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Whole-genome sequencing in medicinal plants:current progress and prospect

Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang Leng Wei Sun Baocai Liu Xue Feng Xiwen Li Shilin Chen institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China institute of agricultural bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant Genome”to decipher their genetic code.However,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity.Whole genomes of 123 medicinal plants were published until September 2022.These published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing strategies.More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes.Diploid species account for a majority of sequenced medicinal plants.The whole genomes of plants in the Poaceae family are the most studied.Almost 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal effects.Medicinal plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to complete.In addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome.Herein,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants.Moreover,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were reviewed.We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

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Mulberry leaf supplementation inhibits skatole deposition by regulating gut microbiota and upregulating liver cytochrome P4501A1 expression in finishing pigs

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Animal Nutrition 2024年第1期16卷 34-44页

作者： Yuqing Sun Xiaoming Men Tianbao Lin Bo Deng Shi Zhong Jinxi Huo Kaipeng Qin Zhiqiang Lv Ziwei Xu Yougui Li institute of Sericulture and Tea Zhejiang Academy of Agricultural Sciences institute of Animal Husbandry and Veterinary Science Zhejiang Academy of Agricultural Sciences

Skatole, a strong fecal odor substance, is generated through microbial degradation of tryptophan in the animal hindgut. It easily accumulates in adipose tissue and affects meat quality. In this study, the effect of mulberry leaf supplementation on skatole in finishing pigs was studied. In a 35-day trial, 20 finishing pigs (barrows and gilts) were fed with a basal diet or basal diet with 6% mulberry leaves. Growth performance of the pigs (n=10) was automatically recorded by a performance-testing feeder system and 8 pigs in each treatment were slaughtered and sampled for the remaining tests. Skatole and short-chain fatty acids were detected using HPLC and gas chromatography, respectively. Fecal microbiota were analyzed using 16S r RNA gene sequencing. The metabolomics analysis of feces and serum was performed with UHPLC-MS/MS. The major cytochrome P450 (CYP) enzymes that catalyze skatole degradation in the liver were tested by using RT-PCR and Western blot. Effects of major bioactive compounds in mulberry leaves on the CYP genes were verified in the hepatic cell line Hep G2 in an in vitro test (n=3). In finishing pigs, mulberry leaf supplementation had no significant effect on the average daily gain, average daily feed intake, and feed conversion ratio (P>0.05), but reduced skatole levels in feces, serum, and backfat (P<0.05), and increased acetic acid levels in feces (P=0.027). Mulberry leaf supplementation decreased the relative abundance of the skatole-producing bacteria Megasphaera and Olsenella (P<0.05). Indole-3acetic acid, the intermediate that is essential for skatole production, was significantly reduced in feces by mulberry leaf supplementation (P<0.05) and was positively correlated with skatole content in feces (P=0.004). In pigs treated with mulberry leaves, liver CYP1A1 expression was increased (P<0.05) and was negatively correlated with skatole content in backfat (P=0.045). The in vitro test demonstrated that mulberry leaf polyphenols and polysaccharides could directly stimulate CYP1A1 expression in h

关键词： Pig Skatole Mulberry leaf Microbiota Cytochrome P450

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Autophagy receptor ZmNBR1 promotes the autophagic degradation of ZmBRI1a and enhances drought tolerance in maize

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Journal of Integrative Plant Biology 2024年第6期66卷 1068-1086页

作者： Yang Xiang Guangdong Li Qian Li Yingxue Niu Yitian Pan Yuan Cheng Xiangli Bian Chongyang Zhao Yuanhong Wang Aying Zhang College of Life Sciences Nanjing Agricultural University State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization Nanjing Agricultural University Sanya institute of Nanjing agricultural University Nanjing Agricultural University

Drought stress is a crucial environmental factor that limits plant growth, development, and productivity.Autophagy of misfolded proteins can help alleviate the damage caused in plants experiencing drought.However, the mechanism of autophagy-mediated drought tolerance in plants remains largely unknown.Here, we cloned the gene for a maize(Zea mays)selective autophagy receptor, NEXT TO BRCA1GENE 1(ZmNBR1), and identified its role in the response to drought stress. We observed that drought stress increased the accumulation of autophagosomes. RNA sequencing and reverse transcriptionquantitative polymerase chain reaction showed that ZmNBR1 is markedly induced by drought stress. ZmNBR1 overexpression enhanced drought tolerance, while its knockdown reduced drought tolerance in maize. Our results established that ZmNBR1 mediates the increase in autophagosomes and autophagic activity under drought stress.ZmNBR1 also affects the expression of genes related to autophagy under drought stress. Moreover, we determined that BRASSINOSTEROID INSENSITIVE1A(ZmBRI1a), a brassinosteroid receptor of the BRI1-like family, interacts with ZmNBR1. Phenotype analysis showed that ZmBRI1a negatively regulates drought tolerance in maize, and genetic analysis indicated that ZmNBR1 acts upstream of ZmBRI1a in regulating drought tolerance. Furthermore, ZmNBR1facilitates the autophagic degradation of ZmBRI1a under drought stress. Taken together, our results reveal that ZmNBR1 regulates the expression of autophagy-related genes, thereby increasing autophagic activity and promoting the autophagic degradation of ZmBRI1a under drought stress, thus enhancing drought tolerance in maize. These findings provide new insights into the autophagy degradation of brassinosteroid signaling components by the autophagy receptor NBR1 under drought stress.

关键词： autophagy receptor drought tolerance Zea mays ZmBRI1a ZmNBR1

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Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng agricultural Genomics institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw materials.The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding.Notably,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress resistance.However,a considerable gap remains between pea functional genomics and molecular breeding.This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

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Cross-resistance and genetics of field-evolved resistance to chlorfenapyr in Plutella xylostella

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Insect Science 2024年第2期31卷 533-541页

作者： Cheng Qian Jialin Li Shuwen Wu Yihua Yang Yidong Wu Xingliang Wang Sanya institute of Nanjing agricultural Universty SanyaHainanChinaand College of Plant Protection Nanjing Agricultural UniversNanjingChina

Chlorfenapyr is a broad-spectrum halogenated pyrrole insecticide with a unique mode of action.Due to the misuse and overuse of this chemical,resistance has been reported in several arthropods,including Plutella xylostella,which is one of the most destructive insect pests afflicting crucifers worldwide.A better understanding of the cross-resistance and genetics of field-evolved chlorfenapyr resistance could effectively guide resistance management practices.Here,the chlorfenapyr resistance of a fieldderived population of P xylostella was introgressed into the susceptible IPP-S strain using a selection-assisted multigenerational backcrossing approach.The constructed nearisogenic strain,TH-BCsF2,shared 98.4%genetic background with the recurrent parent IPP-S strain.The TH-BCsF2 strain showed 275-fold resistance to chlorfenapyr,but no significant cross-resistance to spinosad,abamectin,chlorpyrifos,β-cypermethrin,indoxacarb,chlorantraniliprole,or broflanilide(no more than 4.2-fold).Genetic analysis revealed that resistance was autosomal,incompletely dominant,and conferred by 1 major gene or a few tightly linked loci.The synergism of metabolic inhibitors(PBO,DEM,and DEF)to chlorfenapyr was very weak(<1.7-fold),and the metabolic enzyme activities in the TH-BCsF2 strain were not significantly elevated compared with the IPP-S strain.The results enhances our understanding of the genetic traits of chlorfenapyr resistance,and provides essential information for improving resistance management strategies.

关键词： chlorfenapyr cross-resistance mode of inheritance near-isogenic line Plutellaxylostella

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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

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Promoting grain production through high-standard farmland construction:Evidence in China

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Journal of Integrative Agriculture 2024年第1期23卷 324-335页

作者： Shuai Hao Guogang Wang Yantao Yang Sicheng Zhao Shengnan Huang Liping Liu Huanhuan Zhang institute of agricultural Economics and Development Chinese Academy of Agricultural SciencesBeijing 100081China

Food security is a strategic priority for a country’s economic development.In China,high-standard farmland construction(HSFC)is an important initiative to stabilize grain production and increase grain production capacity.Based on panel data from 31 sample provinces,autonomous regions,and municipalities in China from 2005–2017,this study explored the impact of HSFC on grain yield using the difference-in-differences(DID)method.The results showed that HSFC significantly increased total grain production,which is robust to various checks.HSFC increased grain yield through three potential mechanisms.First,it could increase the grain replanting index.Second,it could effectively reduce yield loss due to droughts and floods.Last,HSFC could strengthen the cultivated land by renovating the low-and medium-yielding fields.Heterogeneity analysis found that the HSFC farmland showed a significant increase in grain yield only in the main grain-producing areas and balanced areas.In addition,HSFC significantly increased the yields of rice,wheat,and maize while leading to a reduction in soybean yields.The findings suggest the government should continue to promote HSFC,improve construction standards,and strictly control the“non-agriculturalization”and“non-coordination”of farmland to increase grain production further.At the same time,market mechanisms should be used to incentivize soybean farming,improve returns and stabilize soybean yields.

关键词： high-standard farmland farmland construction food security food production area difference-in-differences

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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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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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Retinoic acid alleviates rotavirus-induced intestinal damage by regulating redox homeostasis and autophagic flux in piglets

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Animal Nutrition 2024年第1期16卷 409-421页

作者： Xin Lai Aimin Wu Bing Yu Hui Yan Junqiu Luo Ping Zheng Jie Yu Daiwen Chen institute of Animal Nutrition Sichuan Agricultural University Key Laboratory for Animal Disease-resistance Nutrition of China Ministry of Education Sichuan Agricultural University

Rotaviruses(RV) are a major cause of severe gastroenteritis, particularly in neonatal piglets. Despite the availability of effective vaccines, the development of antiviral therapies for RV remains an ongoing challenge. Retinoic acid(RA), a metabolite of vitamin A, has been shown to have anti-oxidative and antiviral properties. However, the mechanism by which RA exerts its intestinal-protective and antiviral effects on RV infection is not fully understood. The study investigates the effects of RA supplementation in Duroc × Landrace × Yorkshire(DLY) piglets challenged with RV. Thirty-six DLY piglets were assigned into six treatments, including a control group, RA treatment group with two concentration gradients(5and 15 mg/d), RV treatment group, and RV treatment group with the addition of different concentration gradients of RA(5 and 15 mg/d). Our study revealed that RV infection led to extensive intestinal architecture damage, which was mitigated by RA treatment at lower concentrations by increasing the villus height and villus height/crypt depth ratio(P < 0.05), enhancing intestinal stem cell signaling and promoting intestinal barrier functions. In addition, 15 mg/d RA supplementation significantly increased NRF2 and HO-1 protein expression(P < 0.05) and GSH content(P < 0.05), indicating that RA supplementation can enhance anti-oxidative signaling and redox homeostasis after RV challenge. Additionally,the research demonstrated that RA exerts a dual impact on the regulation of autophagy, both stimulating the initiation of autophagy and hindering the flow of autophagic flux. Through the modulation of autophagic flux, RA influence the progression of RV infection. These findings provide new insights into the regulation of redox hemostasis and autophagy by RA and its potential therapeutic application in RV infection.

关键词： Rotavirus Piglet Retinoic acid Intestinal barrier Redox hemostasis Autophagic flux

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