","PeriodicalId":16305,"journal":{"name":"Journal of Integrative Agriculture","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140127744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}