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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng State Key Laboratory of crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

TaRLK-6A promotes Fusarium crown rot resistance in wheat

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Journal of Integrative Plant Biology 2024年第1期66卷 12-16页

作者： Haijun Qi Xiuliang Zhu Wenbiao Shen Xia Yang Chaozhong Zhang Genying Li Feng Chen Xuening Wei Zengyan Zhang Institute of Special Animal and Plant sciences Chinese Academy of Agricultural SciencesChangchun 130000China The National Key Facility for crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China College of Life Science Nanjing Agricultural UniversityNanjing 210095China Agronomy College/National Key Laboratory of Wheat and Maize crop Science/CIMMYT‐China(Henan)Joint Center of Wheat and Maize Henan Agricultural UniversityZhengzhou 450002China department of Plant sciences University of CaliforniaDavisCA 95616USA crop Research Institute Shandong Academy of Agricultural SciencesJinan 250100China

Fusariumcrown rot(FCR),mainly caused by the soil‐borne fungus Fusarium pseudograminearum,is a devastatingdisease of wheat(Triticum aestivum(Ta)).Fusariumcrown rotcauses substantial yield losses and generates mycotoxins inwheat grains that can cause serious health problems in hu-mans and livestock(Powell et al.,2017).Identifying genes thatprovide resistance *** character-izing the molecular mechanisms underlying such resistance arekey to breeding wheat varieties that are resistant to this dev-astating fungus.

关键词： aestivum breeding soil

Winter wheat yield improvement by genetic gain across different provinces in China

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Journal of Integrative Agriculture 2024年第2期23卷 468-483页

作者： Wei Chen Jingjuan Zhang Xiping Deng Key Laboratory of Disaster Monitoring and Mechanism Simulating of Shaanxi Province/School of Geography and Environment Baoji University of Arts and SciencesBaoji 721013China Centre for crop and Food Innovation Murdoch University90 South StreetMurdochWA 6150Australia State Key Laboratory of Soil Erosion and dryland Farming on the Loess Plateau Northwest A&F UniversityYangling 712100China

The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide,with remarkable progress in *** on two sets of data,production yield from the National Bureau of Statistics of China and experimental yield from literature,this study aims to(1)illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China,(2)explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China,and(3)compare the yield gap between experimental yield and production *** results show that both the production and experimental yields significantly increased along with the variety *** national annual yield increase ratio for the production yield was 1.67%from 1978 to 2018,varying from 0.96%in Sichuan Province to 2.78%in Hebei Province;such ratio for the experimental yield was 1.13%from 1937 to *** yield gap between experimental and production yields decreased from the 1970s to the *** study reveals significant increases in some yield components consequent to variety replacement,including thousand-grain weight,kernel number per spike,and grain number per square meter;however,no change is shown in spike number per square *** biomass and harvest index consistently and significantly increased,whereas the plant height decreased significantly.

关键词： genetic gain winter wheat yield yield components

Parkland trees on smallholder farms ameliorate soil physical-chemical properties in the semi-arid area of Tigray,Ethiopia

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Journal of Arid Land 2024年第1期16卷 1-13页

作者： Selam LJALEM Emiru BIRHANE Kassa TEKA Daniel H BERHE department of Land Resources Management and Environmental Protection College of Dryland Agriculture and Natural ResourcesMekelle UniversityMekelle 231Ethiopia Institute of Climate and Society Mekelle UniversityMekelle 231Ethiopia Faculty of Environmental sciences and Natural Resource Management Norwegian University of Life Sciences(NMBU)Ås 1432Norway department of Natural Resources Management Adigrat UniversityAdigrat 50Ethiopia

Proposed agroforestry options should begin with the species that farmers are most familiar with,which would be the native multipurpose trees that have evolved under smallholder farms and socioeconomic *** African birch(Anogeissus leiocarpa(DC.)Guill.&Perr.)and pink jacaranda(Stereospermum kunthianum Cham.)trees are the dominant species in the agroforestry parkland system in the drylands of Tigray,*** farmers highly value these trees for their multifunctional uses including timber,firewood,charcoal,medicine,*** trees also could improve soil ***,the amount of soil physical and chemical properties enhanced by the two species must be determined to maintain the sustainable conservation of the species in the parklands and to scale up to similar agroecological ***,we selected twelve isolated trees,six from each species that had similar dendrometric characteristics and were growing in similar environmental *** divided the canopy cover of each tree into three radial distances:mid-canopy,canopy edge,and canopy gap(control).At each distance,we took soil samples from three different *** collected 216 soil samples(half disturbed and the other half undisturbed)from each canopy position and soil *** density(BD),soil moisture content(SMC),soil organic carbon(SOC),total nitrogen(TN),available phosphorus(AP),available potassium(AK),p H,electrical conductivity(EC),and cation exchange capacity(CEC)were *** revealed that soil physical and chemical properties significantly improved except for soil texture and EC under both species,CEC under ***,and soil p H under ***,all the studied soils were improved under both species canopy as compared with canopy ***,TN,AP,and AK under canopy of these trees were respectively 24.1%,11.1%,55.0%,and 9.3% higher than those soils under *** two parkland agroforestry species significantly enhanced soil fertility near the canopy of top

关键词： agroforestry bulk density carbon stock dispersed tree soil texture tree canopy

Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

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Journal of Integrative Agriculture 2024年第3期23卷 769-780页

作者： Shuliang Jiao Qinyan Li Fan Zhang Yonghong Tao Yingzhen Yu Fan Yao Qingmao Li Fengyi Hu Liyu Huang Key Laboratory of Biology and Germplasm Innovation of Perennial Rice Ministry of Agriculture and Rural Affairs/School of AgricultureYunnan UniversityKunming 650091China State Key Laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Wenshan Academy of Agricultural sciences Wenshan 663000China

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides

关键词： Green Revolution Semidwarf 1 high-yield breeding upland rice plant height

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

The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

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The crop Journal 2024年第2期12卷 515-528页

作者： Dandan Hu Jin Lu Wenwen Li Yinghui Yang Junxiong Xu Han Qin Hao Wang Yan Niu Huaiqi Zhang Qingqing Liu Xiangxiang He Annaliese S.Mason JChris Pires Zhiyong Xiong Jun Zou National Key Laboratory of crop Genetic Improvement College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina College of Agronomy Henan Agricultural UniversityZhengzhou 450002HenanChina Key Laboratory of Herbage and Endemic crop Biotechnology Inner Mongolia UniversityHohhot 010070Inner MongoliaChina Plant Breeding department University of BonnBonn 53115Germany department of Soil and crop sciences Colorado State UniversityFort CollinsCO 80523USA

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop *** synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding ***,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome *** observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger ***,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic ***,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for *** results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

关键词： Allopolyploid Large Genome structural variation Linkage mapping Synthetic polyploids Inheritance and segregation

Proteomics analysis of coronary atherosclerotic heart disease with different Traditional Chinese Medicine syndrome types before and after percutaneous coronary intervention

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Journal of Traditional Chinese Medicine 2024年第3期44卷 554-563页

作者： WANG Zhibo LI Ying WANG Daoping MA Bo MIAO Lan REN Junguo LIU Jinghua LIU Jianxun Beijing Key Laboratory of Pharmacology of Chinese Materia Region Institute of Basic Medical SciencesXiyuan HospitalChina Academy of Chinese Medical SciencesNational Clinical Research Center of Cardiovascular Disease of Traditional Chinese Medicine the National Key Facility for crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural Science department of Cardiology Beijing Anzhen HospitalCapital Medical University

OBJECTIVE: To investigate the underlying protein molecular mechanisms of "Qi stagnation and blood stasis syndrome"(QS) and "Qi deficiency and blood stasis syndrome"(QD), as two subtypes of coronary artery disease(CAD) in Traditional Chinese Medicine(TCM),following percutaneous coronary intervention(PCI).METHODS: In this study, a total of 227 CAD patients with QS and 211 CAD patients with QD were enrolled; all participants underwent PCI. Label-free quantification proteomics were employed to analyze the changes in serum in two subtypes of CAD patients before and 6 months after PCI, aiming to elucidate the intervention mechanism of PCI in treating CAD characterized by two different TCM ***: Biochemical analysis revealed significant changes in tumor necrosis factor-α, high density lipoprotein cholesterol, blood stasis clinical symptoms observation, and Gensini levels in both patient groups post-PCI; Proteomic analysis identified 79 and 95 differentially expressed proteins in the QS and QD patient groups, respectively, compared to their control *** C8 alpha chain, complement factor H,apolipoprotein H, apolipoprotein B, plasminogen,carbonic anhydrase 2, and complement factor Ⅰ were altered in both comparison groups. Furthermore,enrichment analysis demonstrated that cell adhesion and connectivity-related processes underwent changes in QS patients post-PCI, whereas lipid metabolism-related pathways, including the peroxisome proliferator-activated receptor signaling pathway and extracellular matrix receptor interaction, underwent changes in the QD *** protein-protein interaction network analysis further enriched 52 node proteins, including apolipoprotein B,lipoprotein(a), complement C5, apolipoprotein A4,complement C8 alpha chain, complement C8 beta chain,complement C8 gamma chain, apolipoprotein H,apolipoprotein A-Ⅱ, albumin, complement C4-B,apolipoprotein C3, among others. The functional network of these proteins is posited to contribute t

关键词： Traditional Chinese Medicine syndrome coronary atherosclerotic heart disease peptide mapping percutaneous coronary intervention proteomics

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Responses of arbuscular mycorrhizal fungi to straw return and nitrogen fertilizer reduction in a rainfed maize field

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Pedosphere 2024年第2期34卷 351-360页

作者： Zhenling PENG Hao XI Lin MAO Huyuan FENG Jianjun ZHANG Yongjun LIU State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems College of EcologyLanzhou UniversityLanzhou 730000China College of Life sciences Northwest Normal UniversityLanzhou 730070China School of Life sciences Lanzhou UniversityLanzhou 730000China dryland Agriculture Institute Gansu Academy of Agricultural SciencesLanzhou 730070China

Straw return can be used to reduce fertilizer input and improve agricultural sustainability and soil ***,how straw return and reduced fertilizer application affect beneficial soil microbes,particularly arbuscular mycorrhizal fungi(AMF),remains poorly ***,we conducted a five-year field experiment in a rainfed maize field on the Loess Plateau of northwestern *** tested four treatments with straw return combined with four nitrogen(N)application rates,i.e.,100%,80%,60%,and 0%of the common N application rate(225 kg N ha^(-1)year^(-1))in this region,and two reference treatments(full or no N application),with three replicates for each *** colonization was quantified and AMF communities colonizing maize roots were characterized using Illumina *** virtual taxa(VTs)of AMF were identified in root samples,among which VT113(related to Rhizophagus fasciculatus)and VT156(related to Dominikia gansuensis)were the predominant *** root length colonization and AMF VT richness were sensitive to N fertilization,but not to straw return;furthermore,both gradually increased with decreasing N application *** VT composition of the AMF community was also affected by N fertilization,but not by straw return,and the community variation could be well explained by soil available N and phosphorus ***,60%,80%,and full N fertilization produced similar maize ***,our study revealed the response patterns of AMF to straw return and N fertilizer reduction and showed that straw return combined with N fertilizer reduction may be a promising practice to maintain mycorrhizal symbiosis concomitantly with crop productivity.

关键词： agricultural sustainability crop productivity mycorrhizal colonization mycorrhizal symbiosis root length colonization virtual taxon