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

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 species.However,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 populations.To this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations.OcBSA 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 population.Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy.In addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and rice.We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study.The 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 color.Taken 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 species.For 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

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Northward Shift in Landfall Locations of Tropical Cyclones over the Western North Pacific during the Last Four Decades

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Advances in Atmospheric Sciences 2022年第2期39卷 304-319页

作者： Ting chen shumin chen Mingsen ZHOU Chaoyong TU Aoqi ZHANG Yilun chen Weibiao LI School of Atmospheric Sciences Sun Yat-sen UniversityGuangzhou 510275China Southern Laboratory of Ocean Science and Engineering Zhuhai 519082China Guangzhou Institute of Tropical and Marine Meteorology China Meteorological AdministrationGuangzhou 510062China

This study analyzes landfall locations of tropical cyclones(TCs)over the western North Pacific during 1979–2018.Results demonstrate that the landfall locations of TCs over this region have shifted northward during the last four decades,primarily due to the shift of landfalling TC tracks,with the decreasing/increasing proportion of westward/northward TC tracks.In particular,the northward shift of the landfalling TCs was not related to their formation locations,which have not markedly changed,whereas"no-landed"TCs have significantly shifted northward.TC movement was significantly and positively correlated to the zonal component of the steering flow,while the correlation between TC movement and the meridional component of the steering flow was relatively unobvious.The westward steering flow in the tropical central Pacific that occurred around the formation and early development of the westward TCs was significantly weakened,which was unfavorable for their westward movement,thereby,causing the higher proportions of northward moving tracks.This weakened westward flow was related to the northward shift of the subtropical high ridge,which was caused by significant weakening of the southern part of the subtropical high.The vertical wind shear,sea surface temperature,and convective available potential energy also showed that the northern region of the western North Pacific became more favorable for TC development,whereas the upper divergence,low-layer relative vorticity,and accumulated water vapor content were not obviously related to the northward shift of TCs.

关键词： tropical cyclone track landfall location northward shift steering flow background environment

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Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei(Rubus corchorifolius)

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1106-1118页

作者： Yinqing Yang Kang Zhang Ya Xiao Lingkui Zhang Yile Huang Xing Li shumin chen Yansong Peng Shuhua Yang Yongbo Liu Feng cheng Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural CropsMinistry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China Biotechnology Research Center Xiangxi Academy of Agricultural SciencesJishou 416000China Lushan Botanical Garden Chinese Academy of SciencesJiujiang 332900China State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment Chinese Research Academy of Environmental SciencesBeijing 100012China

Rubus corchorifolius(Shanmei or mountain berry,2n=14)is widely distributed in China,and its fruits possess high nutritional and medicinal values.Here,we reported a highquality chromosome-scale genome assembly of Shanmei,with contig size of 215.69 Mb and 26,696 genes.Genome comparison among Rosaceae species showed that Shanmei and Fupenzi(Rubus chingii Hu)were most closely related,followed by blackberry(Rubus occidentalis),and that environmental adaptation-related genes were expanded in the Shanmei genome.Further resequencing of 101 samples of Shanmei collected from four regions in the provinces of Yunnan,Hunan,Jiangxi,and Sichuan in China revealed that among these samples,the Hunan population of Shanmei possessed the highest diversity and represented the more ancestral population.Moreover,the Yunnan population underwent strong selection based on the nucleotide diversity,linkage disequilibrium,and historical effective population size analyses.Furthermore,genes from candidate genomic regions that showed strong divergence were significantly enriched in the flavonoid biosynthesis and plant hormone signal transduction pathways,indicating the genetic basis of adaptation of Shanmei to the local environment.The high-quality assembled genome and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.

关键词： Rubus corchorifolius Genome assembly Resequencing Divergence Genome evolution

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Improved outcomes in E2A::HLF positive B-cell acute lymphoblastic leukemia by chimeric antigen receptor T cell therapy and BCL-2 inhibitor

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Chinese Medical Journal 2023年第11期136卷 1382-1384页

作者： shumin chen Ye Li Zheng Wang Lin Feng Yueping Jia Xiaodong Mo Yu Wang Qian Jiang Xiaojun Huang Yueyun Lai Peking University Institute of Hematology Peking University People’s HospitalBeijing 100044China Department of Pediatrics Peking University People’s HospitalBeijing 100044China Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies Chinese Academy of Medical Sciences(2019RU029)Beijing 100044China

To the Editor:The fusion gene E2A::HLF(TCF3::HLF)is formed by t(17;19)(q21-22;p13),which presents in<1%of B-cell acute lymphoblastic leukemia(B-ALL)and mainly occurs in older children and adolescents.[1]Such patients were often accompanied by drug resistance and early relapse,which confer an extremely poor prognosis,and even intensive chemotherapy and hematopoietic stem cell transplantation(HSCT)cannot improve their survival.[2]A few studies suggested that chimeric antigen receptor T(CAR-T)cell therapy or BCL-2 inhibitors might benefit such patients.

关键词： HLF lymphoblastic acute

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Morphological Characteristics of Precipitation Areas over the Tibetan Plateau Measured by TRMM PR

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Advances in Atmospheric Sciences 2021年第4期38卷 677-689页

作者： Yilun chen Aoqi ZHANG Yunfei FU shumin chen Weibiao LI Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies School of Atmospheric SciencesSun Yat-sen UniversityZhuhai 519000China School of Earth and Space Sciences University of Science and Technology of ChinaHefei 230026China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519000China

The multidimensional morphological characteristics(including scale, horizontal shape and 3 D morphology) of precipitation areas over the Tibetan Plateau in summer were studied using 15 years(1998–2012) of observational data from the precipitation radar onboard the Tropical Rainfall Measuring Mission satellite. As the scale of the precipitation area increased from 20 to 150 km, the near-surface rain rate(RRav) of the precipitation area increased by up to 78%(from ~1.12 to ~2 mm h~(-1)). Linear precipitation areas had the lowest median RRav(~1 mm h~(-1) over the eastern Tibetan Plateau),whereas square-shaped precipitation areas had the highest median RRav(~1.58 mm h~(-1) over the eastern Tibetan Plateau).The 3D morphology was defined as the ratio of the average vertical scale to the average horizontal scale, where a large value corresponds to thin and tall, and a small value corresponds to plump and short. Thin-and-tall precipitation areas and plump-and-short precipitation areas had a greater median RRav, whereas the precipitation areas with a moderate 3D morphology had the lowest median RRav. The vertical structure of the precipitation-area reflectivity was sensitive to both size and 3D morphology, but was not sensitive to the horizontal shape. The relationship between RRav and the morphological characteristics was most significant over the southern slopes of the Tanggula Mountains and the Tibetan Plateau east of 100°E. The morphological characteristics of precipitation areas are therefore closely related to the intensity of precipitation and could potentially be used to forecast precipitation and verify numerical models.

关键词： precipitation areas morphological characteristics Tibetan Plateau TRMM PR

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Satellite Observations of Reflectivity Maxima above the Freezing Level Induced by Terrain

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Advances in Atmospheric Sciences 2021年第4期38卷 627-640页

作者： Aoqi ZHANG Weibiao LI shumin chen Yilun chen Yunfei FU Guangdong Province Key Laboratory for Climate Change and Natural Disaster Studies School of Atmospheric SciencesSun Yat-sen UniversityGuangzhou 510275China Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai) Zhuhai 519082China School of Earth and Space Sciences University of Science and Technology of ChinaHefei 230026China

Previous studies have recognized reflectivity maxima above the freezing level(RMAF) within stratiform precipitation over mountain slopes, however, quantitative studies are limited due to the lack of adequate identification criteria. Here, we establish an identification method for RMAF precipitation and apply it to the Tropical Rainfall Measuring Mission(TRMM) Precipitation Radar(PR) observations. Using the TRMM 2A25 product from 1998 to 2013, we show that the RMAF structure in reflectivity profiles can be effectively identified. RMAF exists not only in stratiform precipitation but also in convective precipitation. RMAF frequency is positively correlated with elevation, which is thought to be caused by enhanced updrafts in the middle layers of stratiform precipitation, or in the low to middle layers of convective precipitation over mountains. The average RMAF heights in stratiform and convective precipitation were 1.35 and 2.01 km above the freezing level, respectively, which is lower than previous results. In addition, our results indicate that the RMAF structure increased the echo top height and enhanced precipitation processes above the RMAF height, but it suppressed the downward propagation of ice particles and the near-surface rain rate. Future studies of orographic precipitation should take into account the impact of the RMAF structure and its relevant dynamic triggers.

关键词： orographic precipitation reflectivity maxima above the freezing level precipitation structure TRMM PR

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Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits

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Molecular Plant 2022年第5期15卷 913-924页

作者： Xiaoxue Sun Xing Li Yin Lu Shan Wang Xiaomeng Zhang Kang Zhang Xiangjie Su Mengyang Liu Daling Feng Shuangxia Luo Aixia Gu Yu Fu Xueping chen Shuxin Xuan Yanhua Wang Donghui Xu shumin chen Wei Ma Shuxing Shen Feng cheng Jianjun Zhao State Key Laboratory of North China Crop Improvement and Regulation Key Laboratory of Vegetable Germplasm Innovation and Utilization of HebeiCollaborative Innovation Center of Vegetable Industry in HebeiCollege of HorticultureHebei Agricultural UniversityBaoding 071000China Institute of Vegetables and Flowers Chinese 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 271000China

Chinese cabbage(Brassica rapa ssp.pekinensis)is an economically important vegetable crop throughout the world,especially in Asia.High-quality genome sequences are available for Chinese cabbage,but gene functional studies remain challenging.To promote functional genomic studies of Chinese cabbage,we generated an ethyl methane sulfonate(EMS)mutant population of~8000 M_(2) plants using the double haploid inbred line A03 as the parent.The genome of A03 was sequenced and used as a reference for high-throughput functional characterization of gene mutations at the whole-genome level.A total of 300 M_(2) to M_(5) EMS mutants were phenotypically screened and then sequenced,revealing 750629 SNPs and 46272 InDel mutations that cover 98.27%of all predicted genes in the A03 genome.A forward-genetics approach was successfully used to identify two genes with chloroplast-related functions that are responsible for the yellow leaf mutant trait.A reverse-genetics approach was also used to identify associations between mutations in five genes of the glucosinolate biosynthetic pathway and variations in glucosinolate content of the mutant plants.In addition,we built the Chinese cabbage EMS mutation database(CCEMD,***/EMSmutation/home)to increase the usability of this mutant population resource.In summary,we performed large-scale screening of a heading Chinese cabbage EMS mutant collection at the phenotypic and genotypic levels,which will facilitate gene mining of Chinese cabbage and might also be useful for the study of other Brassica crops.

关键词： Chinese cabbage EMS morphological variations whole-genome sequencing functional genomics

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“治脑调神”刺法治疗神志病探析及其临床应用

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中华中医药杂志 2024年第5期39卷 2630-2632页

作者：陈淑敏王莹莹中国中医科学院针灸研究所北京100700 中国中医科学院国医大师程莘农传承工作室北京100700

中国中医科学院国医大师程莘农传承工作室在程院士“一窍开百窍法”治疗脑病的学术观点基础上,结合“凡刺之法,先必本于神”和现代医学“身心疾病模式”,提出“主穴在脑、配穴在心”整体调理的“治脑调神”刺法,在神志病治疗中效果较佳... 详细信息

中国中医科学院国医大师程莘农传承工作室在程院士“一窍开百窍法”治疗脑病的学术观点基础上,结合“凡刺之法,先必本于神”和现代医学“身心疾病模式”,提出“主穴在脑、配穴在心”整体调理的“治脑调神”刺法,在神志病治疗中效果较佳。文章通过分析“治脑调神”刺法治疗神志病的理论内涵及临床应用特色,提出组穴上安脑神为主,调心神为要;针法上强调得气以调神;情绪不良者加以背俞穴快针,以调五脏;日久不愈者重用奇经穴,以交会经气;并指出临床可拓宽调治脑神法的运用思路,以丰富针刺调神法治疗,提高临床疗效。

关键词：程莘农治脑调神神志病临证经验

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Atmospheric Response to Mesoscale Ocean Eddies over the South China Sea

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Advances in Atmospheric Sciences 2018年第9期35卷 1189-1204页

作者： Haoya LIU Weibiao LI shumin chen Rong FANG Zhuo LI School of Atmospheric Sciences Sun Yat-Sen University

The South China Sea（SCS） is an eddy-active area. Composite analyses based on 438 mesoscale ocean eddies during 2000–2012 revealed the status of the atmospheric boundary layer is influenced remarkably by such eddies. The results showed cold-core cyclonic（warm-core anticyclonic） eddies tend to cool（warm） the overlying atmosphere and cause surface winds to decelerate（accelerate）. More than 5% of the total variance of turbulent heat fluxes, surface wind speed and evaporation rate are induced by mesoscale eddies. Furthermore, mesoscale eddies locally affect the columnar water vapor, cloud liquid water, and rain rate. Dynamical analyses indicated that both variations of atmospheric boundary layer stability and sea level pressure are responsible for atmospheric anomalies over mesoscale eddies. To reveal further details about the mechanisms of atmospheric responses to mesoscale eddies, atmospheric manifestations over a pair of cold and warm eddies in the southwestern SCS were simulated. Eddy-induced heat flux anomalies lead to changes in atmospheric stability. Thus, anomalous turbulence kinetic energy and friction velocity arise over the eddy dipole, which reduce（enhance） the vertical momentum transport over the cold（warm） eddy, resulting in the decrease（increase） of sea surface wind. Diagnoses of the model＇s momentum balance suggested that wind speed anomalies directly over the eddy dipole are dominated by vertical mixing terms within the atmospheric boundary layer, while wind anomalies on the edges of eddies are produced by atmospheric pressure gradient forces and atmospheric horizontal advection terms.

关键词： mesoscale ocean eddies air-sea interaction atmospheric responses South China Sea

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信息不对称下新产品研发的合同设计

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系统科学与数学 2024年第6期44卷 1675-1688页

作者：陈丹梅李仲飞陈树敏上海应用技术大学理学院上海201418 南方科技大学商学院深圳518055 广东工业大学管理学院广州510520

假设企业研发一种新产品,其研发成功的时间具有不确定性.文章运用实物期权方法和委托代理理论,分析信息不对称下新产品研发的合同设计问题,得到了最优合同的显式解.在此基础上,文章进一步分析了信息不对称对委托人价值、新产品研发的退... 详细信息

假设企业研发一种新产品,其研发成功的时间具有不确定性.文章运用实物期权方法和委托代理理论,分析信息不对称下新产品研发的合同设计问题,得到了最优合同的显式解.在此基础上,文章进一步分析了信息不对称对委托人价值、新产品研发的退出时机的影响.研究结果表明,信息不对称减少了委托人的价值,使得高成本的新产品的研发退出时机提前;新产品研发成功的平均时间越短,委托人的价值越大.

关键词：信息不对称实物期权委托代理最优择时

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