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The Crop Journal 2024年第1期12卷 222-231页

作者： Huawei Shi Weichong Wang Lifeng Gao Jirong Wu Chengmei Hu Huishu Yan Yugang Shi Ning Li Youzhi Ma Yongbin Zhou Zhaoshi Xu Jun Chen Wensi Tang Kai Chen Daizhen Sun Yuxiang Wu Ming Chen College of agriculture Shanxi Agricultural UniversityJinzhong 030801ShanxiChina National key Facility for Crop Gene resources and genetic Improvement Key Laboratory of Biology and Genetic Improvement of Triticeae CropsMinistry of AgricultureInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Nitrogen(N)fertilizer application is essential for crop-plant growth and *** genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by *** subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling *** the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition *** SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type *** developed two functional markers for Hap 1,the favorable allele of TaBOX.

关键词： Wheat NUE Genome-wide association study Nitrogen sensitive index Chlorate inhibition rate

OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

Glycolysis and gluconeogenesis are involved of glucose metabolism adaptation during fasting and re-feeding in black carp(Mylopharyngodon piceus)

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Aquaculture and Fisheries 2024年第2期9卷 226-233页

作者： Yafan Dai Yubang Shen Jiamin Guo Hao Yang Feng Chen Wei Zhang Wenhui Wu Xiaoyan Xu Jiale Li key laboratory of Freshwater aquatic genetic resources Ministry of Agriculture and Rural AffairsShanghai Ocean UniversityShanghai201306China Shanghai Engineering Research Centre of Aquaculture Shanghai Ocean UniversityShanghai201306China

Both in nature and in aquaculture,fish may experience periods of food scarcity or *** metabolic regulation of fish when nutritional state changes is a complex process that involves many *** study glucose metabolism adaptability during fasting and re-feeding in the black carp(Mylopharyngodon piceus),we measured changes in some biochemical indicators related to glucose *** fish were sampled on days 0,1,3,5,and 10 of fasting(F,S1,S3,S5,and S10,respectively)and days 1,3,and 5 of re-feeding(RF1,RF3,and RF5,respectively).The serum glucose concentration decreased significantly at S1,reached the lowest point at S10,and increased significantly at RF1(P<0.05).The concentration of liver glycogen decreased significantly at S1 and reached the lowest level at S3,whereas the muscle glycogen level decreased significantly at S5 and reached the lowest value at S10(P<0.05).Both liver and muscle glycogen levels returned to the pre-fasting level at RF5(P<0.05).Regarding glycolysis,the concentrations of pyruvate kinase(PK)and hexokinase(HK)decreased significantly at S5 and increased significantly at RF5 and RF1,respectively(P<0.05).The concentrations of glucokinase(GCK)and insulin decreased significantly at S1 and increased significantly at RF1 and RF3,respectively(P<0.05).The mRNA expression levels of liver GCK and glucose transporter 2(GLUT2)decreased significantly at S1 and increased significantly at RF1 and RF5,respectively(P<0.05).As for gluconeogenesis,the concentration of glucose-6-phosphatase(G6PC)increased significantly at S1 and decreased significantly at RF1(P<0.05).The concentrations of glucagon and glucocorticoid(GC)increased significantly at S3 and significantly decreased at RF1 and RF5,respectively(P<0.05).The mRNA expression levels of liver G6PC and phosphoenolpyruvate carboxykinase(PEPCK)increased significantly at S3 and S1,and both decreased significantly at RF1(P<0.05).These results indicate that coordination between glycolysis and gluconeogen

关键词： Mylopharyngodon piceus Fasting Glucose metabolism Glycolysis Gluconeogenesis

Aquaculture species diversification in China

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Aquaculture and Fisheries 2024年第2期9卷 206-217页

作者： Gen Hua Yue Yi Xuan Tay Joey Wong Yubang Shen Junhong Xia Temasek Life Sciences laboratory National University of Singapore1 Research Link117604Singapore key laboratory of Freshwater aquatic genetic resources Ministry of Agriculture and Rural AffairsShanghai Ocean UniversityShanghai201306China State key laboratory of Biocontrol Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic AnimalsCollege of Life SciencesSun Yat-Sen UniversityGuangzhou510275China

China has been the top aquaculture producer in the world since *** 800 species and 240 improved varieties have been used in China’s aquaculture,which is the most diverse collection of species on this *** diversification,along with other aquaculture technologies,contributes significantly to the increase of China’s aquaculture production,whereas the use of too many species in aquaculture has resulted in some issues related to the environment and *** provide an updated overview of the species currently used in Chinese aquaculture in this *** examine critically the main drivers of species diversification in China with *** also introduce Chinese approaches to improve and certify new species and varieties for commercial *** believe that further species diversification is not a priority in China’s aquaculture,while further improvement of aquaculture technologies for major and native species is essential for green,profitable,and sustainable(GPS)*** implications of China’s experiences with species diversification for global aquaculture species diversification are discussed.

关键词： Fish Species Diversification Improvement Future

OsPPG encodes a pseudouridine-5'-phosphate glycosidase and regulates rice spikelet development

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The Crop Journal 2024年第3期12卷 698-708页

作者： Rui Chen Dagang Tian Yarong Lin Jiaqing Huang Qinqin Yang Yupei Li Huaqing Liu Shaohua Yang Jingyang Chen Shufen Zhou Feng Wang Shubiao Zhang key laboratory of genetics Breeding and Multiple Utilization of CropsMinistry of Education/Key Laboratory of Biological Breeding for Fujian and Taiwan CropsMinistry of Agriculture and Rural AffairsFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Fujian key laboratory of genetic Engineering for agriculture Biotechnology Research InstituteFujian Academy of Agricultural SciencesFuzhou 350003FujianChina Institute of resources Environment and Soil FertilizerFujian Academy of Agricultural SciencesFuzhou 350013FujianChina

Florets are the basic structural units of spikelets,and their morphogenesis determines the yield and quality of rice ***,whether and how pseudouridine-5’-phosphate glycosidase participates in rice spikelet development remains an open *** this study,we identified a novel gene,OsPPG,which encodes a peroxisome-localized pseudouridine-5’-phosphate glycosidase and regulates the development of rice *** mutants exhibited abnormal sterile lemma,lemma,palea,lodicule,stamens,and pistils;male sterility;shorter panicles;and reduced plant *** was found to regulate several OsMADS genes,thereby affecting the morphogenesis of rice ***,metabolomics revealed that the OsPPG gene was involved in the decomposition of pseudouridine via the pyrimidine metabolism pathway and may affect the jasmonic acid signaling *** results suggest that OsPPG is a key regulator of rice spikelet development.

关键词： OsPPG Reproductive regulation Spikelet development Rice

Identification of serum immunoglobulin M(IgM)of crucian carp(Carassius auratus gibelio)and immune response to cyprinid herpesvirus 2 infection

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Aquaculture and Fisheries 2024年第2期9卷 172-180页

作者： Shuran Wang Haotian Wu Longlong Wang Pinhua Wang Liqun Lu Yousheng Jiang Ye Zhang Dan Xu National Pathogen Collection Center for aquatic Animals Shanghai Ocean UniversityShanghai201306China key laboratory of aquatic genetic resources of the ministry of agriculture Shanghai Ocean UniversityShanghai201306China National Demonstration Center for Experimental Fisheries Science Education Shanghai Ocean UniversityShanghai201306China

Crucian carp(Carassius auratus gibelio),an extensively cultivated freshwater fish,was one of the model species for the study of fish *** antibodies were advantageous molecular tools for studying teleost immune ***,polyclonal antibodies reacting with immunoglobulins(Ig)were used successfully in studies of the teleost *** the present study,we produced polyclonal antibody against CH2 domains of crucian carp IgM,and measured the in vivo dynamics of IgM mRNA caused by CyHV-2 *** recombinant protein IgM with relative molecular weight about 53 KD was correctly expressed in prokaryotic *** specificity of the polyclonal antibody was evaluated by Western blotting and results revealed that the antibody not only specifically recognized crucian carp serum but also cross-reacted with grass carp *** RT-PCR analysis demonstrated the expression of IgM mRNA changed significantly after CyHV-2 *** expression of IgM in the kidney increased and reached a maximum at 6 h post-infection(hpi),while dropped to a low level at 5 days post-infection(dpi).In conclusion,the expression of IgM was significantly upregulated in the kidney of crucian carp infected with CyHV-2,indicating that IgM played a potential role in systemic immunity against viral *** antibody against crucian carp IgM had certain clinical relevance,which might provide insight into the early stage of virus infection and prevention of the disease.

关键词： Immunoglobulin M Crucian carp Polyclonal antibody Cyprinid herpesvirus 2 Immunoprotection

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

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The Crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que key laboratory of Sugarcane Biology and genetic Breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National key laboratory for Tropical Crop Breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen ***,the resistance mechanisms of WRKY genes in sugarcane remain *** the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense *** identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar *** gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)***,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium ***,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani *** and caused down-regulated expression of immune marker-related *** analysis indicated suppressed expression of most JAZ genes in the signal transduction ***4 interacted with ScJAZ13 to repress its *** thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling *** present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice

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The Crop Journal 2024年第1期12卷 68-78页

作者： Liyu Huang Yachong Bao Shiwen Qin Min Ning Qinyan Li Qingmao Li Shilai Zhang Guangfu Huang Jing Zhang Wensheng Wang Binying Fu Fengyi Hu key laboratory of Biology and Germplasm Innovation of Perennial Rice from ministry of agriculture and Rural Affairs School of AgricultureYunnan UniversityKunming 650091YunnanChina National key Facility for Crop Gene resources and genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated *** previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is *** this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland ***2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought ***2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland ***2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.

关键词： Upland rice Dryland adaptation ABA Root development Drought tolerance

High expression circRALGPS2 in atretic follicle induces chicken granulosa cell apoptosis and autophagy via encoding a new protein

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Journal of Animal Science and Biotechnology 2024年第3期15卷 971-986页

作者： Haorong He Yuanhang Wei Yuqi Chen Xiyu Zhao Xiaoxu Shen Qing Zhu Huadong Yin key laboratory of Livestock and Poultry Multi‑Omics Ministry of Agriculture and Rural AffairsCollege of Animal Science and TechnologySichuan Agricultural UniversityChengduSichuan 611130China Farm Animal genetic resources Exploration and Innovation key laboratory of Sichuan Province Sichuan Agricultural UniversityChengduSichuan 611130China

Background The reproductive performance of chickens mainly depends on the development of ***-mal follicle development can lead to decreased reproductive performance and even ovarian disease among *** is the only non-human animal with a high incidence of spontaneous ovarian *** recent years,the involvement of circRNAs in follicle development and atresia regulation has been *** In the present study,we used healthy and atretic chicken follicles for circRNA *** results showed differential expression of *** was then confirmed that circRALGPS2 can translate into a protein,named cir-cRALGPS2-212aa,which has IRES ***,we found that circRALGPS2-212aa promotes apoptosis and autophagy in chicken granulosa cells by forming a complex with PARP1 and *** Our results revealed that circRALGPS2 can regulate chicken granulosa cell apoptosis and autophagy through the circRALGPS2-212aa/PARP1/HMGB1 axis.

关键词： Apoptosis Autophagy Chicken CircRALGPS2 Follicle atresia PARP1 RNC-seq