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Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean

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Journal of Integrative Plant Biology 2023年第1期65卷 117-132页

作者： Delin Li Dong Bai Yu Tian Ying-Hui Li Chaosen Zhao Qi Wang Shiyu Guo Yongzhe Gu xiaoyan luan Ruizhen Wang Jinliang Yang Malcolm J.Hawkesford James C.Schnable Xiuliang Jin Li-Juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop Science Chinese Academy of Agricultural SciencesBeijing 100081 China Crops Research Institute of Jiangxi Academy of Agricultural Sciences Nanchang 330200 China College of Agriculture Northeast Agricultural University Harbin 150030 China Soybean Research Institute Heilongjiang Academy of Agricultural Sciences Harbin 150086 China Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln Nebraska 68583 USA Plant Sciences Department Rothamsted ResearchWest CommonHarpendenHertfordshire AL52JQ UK

Advances in plant phenotyping technologies are dramatically reducing the marginal costs of collecting multiple phenotypic measurements across several time points.Yet,most current approaches and best statistical practices implemented to link genetic and phenotypic variation in plants have been developed in an era of single-time-point data.Here,we used time-series phenotypic data collected with an unmanned aircraft system for a large panel of soybean(Glycine max(L.)Merr.)varieties to identify previously uncharacterized loci.Specifically,we focused on the dissection of canopy coverage(CC)variation from this rich data set.We also inferred the speed of canopy closure,an additional dimension of CC,from the time-series data,as it may represent an important trait for weed control.Genome-wide association studies(GWASs)identified 35 loci exhibiting dynamic associations with CC across developmental stages.The time-series data enabled the identification of 10 known flowering time and plant height quantitative trait loci(QTLs)detected in previous studies of adult plants and the identification of novel QTLs influencing CC.These novel QTLs were disproportionately likely to act earlier in development,which may explain why they were missed in previous single-time-point studies.Moreover,this time-series data set contributed to the high accuracy of the GWASs,which we evaluated by permutation tests,as evidenced by the repeated identification of loci across multiple time points.Two novel loci showed evidence of adaptive selection during domestication,with different genotypes/haplotypes favored in different geographic regions.In summary,the time-series data,with soybean CC as an example,improved the accuracy and statistical power to dissect the genetic basis of traits and offered a promising opportunity for crop breeding with quantitative growth curves.

关键词： canopy coverage dynamic regulation GWAS soybean time series unmanned aircraft system

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400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂对苹果褐斑病的田间药效评价

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农药 2024年第6期63卷 451-453页

作者：陈敏栾炳辉吕晓艳刘保友山东省烟台市农业科学研究院山东烟台265500 烟台大学生命科学学院山东烟台264005 烟台市中国社科院农村发展研究中心山东烟台264001

[目的]评价新型杀菌剂400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂对苹果褐斑病的防治效果。[方法]于山东栖霞进行了连续2年的田间药效试验。[结果]400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂225、300、360 g a.i./hm2处理对苹果褐斑病表现出较好... 详细信息

[目的]评价新型杀菌剂400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂对苹果褐斑病的防治效果。[方法]于山东栖霞进行了连续2年的田间药效试验。[结果]400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂225、300、360 g a.i./hm2处理对苹果褐斑病表现出较好的防治效果,末次药后14 d,防效均在92.38%以上,且对供试苹果品种安全无药害。[结论]400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂可有效防治苹果褐斑病,为新型药剂的推广应用提供了依据。

关键词： 400 g/L氯氟醚菌唑·吡唑醚菌酯悬浮剂苹果褐斑病田间药效

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Geographical distribution of GmTfl1 alleles in Chinese soybean varieties

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The Crop Journal 2015年第5期3卷 371-378页

作者： Guifeng Liu Lin Zhao Benjamin J.Averitt Ying Liu Bo Zhang Ruzhen Chang Yansong Ma xiaoyan luan Rongxia Guan Lijuan Qiu Soybean Research Institute Northeast Agricultural University Department of Crop and Soil Environmental Sciences VA Polytechnic Institute and State University The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Institute of Crop ScienceChinese Academy of Agricultural Sciences Heilongjiang Academy of Agricultural Sciences

Stem growth habit is an important agronomic trait in soybean and is subject to artificial selection. This study aimed to provide a theory for genotypic selection of stem growth habit for breeding purposes by analyzing the alleles of Gm Tfl1 gene in Chinese soybean varieties and establishing a database of Gm Tfl1 variation. Using knowledge of insertion and deletion(Indel) in the non-coding region and four single-nucleotide polymorphisms(SNPs) in the coding sequences of the Gm Tfl1 gene, four CAPS and one Indel markers were developed and used to test 1120 Chinese soybean varieties. We found that the dominant Gm Tfl1 allele was prevalent in accessions from the Northern ecoregion, whereas the recessive allele, Gmtfl1, was more common in the Southern ecoregion, and the proportions of Gm Tfl1 and recessive alleles were respectively 40.1% and 59.9% in the Huang-Huai ecoregion. The proportion of Gm Tfl1 decreased and that of Gmtfl1 increased, gradually from north to south. Allele Gm Tfl1-a was present in higher proportions in the Huang-Huai spring, Huang-Huai summer, and Northern spring sub-ecoregions than that in the other sub-ecoregions. Gm Tfl1-b was common in the Northeast spring, Northern spring and Southern summer sub-ecoregions. Gmtfl1-ta was found mainly in the Huang-Huai spring,Huang-Huai summer and Southern spring sub-ecoregions. The Gmtfl1-ab allele was distributed in all six soybean sub-ecoregions. The Gmtfl1-bb allele was distributed mainly in the Huang-Huai spring and summer and Southern spring and summer sub-ecoregions,but the Gmtfl1-tb allele was detected only in the Huang-Huai summer sub-ecoregion. The distributions of Gm Tfl1 and Gmtfl1 have shown no large changes in nearly 60 years of breeding, but the frequency of the recessive genotype Gmtfl1 has shown a rising trend in the last 20 years. This study provides a theoretical foundation for breeding new soybean varieties for different ecoregions.

关键词： Soybean Stem growth habit Gm Tfl1 Distribution

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大豆新品种黑农84品质性状的环境稳定性分析

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大豆科学 2024年第1期43卷 1-12页

作者：王婉刘鑫磊孙君明栾晓燕邱丽娟中国农业科学院作物科学研究所/农作物基因资源与遗传改良国家重大科学工程/农业部北京大豆生物学重点实验室北京100081 黑龙江省农业科学院大豆研究所黑龙江哈尔滨150086

为明确黑农84的品质稳定性,为新品种的推广应用提供依据,本研究分析了黑农84不同年份、不同地点种植的品质性状变异。结果显示:黑农84是具备高蛋白、低脂肪、高亚麻酸、高异黄酮、高蔗糖和低水苏糖特性的优质功能型品种。在检测的27个... 详细信息

为明确黑农84的品质稳定性,为新品种的推广应用提供依据,本研究分析了黑农84不同年份、不同地点种植的品质性状变异。结果显示:黑农84是具备高蛋白、低脂肪、高亚麻酸、高异黄酮、高蔗糖和低水苏糖特性的优质功能型品种。在检测的27个品质性状中,16个性状(蛋白质和脂肪含量,蛋脂总量,棕榈酸、硬脂酸、油酸、亚油酸和亚麻酸含量,维生素E含量,水溶性糖,γ-维生素E,δ-维生素E,果糖、葡萄糖、蔗糖和水苏糖含量)的变异系数小于10%,较为稳定。两年的遗传多样性指数变异范围分别为1.08~1.98和1.07~1.73,平均值分别为1.62和1.59,其中α-大豆苷的遗传多样性指数最高(1.98和1.73),棉子糖的遗传多样性指数均最小(1.08和1.07)。黑农84品质性状聚类均可以分为两类,第一类中蛋白质和α-维生素E含量较高,脂肪和异黄酮含量较低;第二类中大豆苷、m-大豆苷、α-大豆苷和m-染料木苷含量较低。黑农84优质性状的环境稳定性为该品种的遗传育种和加工应用等提供了理论依据。

关键词：黑农84 品质性状遗传多样性指数聚类分析环境稳定性

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Genome-wide signatures of the geographic expansion and breeding of soybean

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Science China(Life Sciences) 2023年第2期66卷 350-365页

作者： Ying-Hui Li Chao Qin Li Wang Chengzhi Jiao Huilong Hong Yu Tian Yanfei Li Guangnan Xing Jun Wang Yongzhe Gu Xingpeng Gao Delin Li Hongyu Li Zhangxiong Liu Xin Jing Beibei Feng Tao Zhao Rongxia Guan Yong Guo Jun Liu Zhe Yan Lijuan Zhang Tianli Ge Xiangkong Li Xiaobo Wang Hongmei Qiu Wanhai Zhang xiaoyan luan Yingpeng Han Dezhi Han Ruzhen Chang Yalong Guo Jochen C.Reif Scott A.Jackson Bin Liu Shilin Tian Li-juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000China Novogene Bioinformatics Institute Beijing 100098China State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute Nanjing Agricultural UniversityNanjing 210095China Soybean Research Institute/MOA National Center for Soybean Improvement/MOA Key Laboratory for Biology and Genetic Improvement of Soybean(General)/State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China College of Agriculture Yangtze UniversityJingzhou 451199China School of Agronomy Anhui Agricultural UniversityHefei 230036China Jilin Academy of Agricultural Sciences Changchun 130119China Hulun Buir Institution of Agricultural Sciences Hulun Buir 021008China Soybean Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086China Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry) Northeast Agricultural UniversityHarbin 150030China Heihe Branch of Heilongjiang Academy of Agricultural Sciences Harbin 150086China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Department of Breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben DE D-06466Germany Center for Applied Genetic Technologies University of GeorgiaAthens 30602USA Department of Ecology/Tibetan Centre for Ecology and Conservation at WHU-TU/Hubei Key

Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.

关键词： soybean adaptation introgression flowering time breeding

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FERONIA is involved in phototropin 1-mediated blue light phototropic growth in Arabidopsis

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Journal of Integrative Plant Biology 2022年第10期64卷 1901-1915页

作者： Chiyu Li Jia Chen xiaoyan Li Xin Zhang Ying Liu Sirui Zhu Long Wang Heping Zheng Sheng luan Jiada Li Feng Yu School of Life Sciences Central South UniversityChangsha 410078China State Key Laboratory of Chemo/Biosensing and Chemometrics College of BiologyHunan UniversityChangsha 410082China Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan UniversityChangsha 410082China Department of Plant and Microbial Biology University of CaliforniaBerkeleyCA94720USA State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China

Plant shoot phototropism is triggered by the formation of a light-driven auxin gradient leading to bending growth.The blue light receptor phototropin 1(phot1)senses light direction,but how this leads to auxin gradient formation and growth regulation remains poorly understood.Previous studies have suggested phot1’s role for regulated apoplastic acidification,but its relation to phototropin and hypocotyl phototropism is unclear.Herein,we show that blue light can cause phot1 to interact with and phosphorylate FERONIA(FER),a known cell growth regulator,and trigger downstream phototropic bending growth in Arabidopsis hypocotyls.fer mutants showed defects in phototropic growth,similar to phot1/2 mutant.FER also interacts with and phosphorylates phytochrome kinase substrates,the phot1 downstream substrates.The phot1-FER pathway acts upstream of apoplastic acidification and the auxin gradient formation in hypocotyl under lateral blue light,both of which are critical for phototropic bending growth in hypocotyls.Our study highlights a pivotal role of FER in the phot1-mediated phototropic cell growth regulation in plants.

关键词： blue light FERONIA H+and auxin gradience formation hypocotyl phototropin 1 phototropism

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High-temperature mechanical behavior of ultra-coarse cemented carbide with grain strengthening

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Journal of Materials Science & Technology 2022年第9期104卷 8-18页

作者： Huaxin Hu Xuemei Liu Jinghong Chen Hao Lu Chao Liu Haibin Wang Junhua luan Zengbao Jiao Yong Liu xiaoyan Song Faculty of Materials and Manufacturing Key Laboratory of Advanced Functional MaterialsMinistry of Education of ChinaBeijing University of TechnologyBeijing 100124China Xiamen Tungsten Co. Ltd.Xiamen 361009China Department of Materials Science and Engineering City University of Hong KongHong KongChina Department of Mechanical Engineering The Hong Kong Polytechnic UniversityHong KongChina State Key Laboratory of Powder Metallurgy Central South UniversityChangsha 410083China

Ultra-coarse grained cemented carbides are often used under conditions of concurrently applied stress and high temperature.Improvement of high-temperature mechanical performance of ultra-coarse grained cemented carbides is highly desirable but still a big challenge.In this study,it is proposed that the hightemperature compression strength of ultra-coarse cemented carbides can be enhanced by modulating hard matrix grains by activated Ta C nanoparticles,through solid solution strengthening of Ta atoms.Based on the designed experiments and microstructural characterizations combined with finite element simulations,the grain morphology,stress distribution and dislocation configuration were studied in detail for ultra-coarse grained cemented carbides.The mechanisms of Ta dissolving in WC crystal and strengthening ultra-coarse grains through interaction with dislocations were disclosed from the atomic scale.This study opens a new perspective to modulate hard phases of cemented carbides for improving their hightemperature performance,which will be applicable to a variety of cermet and ceramic-based composite materials.

关键词： Ultra-coarse cemented carbides High-temperature compressive behavior Strengthening of hard-phase grains Dislocation motion

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嗜酸性肉芽肿性多血管炎患者的多发性脑梗死:1例报道并文献复习

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国际脑血管病杂志 2024年第1期32卷 71-74页

作者：栾海辉宋晓燕盛帅刘青霞甄明清烟台业达医院神经内一科 264006 烟台业达医院血液风湿免疫科 264006 烟台业达医院感染疾病科 264006

嗜酸性肉芽肿性多血管炎(eosinophilic granulomatosis with polyangiitis,EGPA)是一种免疫介导的全身多系统炎性疾病,主要表现为哮喘、外周血和组织中嗜酸性粒细胞增多以及中小血管坏死性肉芽肿性炎症[1,2,3,4]。EGPA的发病年龄高峰在4... 详细信息

嗜酸性肉芽肿性多血管炎(eosinophilic granulomatosis with polyangiitis,EGPA)是一种免疫介导的全身多系统炎性疾病,主要表现为哮喘、外周血和组织中嗜酸性粒细胞增多以及中小血管坏死性肉芽肿性炎症[1,2,3,4]。EGPA的发病年龄高峰在40~60岁,年发病率为(0.5~4.2)/100万,患病率为(10.7~13.0)/100万[5]。因其临床罕见,故易造成误诊或漏诊。EGPA引起脑梗死的病例相对少见,且机制尚不明确。本文通过报道1例合并多发性脑梗死的EGPA患者并进行文献复习,期望加强临床医师对该病的了解。

关键词：多发性脑梗死肉芽肿性炎症嗜酸性粒细胞增多嗜酸性肉芽肿性多血管炎临床医师免疫介导坏死性

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swSpAMM:optimizing large-scale sparse approximate matrix multiplication on Sunway Taihulight

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Frontiers of Computer Science 2023年第4期17卷 29-41页

作者： xiaoyan LIU Yi LIU Bohong YIN Hailong YANG Zhongzhi luan Depei QIAN State Key Laboratory of Software Development Environment Beijing 100191China School of Computer Science and Engineering Beihang UniversityBeijing 100191China

Although matrix multiplication plays an essential role in a wide range of applications,previous works only focus on optimizing dense or sparse matrix multiplications.The Sparse Approximate Matrix Multiply(SpAMM)is an algorithm to accelerate the multiplication of decay matrices,the sparsity of which is between dense and sparse matrices.In addition,large-scale decay matrix multiplication is performed in scientific applications to solve cutting-edge problems.To optimize large-scale decay matrix multiplication using SpAMM on supercomputers such as Sunway Taihulight,we present swSpAMM,an optimized SpAMM algorithm by adapting the computation characteristics to the architecture features of Sunway Taihulight.Specifically,we propose both intra-node and inter-node optimizations to accelerate swSpAMM for large-scale execution.For intra-node optimizations,we explore algorithm parallelization and block-major data layout that are tailored to better utilize the architecture advantage of Sunway processor.For inter-node optimizations,we propose a matrix organization strategy for better distributing sub-matrices across nodes and a dynamic scheduling strategy for improving load balance across nodes.We compare swSpAMM with the existing GEMM library on a single node as well as large-scale matrix multiplication methods on multiple nodes.The experiment results show that swSpAMM achieves a speedup up to 14.5×and 2.2×when compared to xMath library on a single node and 2D GEMM method on multiple nodes,respectively.

关键词： approximate calculation sunway processor performance optimization

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Socioeconomic disparities of patients with acute kidney injury:subgroup analysis of local hospitals in China from a national survey

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Chinese Medical Journal 2022年第24期135卷 3016-3018页

作者： Lihua Wu Jinwei Wang Yaqi Ma Fengwu luan Mengting Wang Zhihong Feng Yanhong Tian Lu Li Rui Chu Xiaolong Yin Yan Wang Yanmei Li xiaoyan Guo Xiaoling Zhou Min Yu Yinyin Yan Li Yang Menghua Chen Department of Nephrology General Hospital of Ningxia Medical UniversityNingxia 750004China Renal Division Peking University First HospitalBeijing 100034China

To the Editor:Acute kidney injury(AKI)is a common public health problem worldwide,which can adversely affect patients’quality of life and even lead to death.^([1])Academic hospitals play an important role in admitting and providing treatment for patients with AKI,but limited data exist regarding the characteristics of patients in county-level local hospitals.Our research group initiated a comprehensive survey as part of the International Society of Nephrology’s"0 by 25"project(eliminating all deaths related to untreated AKI by 2025)for investigating the disease burden of AKI and its associated risk factors and prognosis through 22 province-level regions of China in 2013.

关键词： patients kidney injury

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