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Journal of genetics and genomics 2024年第6期51卷 665-668页

作者： Botao Ye Yangyang Liu Ziying Wang Liping Shen Changbin Yin Kuocheng Shen Jiaqiang Sun Xiaowan Xu Mengjing Sun Jianhui Wu Zhonghu He Xuchang Yu Fei Lu Yuanfeng Hao Zifeng Guo key laboratory of plant Molecular physiology Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China China National Botanical Garden Beijing 100093China State key laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China Institute of crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China State key laboratory of crop Stress Biology for Arid Areas Northwest A&F UniversityYanglingShaanxi 712100China International Maize and Wheat Improvement Center China Office c/o CAASBeijing 100081China CAS-JIC Centre of Excellence for plant and Microbial Science Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Common wheat(Triticum aestivum L.,2n=6x=42,AABBDD)is one of the most widely grown crops worldwide,providing about 20%of the daily calories and protein consumed by humans(Shiferaw et al.,2013).The world population is projected to reach 9.8 billion in 2050(https://***/en/desa/world-population-projectedreach-98-billion-2050-and-112-billion-2100);thus,to meet the challenges of global food and nutritional security,wheat yields must continue to be increased through breeding programs and improved agricultural techniques(Hunter et al.,2017).

关键词： breeding crops wheat

HEMU:An integrated comparative genomics database and analysis platform for Andropogoneae grasses

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plant Communications 2024年第4期5卷 133-136页

作者： Yuzhi Zhu Zijie Wang Zanchen Zhou Yuting Liu Xiang Gao Weilong Guo Junpeng Shi School of Agriculture Shenzhen Campus of Sun Yat-sen UniversitySun Yat-sen UniversityShenzhen 518107China Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)and Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China These authors contributed equally to this article.

Dear Editor,Tribe Andropogoneae within the family Poaceae encompasses92 genera and 1200 species of substantial agronomic and ecological importance,as represented by maize(Zea mays),sorghum(Sorghum bicolor),sugarcane(... 详细信息

关键词： mays) crops pogon

Development of a single transcript CRISPR/Cas9 toolkit for efficient genome editing in autotetraploid alfalfa

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The crop Journal 2024年第3期12卷 788-795页

作者： Haixia Zhao Siyi Zhao Yingping Cao Xiping Jiang Lijuan Zhao Zhimeng Li Mengqi Wang Ruijuan Yang Chuanen Zhou Zhaoming Wang Feng Yuan Dongmei Ma Hao Lin Wenwen Liu Chunxiang Fu CAS key laboratory of Biofuels Shandong Provincial Key Laboratory of Energy GeneticsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao 266101ShandongChina Shandong Energy Institute Qingdao 266101ShandongChina Qingdao New Energy Shandong laboratory Qingdao 266101ShandongChina University of Chinese Academy of Sciences Beijing 100049China The key laboratory of plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdao 266101ShandongChina key laboratory of Forage Breeding and Seed Production of Inner Mongolia Inner Mongolia M-Grass Ecology and Environment(Group)Co.Ltd.Hohhot 010016Inner MongoliaChina School of Ecology Environment Ningxia UniversityYinchuan 750021NingxiaChina Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China

Alfalfa(Medicago sativa.L.)is a globally significant autotetraploid legume forage ***,despite its importance,establishing efficient gene editing systems for cultivated alfalfa remains a formidable *** this study,we pioneered the development of a highly effective ultrasonic-assisted leaf disc transformation system for Gongnong 1 alfalfa,a variety widely cultivated in Northeast ***,we created a single transcript CRISPR/Cas9(CRISPR_2.0)toolkit,incorporating multiplex gRNAs,designed for gene editing in Gongnong *** Cas9 and gRNA scaffolds were under the control of the Arabidopsis ubiquitin-10 promoter,a widely employed polymeraseⅡconstitutive promoter known for strong transgene expression in *** assess the toolkit’s efficiency,we targeted PALM1,a gene associated with a recognizable multifoliate *** the CRISPR_2.0 toolkit,we directed PALM1 editing at two sites in the wild-type Gongnong *** indicated a 35.1%occurrence of editing events all in target 2 alleles,while no mutations were detected at target 1 in the transgenic-positive *** explore more efficient sgRNAs,we developed a rapid,reliable screening system based on Agrobacterium rhizogenes-mediated hairy root transformation,incorporating the visible reporter *** screening system demonstrated that most purple visible hairy roots underwent gene ***,sgRNA3,with an 83.0%editing efficiency,was selected using the visible hairy root *** anticipated,tetra-allelic homozygous palm1 mutations exhibited a clear multifoliate *** palm1 lines demonstrated an average crude protein yield increase of 21.5%compared to trifoliolate *** findings highlight the modified CRISPR_2.0 system as a highly efficient and robust gene editing tool for autotetraploid alfalfa.

关键词： Alfalfa Gene editing CRISPR_2.0 toolkit Hairy root system Tetra-allelic homozygous mutants

Copy number variation of NAL23 causes narrow-leaf development in rice

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Journal of genetics and genomics 2024年第8期51卷 880-883页

作者： Degui Zhou Yajing Li Xianrong Xie Wenyan Ding Libin Chen Tie Li Jianian Tang Xiyu Tan Weizhi Liu Yueqin Heng Yongyao Xie Letian Chen Qi Liu Shaochuan Zhou Jing Zhao Gong Zhang Jiantao Tan Yaoguang Liu Rongxin Shen State key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern AgricultureCollege of Life SciencesSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong key laboratory of New Technology in Rice Breeding Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong 510640China key laboratory of functional Protein Research of Guangdong Higher Education Institutes and MOE key laboratory of Tumor Molecular Biology Institute of Life and Health EngineeringJinan UniversityGuangzhouGuangdong 510632China

Leaf shape is a key trait for plant architecture relating to photosynthesis and transpiration in plants(Lawson et al.,2020).Erect leaves with proper leaf length and width,particularly the upper three leaves in cereal crops,could significantly improve light absorption efficiency in canopy and ultimately increase crop yield(Jiao et al.,2010).Rice leaves initiate at the peripheral zone of shoot apical meristem,then develop along the proximal-distal,adaxial-abaxial,and mediallateral axes to form a flat symmetric architecture(Du et al.,2018).

关键词： crops cereal narrow

Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance

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Science China(Life Sciences) 2024年第1期67卷 149-160页

作者： Haofei Luo Xiaofei Wang Changqing You Xuedan Wu Duofeng Pan Zhiyao Lv Tong Li Dongmei Zhang Zhongbao Shen Xiaodong Zhang Guodao Liu Kaixuan He Qingtong Ye Yajun Jia Qinghua Zhao Xian Deng Xiaofeng Cao Xianwei Song Gai Huang State key laboratory of plant genomics and National Center for plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed Lab Sanya 572025China University of Chinese Academy of Sciences Beijing 100049China Institute of Forage and Grassland Sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China Shandong Academy of Agricultural Sciences Jinan 250100China National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land Dongying 257345China Shandong Green Manure Ecological Technology Co. LtdDongying 257345China State key laboratory of Tropical crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal ***,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline *** understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of *** spanning~2,087 *** assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric *** genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years *** genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A *** further identified four specific alkali-induced phosphate transporter genes in ***;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline *** work highlights the significance of *** as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

关键词： Sesbania cannabina alkaline stress telomere-to-telomere genome legume green manure phosphate transporter allotetraploid

通过机器学习开发基于作物基因型的抗病表型精准预测方法（英文）

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Engineering 2024年第9期 100-110页

作者：刘琪左世敏彭沙莎张昊彭烨李魏熊叶辉林润茂冯志明李慧慧杨俊王国梁康厚祥 State key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant Protection Chinese Academy of Agricultural Sciences Zhongshan Biological Breeding laboratory & jiangsu key laboratory of crop genomics and Molecular Breeding Agricultural College of Yangzhou University Hunan provincial key laboratory of crop Germplasm Innovation and Utilization and College of Agronomy Hunan Agricultural University State key laboratory of crop Gene Resources and Breeding Institute of Crop Sciences Chinese Academy of Agricultural Sciences College of plant Protection Hunan Agricultural University key laboratory of Green Prevention and Control of Tropical plant Diseases and Pests Ministry of Education College of Plant Protection Hainan University MARA key laboratory of Surveillance and Management for plant Quarantine Pests Department of Plant Biosecurity College of Plant Protection China Agricultural University Department of plant Pathology Ohio State University

The traditional method of screening plants for disease resistance phenotype is both time-consuming and costly. Genomic selection offers a potential solution to improve efficiency, but accurately predicting plant disease resistance remains a challenge. In this study, we evaluated eight different machine learning(ML)methods, including random forest classification(RFC), support vector classifier(SVC), light gradient boosting machine(light GBM), random forest classification plus kinship(RFC＿K), support vector classification plus kinship(SVC＿K), light gradient boosting machine plus kinship(light GBM＿K), deep neural network genomic prediction(DNNGP), and densely connected convolutional networks(Dense Net), for predicting plant disease resistance. Our results demonstrate that the three plus kinship(K) methods developed in this study achieved high prediction accuracy. Specifically, these methods achieved accuracies of up to 95% for rice blast(RB), 85% for rice black-streaked dwarf virus(RBSDV), and 85% for rice sheath blight(RSB) when trained and applied to the rice diversity panel I(RDPI). Furthermore, the plus K models performed well in predicting wheat blast(WB) and wheat stripe rust(WSR) diseases, with mean accuracies of up to 90% and 93%, respectively. To assess the generalizability of our models, we applied the trained plus K methods to predict RB disease resistance in an independent population, rice diversity panel Ⅱ(RDPⅡ). Concurrently, we evaluated the RB resistance of RDPⅡ cultivars using spray inoculation. Comparing the predictions with the spray inoculation results, we found that the accuracy of the plus K methods reached 91%. These findings highlight the effectiveness of the plus K methods(RFC＿K, SVC＿K, and light GBM＿K) in accurately predicting plant disease resistance for RB, RBSDV, RSB,WB, and WSR. The methods developed in this study not only provide valuable strategies for predicting disease resistance, but also pave the way for using machine learning to str

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Population genetic insights into the conservation of common walnut(Juglans regia)in Central Asia

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plant Diversity 2024年第5期46卷 600-610页

作者： Linjiang Ye Robabeh Shahi Shavvon Hailing Qi Hongyu Wu Pengzhen Fan Mohammad Nasir Shalizi Safiullah Khurram Mamadzhanov Davletbek Yerlan Turuspekov Jie Liu CAS key laboratory for plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina key laboratory of plant Resources and Biodiversity of Jiangxi Province Jingdezhen UniversityJingdezhen 333400JiangxiChina Germplasm Bank of Wild Species&Yunnan key laboratory of crop Wild Relatives Omics Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanChina Department of Biology Faculty of ScienceYasouj UniversityYasouj 75918-74934Iran University of Chinese Academy of Sciences Beijing 100049China Department of Forestry and Environmental Resources North Carolina State UniversityRaleighNC 27695United States Department of Forestry and Natural Resources Faculty of AgricultureKabul UniversityKabul D-1006Afghanistan National Academy of Science of the Kyrgyz Republic Jalal-Abad Scientific CenterJalal-Abad 715600Kyrgyzstan laboratory of Molecular genetics Institute of Plant Biology and BiotechnologyAlmaty 050040Kazakhstan

The common walnut(Juglans regia)is one of the most economically important nut trees cultivated *** its importance,no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated,Central *** this study,we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central *** found moderate genetic diversity of *** across Central Asia,with 46 populations clustered into three groups with a weak relationship between genetic and geographic *** findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that,except for two populations in Gongliu Wild Walnut Valley,humans might have introduced walnut populations to Xinjiang,*** observed distribution of the genetic landscape has probably been affected by historical climate fluctuation,breeding system,and prolonged anthropogenic *** propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in *** findings enhance our understanding of the genetic variation throughout the distribution range of *** in Central Asia,which will provide a key prerequisite for evidence-based conservation and management.

关键词： Central Asia Genetic diversity Germplasm management Gongliu wild walnut valley Juglans regia Western Himalaya

Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

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The crop Journal 2024年第4期12卷 1022-1030页

作者： Fuying Ma Mingyu Liu Peiwen Yan Shicong He Jian Hu Xinwei Zhang Fuan Niu Jinhao Cui Xinyu Yuan Xiaoyun Xin Liming Cao Jinshui Yang Ying Wang Xiaojin Luo State key laboratory of Genetic Engineering and Engineering Research Center of Gene Technology(Ministry of Education) School of Life SciencesFudan UniversityShanghai 200433China Ministry of Education key laboratory for Biodiversity Science and Ecological Engineering Department of Ecology and Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China Institute of crop Breeding and Cultivation Shanghai Academy of Agricultural SciencesShanghai 200241China Ministry of Education Key Laboratory of Crop PhysiologyEcology and Genetic Breeding College of AgronomyJiangxi Agricultural UniversityNanchang 330045JiangxiChina

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and ***,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthet... 详细信息

关键词： Multi-genome analysis Activity of bc1 complex gene Photosynthesis Biomass Osabc1-13 Haplotype

AcWRKY28 mediated activation of AcCPK genes confers salt tolerance in pineapple(Ananas comosus)

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Horticultural plant Journal 2024年第2期10卷 398-412页

作者： Qiao Zhou Samaranayaka Vidana Gamage Nirosha Priyadarshani Rongjuan Qin Han Cheng Tiantian Luo Myat Hnin Wai Mohammad Aqa Mohammadi Yanhui Liu Chang Liu Hanyang Cai Xiaomei Wang Yeqiang Liu Yuan Qin Lulu Wang Guangxi key Lab of Sugarcane Biology State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of AgricultureGuangxi UniversityNanningGuangxi 530004China State key laboratory of Ecological Pest Control for Fujian and Taiwan crops College of Life ScienceCollege of Plant ProtectionCollege of AgricultureCollege of HorticultureFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyCenter for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouFujian 350002China Pingtan Science and Technology Research Institute of Fujian Agriculture and Forestry University PingtanFujian 350400China National Education Commission BMICHColombo00700Sri Lanka Fishery Multiplication Management Station of Lijiang River Water Supply Hub Project GuilinGuangxi 541001China Horticulture Research Institute Guangxi Academy of Agricultural SciencesNanning Investigation Station of South Subtropical Fruit TreesMinistry of AgricultureNanningGuangxi 530007China

Unfavorable environmental cues severely affect crop productivity resulting in significant economic losses to farmers. In plants, multiple regulatory genes, such as the WRKY transcription factor (TF) family, modulate the expression of defense genes. However, the role of the pineapple WRKY genes is poorly understood. Here, we studied the pineapple WRKY gene, AcWRKY28, by generating AcWRKY28 over-expressing transgenic pineapple plants. Overexpression of AcWRKY28 enhanced the salt stress resistance in transgenic pineapple lines. Comparative transcriptome analysis of transgenic and wild-type pineapple plants showed that “plant-pathogen interaction” pathway genes, including 9calcium-dependent protein kinases (CPKs), were up-regulated in AcWRKY28 over-expressing plants. Furthermore, chromatin immunoprecipitation and yeast one-hybrid assays revealed AcCPK12, AcCPK3, AcCPK8, AcCPK1, and AcCPK15 as direct targets of AcWRKY28. Consistently, the study of AcCPK12 over-expressing Arabidopsis lines showed that AcCPK12 enhances salt, drought, and disease resistance. This study shows that AcWRKY28 plays a crucial role in promoting salt stress resistance by activating the expression of AcCPK genes.

关键词： Pineapple AcWRKY AcCPK Transcription factor Salt stress ChIP

Genetic diversity of RNA viruses infecting invertebrate pests of rice

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Science China(Life Sciences) 2024年第1期67卷 175-187页

作者： Haoran Wang Shufen Chao Qing Yan Shu Zhang Guoqing Chen Chonghui Mao Yang Hu Fengquan Yu Shuo Wang Liang Lv Baojun Yang Jiachun He Songbai Zhang Liangsheng Zhang Peter Simmonds Guozhong Feng State key laboratory of Rice Biology and Breeding China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou 311400China State key laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Institute of plant Protection&Soil Fertilizer Hubei Academy of Agricultural SciencesWuhan 430064China Institute of plant Protection Guizhou Academy of Agricultural SciencesGuiyang 550000China Institute of plant Protection Liaoning Academy of Agricultural SciencesShenyang 110161China Sanya Agricultural Technology Extension and Service Centre Sanya 572000China College of Agriculture Yangtze UniversityJingzhou 434000China Fujian provincial key laboratory of Haixia Applied plant Systems Biology Fujian Agriculture and Forestry UniversityFuzhou 350002China genomics and Genetic Engineering laboratory of Ornamental plants College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310012China Nuffield Department of Medicine Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxford OX13SYUnited Kingdom

Invertebrate species are a natural reservoir of viral genetic diversity,and invertebrate pests are widely distributed in crop ***,information on viruses infecting invertebrate pests of crops is *** this report,we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice *** identified 296 new RNA viruses and 13 known RNA *** viruses clustered within 31 families,with many highly divergent viruses constituting potentially new families and *** the identified viruses,13 RNA viruses clustered within the Fiersviridae family of bacteriophages,and 48 RNA viruses clustered within families and genera of *** detected known rice viruses in novel invertebrate hosts at high ***,some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within genera of several plant virus *** potential insect pathogenic RNA viruses were detected in invertebrate *** analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral ***-species transmission of RNA viruses was detected between invertebrate *** identified viral genomes showed extensive variation for invertebrate viral families or ***,the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species,the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.

关键词： invertebrate species metatranscriptome viral diversity viral transmission viral genomes