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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences institute of Wetland agriculture and Ecology Shandong Academy of Agricultural Sciences State key laboratory of Rice Biology China National Rice Research Institute National key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

Amino acids in piglet diarrhea: Effects, mechanisms and insights

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Animal Nutrition 2024年第1期16卷 267-274页

作者： Xihong Zhou Jing Liang Xia Xiong Yulong Yin key laboratory of Agro-ecological Processes in Subtropical Region Institute of Subtropical Agriculture The Chinese Academy of Sciences College of Advanced agricultural sciences University of Chinese Academy of Sciences

Piglet diarrhea is among one of the most serious health problems faced by the pig industry, resulting in significant economic losses. Diarrheal disease in piglets has a multifactorial etiology that is affected by physiology, environment, and management strategy. Diarrhea is the most apparent symptom of intestinal dysfunction. As a key class of essential nutrients in the piglet diet, amino acids confer a variety of beneficial effects on piglets in addition to being used as a substrate for protein synthesis, including maintaining appropriate intestinal integrity, permeability and epithelial renewal, and alleviating morphological damage and inflammatory and oxidative stress. Thus, provision of appropriate levels of amino acids could alleviate piglet diarrhea. Most amino acid effects are mediated by metabolites, gut microbes, and related signaling pathways. In this review, we summarize the current understanding of dietary amino acid effects on gut health and diarrhea incidence in piglets, and reveal the mechanisms involved. We also provide ideas for using amino acid blends and emphasize the importance of amino acid balance in the diet to prevent diarrhea in piglets.

关键词： Piglet Amino acid Diarrhea Gut microbe Immune

Impacts of agri-food e-commerce on traditional wholesale industry:Evidence from China

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Journal of Integrative agriculture 2024年第4期23卷 1409-1428页

作者： Ruyi Yang Jifang Liu Shanshan Cao Wei Sun Fantao Kong institute of agricultural information Chinese Academy of Agricultural SciencesBeijing 100081China institute of Special Animal and Plant sciences Chinese Academy of Agricultural SciencesChangchun 130112China

Rapidly expanding studies investigate the effects of e-commerce on company operations in the retail market.However,the interaction between agri-food e-commerce(AEC)and the traditional agri-food wholesale industry(AWI)has not received enough attention in the existing literature.Based on the provincial panel data from 2013 to 2020 in China,this paper examines the effect of AEC on AWI,comprising three dimensions:digitalization(DIGITAL),agrifood e-commerce infrastructure and supporting services(AECI),and agri-food e-commerce economy(AECE).First,AWI and AEC are measured using an entropy-based combination of indicators.The results indicate that for China as a whole,AWI has remained practically unchanged,whereas AEC exhibits a significant rising trend.Second,the findings of the fixed-effect regression reveal that DIGITAL and AECE tend to raise AWI,whereas AECI negatively affects AWI.Third,threshold regression results indicate that AECI tends to diminish AWI with three-stage inhibitory intensity,which manifests as a first increase and then a drop in the inhibition degree.These results suggest that with the introduction of e-commerce for agricultural product circulation,digital development will have catfish effects that tend to stimulate the vitality of the conventional wholesale industry and promote technical progress.Furthermore,the traditional wholesale industry benefits financially from e-commerce even while it diverts part of the traditional wholesale circulation for agricultural products.

关键词： agri-food e-commerce traditional wholesale industry panel threshold model dual-channel circulation

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Modularized viromimetic polymer nanoparticle vaccines(VPNVaxs) to elicit durable and effective humoral immune responses

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National Science Review 2024年第3期11卷 200-214页

作者： Zichao Huang Xinyu Zhuang Liping Liu Jiayu Zhao Sheng Ma Xinghui Si Zhenyi Zhu Fan Wu Ningyi Jin Mingyao Tian Wantong Song Xuesi Chen key laboratory of Polymer Ecomaterials Changchun Institute of Applied ChemistryChinese Academy of Sciences School of Applied Chemistry and Engineering University of Science and Technology of China Changchun Veterinary Research institute Chinese Academy of Agricultural Sciences Jilin Biomedical Polymers Engineering laboratory State key laboratory of Polymer Physics and Chemistry Changchun Institute of Applied Chemistry Chinese Academy of Sciences

Virus-like particle(VLP) vaccines had shown great potential during the COVID-19 pandemic, and was thought to be the next generation of antiviral vaccine technology due to viromimetic structures. However,the time-consuming and complicated processes in establishing a current recombinant-protein–based VLP vaccine has limited its quick launch to the out-bursting pandemic. To simplify and optimize VLP vaccine design, we herein report a kind of viromimetic polymer nanoparticle vaccine(VPNVax), with subunit receptor-binding domain(RBD) proteins conjugated to the surface of polyethylene glycol-b-polylactic acid(PEG-b-PLA) nanoparticles for vaccination against SARS-CoV-2. The preparation of VPNVax based on synthetic polymer particle and chemical post-conjugation makes it possible to rapidly replace the antigens and construct matched vaccines at the emergence of different viruses. Using this modular preparation system, we identified that VPNVax with surface protein coverage of 20%–25% had the best immunostimulatory activity, which could keep high levels of specific antibody titers over 5 months and induce virus neutralizing activity when combined with an aluminum adjuvant. Moreover, the polymer nano-vectors could be armed with more immune-adjuvant functions by loading immunostimulant agents or chemical chirality design. This VPNVax platform provides a novel kind of rapidly producing and efficient vaccine against different variants of SARS-CoV-2 as well as other viral pandemics.

关键词： vaccine polymer nanomaterials SARS-CoV-2

Several whitefly genome assemblies and an integrated whitefly gene search platform

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Insect Science 2024年第1期31卷 299-306页

作者： Xingnuo Li Peng Liang Mingyue Wu Shaoli Wang Qingjun Wu Wen Xie Youjun Zhang State key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina Sanya academy of Troprical agricultural Sciense SanyaHainanChina National Research institute of Breeding in Hainan Chinese Academy of Agricultural SciencesSanyaHainanChina

Dear Editor,The characteristics and importance of the whitefly Bemisia tabaci as an economic pest seem to continually get more and more attention.Among the whiteflies B.tabaci including,at least 11 genetic groups and 36 morphologically indistinguishable cryptic species,invasive MEAMl(Middle East-Asia Minor 1,"B"type)and MED(the Mediterranean,"Q"type)are the 2 most destructive cryptic species of the B.

关键词： Middle white East

Invasion of fall armyworm led to the succession of maize pests in Southwest China

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Journal of Integrative agriculture 2024年第4期23卷 1300-1314页

作者： Zezheng Fan Yifei Song Shengyuan Zhao Kongming Wu agricultural information institute Chinese Academy of Agricultural SciencesBeijing 100081China Guangdong laboratory for Lingnan Modern agriculture Guangzhou 510642China State key laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China

The invasive fall armyworm Spodoptera frugiperda(J.E.Smith)invaded Asia in 2018,colonizing the tropical and southern subtropical regions as well as migrating with the monsoons into Northeast Asia during spring and summer.This has resulted in widespread infestations,with significant impacts on maize production in various Asian countries.Previous studies have shown that the invasion of this pest can alter the species relationships of maize pests,but the actual impact on maize pest management is still unclear.This study investigated the changes in maize pest occurrence and pesticide use in the annual breeding areas of S.frugiperda in Yunnan Province and the Guangxi Zhuang Autonomous Region of China during 2017-2021,based on surveys and interviews with small farmers in maize production.The results showed that S.frugiperda has emerged as the dominant species among maize pests after invasion and colonization,replacing traditional pests such as Ostrinia furnacalis,Spodoptera litura,Agrotis ypsilon,and Rhopalosiphum maidis.The variety of pesticides used for maize pest control has changed from chlorpyrifos,lambda-cyhalothrin,and acetamiprid to emamectin benzoate-based pesticides with high effectiveness against S.frugiperda.Furthermore,the frequency of maize pest chemical applications has increased from an average of 5.88 to 7.21 times per season,with the amounts of pesticides used in summer and autumn maize being significantly higher than in winter and spring maize,thereby increasing application costs by more than 35%.The results of this study clarified the impact of S.frugiperda invasion on maize pest community succession and chemical pesticide use in tropical and south subtropical China,thereby providing a baseline for modifying the regional control strategies for maize pests after the invasion of this relatively new pest.

关键词： Spodoptera frugiperda annual breeding region sweet waxy corn economic evaluation

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Resilience effects for household food expenditure and dietary diversity in rural western China

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Journal of Integrative agriculture 2024年第2期23卷 384-396页

作者： Xiao Han Kaiyu Lyu Fengying Nie Yuquan Chen institute of agricultural Economics and Development Chinese Academy of Agricultural SciencesBeijing 100081China agricultural information institute Chinese Academy of Agricultural SciencesBeijing 100081China academy of Global Food Economics and Policy China Agricultural UniversityBeijing 100083China

A more resilient livelihood is increasingly recognized as an efficient way to improve vulnerable households’food security and optimize their dietary decisions.This study quantifies rural household resilience in western China,identifies the three pillars(absorptive capacity,adaptive capacity,and transformative capacity)contribution to resilience,and then establishes the estimated Resilience Capacity Index(RCI)linked with food security and dietary diversity supported by the multiple indicator multiple cause(MIMIC)model.Results show that,despite geographical heterogeneity,the RCI consistently increased from 2015 to 2021.Households with a higher RCI inheriting better capacity to deal with risk and shocks are significantly and positively correlated with increasing food expenditure and diversifying food choices.It can be because resilient households will allocate more money to food expenditure instead of saving for livelihood uncertainty.Thus,policymakers can provide more incentives for rural households to adopt more dynamic and effective risk management strategies.This,in turn,could yield positive spillover effects by preventing human capital loss associated with dietary-related chronic diseases and mortality.

关键词： resilience food expenditure dietary diversity China risk management

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Improving error-correcting capability in DNA digital storage via soft-decision decoding

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National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Guangdong Provincial key laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

Development of small intestinal barrier function and underlying mechanism in chinese indigenous and Duroc piglets during suckling and weaning periods

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Animal Nutrition 2024年第1期16卷 429-442页

作者： Sujuan Ding Yating Cheng Md Abul Kalam Azad Qian Zhu Pan Huang Xiangfeng Kong CAS key laboratory of Agro-ecological Processes in Subtropical Region Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process Institute of Subtropical Agriculture Chinese Academy of Sciences College of Advanced agricultural sciences University of Chinese Academy of Sciences

This study explored the developmental changes in small intestinal barrier function and the potential regulatory roles of intestinal microbiota and metabolites in different breeds of piglets during suckling and weaning periods. Taoyuan black(TB), Xiangcun black(XB), and Duroc(DR) piglets(10 litters per breed; half male and half female) were selected for sampling to evaluate the intestinal barrier-related indexes and intestinal microbiota and metabolites at 1, 10, 21(weaned), and 24(3 d after weaning)d old. The results showed that weaning led to severe shedding of small intestinal microvilli and sparse microvilli arrangement. D-lactate level in the ileum of TB and XB piglets during suckling and weaning periods was lower(P key factors for developing small intestinal barrier functions in different breeds of piglets.

关键词： chinese indigenous piglet Duroc piglet Immune function Intestinal barrier function Weaning stress