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Global wild rice germplasm resources conservation alliance:World Wild-Rice Wiring

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Molecular Plant 2024年第4期17卷 516-518页

作者： Xiaoming Zheng Disna Ratnasekera Jiayu Fan Robert J.Henry Beng-Kah Song Kenneth M.Olsen Bal Krishna Joshi Maria Celeste N.Banaticla-Hilario Tonapha Pusadee Adane Getachew Melaku Yeyinou Laura Estelle Loko Koukham Vilayheuang Gavers K.Oppong Samuel Aduse Poku Peterson W.Wambugu Song Ge Aldo Merotto Junior Ohn Mar Aung Ramaiah Venuprasad Ajay Kohli Wenbin Zhou Qian Qian National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Sanya National Research Institute of Breeding in Hainan Chinese Academy of Agricultural SciencesBeijing 100081China International Rice Research Institute DAPO Box 7777Metro Manila 4031Philippines Department of Agricultural Biology Faculty of AgricultureUniversity of RuhunaMatara 81000Sri Lanka Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China Hainan University Haikou 570228China ARC Centre of Excellence for Plant Success in Nature and Agriculture University of QueenslandBrisbaneQLD4072Australia School of Science Monash University Malaysia47500 Bandar SunwaySelangor 47500Malaysia Department of Biology Washington University in St.LouisSt.LouisMO 63130-4899USA National Agriculture Genetic Resources Center(genebank) KhumaltarPO Box 3055KathmanduNepal Plant Biology Division Insttute of Biological SciencesUniversity of the Pilippines Los BanosLos BanosLaguna 4031Philippines Division of Agronomy Department of Plant and Soil SciencesFaculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Bio and Emerging Technology Institute Addis Ababa 1165Ethiopia National University of Sciences TechnologiesEngineering and Mathematics(UNSTIM)Dassa-ZouméBP 14Benin National genebank Rice and Cash Crops Research CenterNAFRIVientiane 0605Lao PDR Plant Sciences and the Bioeconomy Rothamsted ResearchHarpenden AL52JQUK UK Future Food Beacon of Excellence and School of Biosciences and University of Nottingham Nottingham LE125RDUK Department of Plant and Environmental Biology University of GhanaAccraGhana Kenya Agricultural and Livestock Research Organization Genetic Resources Research InstituteNairobi 00200Kenya Institute of Botany Chinese Academy of SciencesBeijing 100093China Federal University of Rio Grande do Sul UFRGSPorto Alegre 91501-970RSBrazil Department of Agricultur

Wild relatives of crop are key genetic resources serving as diversity reservoirs for crop improvement under changing environments.Rice(Oryza sativa)is one of the most important crops in the world,providing staple food for half of the world's population.Wild rice is thus a critical germplasm resource for sustained global food security,ensuring high production yields,improved quality,and stress resistance in the face of climate change.Wild rice is closely related to domesticated rice and has a rich genetic diversity and exceptional adaptability to extreme environments.It has played a pivotal role in the history of rice hybridization and has become a key resource for rice breeding programs.The identification of wild-type cytoplasmic male sterility resources paved the way for the achievement of the“three lines”goal in hybrid rice,leading to a significant increase in rice yields.In addition,the use of resistance alleles found in wild rice is making rice production more resilient to losses caused by environmental stresses.However,wild rice germplasm resources are threatened due to habitat destruction and other anthropogenic factors.At the same time,the lack of centralized distribution of wild rice has hampered the sharing of basic information on wild rice resources and the utilization and conservation of wild rice in each country,as well as collaboration among scientists.

关键词： germplasm breeding crops

CDCP:a visualization and analyzing platform for single-cell datasets

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Journal of Genetics and Genomics 2022年第7期49卷 689-692页

作者： Yuejiao Li Tao Yang Tingting Lai Lijin You Fan Yang Jiaying Qiu Lina Wang Wensi Du Cong Hua Zhicheng Xu Jia Cai Zhiyong Li Yiqun Liu Ling Li Minwen Zhang Jing Chen Lei Zhang Dongsheng Chen Weiwen Wang Shiping Liu Liang Wu Wenjun Zeng Bo Wang Xiaofeng Wei Longqi Liu Fengzhen Chen BGI-Shenzhen ShenzhenGuangdong 518083China China National genebank ShenzhenGuangdong 518120China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

Recently,the rapid advances of single-cell sequencing technologies,including sequencing of single-cell genomics,transcriptomes,epigenetics,and spatial transcriptomes,have empowered researchers to scrutinize cellular h... 详细信息

关键词： cell advances rutin

Haplotype-resolved and chromosome-scale genomes provide insights into co-adaptation between the Amur tiger and Amur leopard

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Zoological Research 2024年第3期45卷 464-467页

作者： Hai-Meng Li Bo-Yang Liu Min-Hui Shi Le Zhang Shang-Chen Yang Sunil Kumar Sahu Liang-Yu Cui Shan-Lin Liu Nicolas Dussex Yue Ma Dan Liu Wei-Yao Kong Hao-Rong Lu Yue Zhao Love Dalén Huan Liu Tian-Ming Lan Guang-Shun Jiang Yan-Chun Xu College of Wildlife and Protected Area Northeast Forestry UniversityHarbinHeilongjiang 150040China State Key Laboratory of Agricultural Genomics BGI ResearchShenzhenGuangdong 518083China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China College of Life Sciences Zhejiang UniversityHangzhouZhejiang 310058China BGI Research WuhanHubei 430074China Department of Entomology College of Plant ProtectionChina Agricultural UniversityBeijing 100193China Centre for Palaeogenetics Svante Arrhenius väg 20CStockholm 10691Sweden Department of Zoology Stockholm UniversityStockholm 10691Sweden Department of Bioinformatics and Genetics Swedish Museum of Natural HistoryStockholm 10691Sweden Heilongjiang Siberian Tiger Park HarbinHeilongjiang 150000China Jinlin Provincial Academy of Forestry Science ChangchunJilin 130033China China National genebank BGI ResearchShenzhenGuangdong 518120China Guangdong Provincial Key Laboratory of Genome Read and Write BGI ResearchShenzhenGuangdong 518083China BGI Life Science Joint Research Center Northeast Forestry UniversityHarbinHeilongjiang 150040China Feline Research Center of National Forestry and Grassland Administration College of Wildlife and Protected AreaNortheast Forestry UniversityHarbinHeilongjiang 150040China National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization HarbinHeilongjiang 150040China

DEAR EDITOR,Big cats,such as Amur tigers(Panthera tigris altaica)and Amur leopards(P.pardus orientalis),are apex predator and have evolved specialized traits for hunting and carnivory(Moya et al.,2022),thus playing a crucial role in maintaining biodiversity and ecosystem integrity by regulating prey-predator dynamics.However,human-induced pressures,habitat fragmentation,and environmental alterations have restricted these species in small and isolated populations.Currently,all extant big cats are categorized as endangered or threatened according to their conservation status.Amur tigers and Amur leopards share overlapping geographic ranges,habitats,and certain prey species in the forests of Northeast Asia(Jiang et al.,2015).To reduce interspecies conflict,these carnivores exhibit differentiated dietary and temporal niches.Amur tigers predominantly prey on large ungulates,while Amur leopards hunt small to medium-sized animals(Sugimoto et al.,2016).Additionally,they occupy different temporal niches,with tigers being active at night and leopards more active during the day.Despite spatial and temporal niche partitioning,interspecific competition between these two species is inevitable.Tigers,benefiting from their greater size,have a competitive advantage over leopards,which can manifest in occasional leopard predation by tigers and declines in leopard populations with increasing tiger density(Jiang et al.,2015).Tigers also displace leopards from marginal habitats in nature reserves where they coexist.

关键词： habitat Panthera resolved

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Vascular Flora from Ecoton Zones of the Slatioara Secular Forest

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Open Journal of Forestry 2023年第1期13卷 75-91页

作者： Marius Dan Șandru Camelia-Maria Golea Dumitru Dorel Blaga genebank “Mihai Cristea” Suceava Romania Stefan cel Mare University of Suceava Suceava Romania

The purpose of this study is to generate essential scientific information regarding the floristic composition and the structures of the ecotone vegetation in the natural forest Codrul Secular Slătioara, because so far no such studies have been carried out in this reserve. Also, the results of this study provide important data, which can be the basis for the development of strategies for the conservation and sustainable use of some herbaceous species, valuable due to genetic and socio-economic, respectively of a regular forest monitoring program. The floristic studies were carried out in the 2020 to 2021 vegetation season. Based on the specialized literature, plant species were identified and then processed from the point of view of bioforms, floristic elements and ecological indices. The economic categories in which the identified species fall were also analyzed. Thus, a total of 292 species belonging to 46 botanical families were identified and their distribution by ecosystems is as follows: in the forest, 90 species were identified, in the lands adjacent to the forest, in the meadows, 202 species were found and in the area of border, 120 species of vascular plants were identified. Most of the species identified in the study area are hemicryptophytes, heliophiles, and eurytherms, which grow on dry to moderately moist, eurytrophic soils. More than 50% of the identified species belong to several categories of useful plants (fodder, medicinal, melliferous, edible).

关键词： Flora Border Bioforms Floristic Elements Ecological Indices Economic Cat-egories

Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies

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Genomics, Proteomics & Bioinformatics 2022年第1期20卷 192-204页

作者： Xiao Du Lili Li Fan Liang Sanyang Liu Wenxin Zhang Shuai Sun Yuhui Sun Fei Fan Linying Wang Xinming Liang Weijin Qiu Guangyi Fan Ou Wang Weifei Yang Jiezhong Zhang Yuhui Xiao Yang Wang Depeng Wang Shoufang Qu Fang Chen Jie Huang National Institutes for food and drug Control(NIFDC) Beijing 10050China BGI-Qingdao BGI-ShenzhenQingdao 266555China GrandOmics Biosciences Beijing 102200China Annoroad Gene Technology(Beijing)Co. Ltd.Beijing 102200China BGI-Shenzhen Shenzhen 518083China MGI BGI-ShenzhenShenzhen 518083China State Key Laboratory of Agricultural Genomics BGI-ShenzhenShenzhen 518083China China National genebank BGI-ShenzhenShenzhen 518120China

The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109×Pacific Bio sciences(PacBio)continuous long reads(CLRs),22×PacBio circular consensus sequencing(CCS)reads,104×Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping platform,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.

关键词： Asian benchmark Reference material Structural variation Haplotype-resolved Sanger validation

Diversity and trait-specific sources for productivity and nutritional traits in the global proso millet(Panicum miliaceum L.) germplasm collection

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The Crop Journal 2018年第5期6卷 451-463页

作者： Mani Vetriventhan Hari D.Upadhyaya genebank International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Department of Agronomy Kansas State University The UWA Institute of Agriculture The University of Western Australia

Proso millet is an important short-duration crop that adapts well to varied climatic conditions and is grown worldwide for food,feed and fodder purposes.Owing to a lack of genetic improvement,the crop has experienced no yield improvement and provides low income to farmers.In this study,200 accessions of proso millet originating in 30 countries were evaluated in two rainy seasons to assess phenotypic diversity for morpho-agronomic and grain nutritional traits and to identify high grain-yielding and grain nutrient-rich accessions.Proso millet diversity was structured by geographical region,by country within region,and by racial group.Race patentissimum showed high diversity and ovatum low diversity,and diverged widely from each other.The lowest divergence was observed between races compactum and ovatum.Eighteen high grain-yielding,10 large-seeded,and 26 two or more grain nutrients-rich accessions were identified,and highly diverse pairs of accessions within and between trait groups were identified.They included IPm 9 and IPm2661 for high grain yield and large seed size;and IPm 2069,IPm 2076,and IPm 2537 for high Fe,Zn,Ca,and protein contents.IPm 2875 had a seed coat that is readily removed by threshing.This study provides valuable information to proso millet researchers about agronomic and nutritional traits in accessions that could be tested for regional adaption and yield for direct release as cultivars,and could be used in breeding for developing high grain-yielding and nutrient-rich cultivars.

关键词： short-duration morpho-agronomic

Levels of Crotonaldehyde and 4-hydroxy-(E)-2-nonenal and Expression of Genes Encoding Carbonyl-Scavenging Enzyme at Critical Node During Rice Seed Aging

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Rice science 2018年第3期25卷 152-160页

作者： FU Shenzao YIN Guangkun XIN Xia WU Shuhua WEI Xinghua LU Xinxiong State Key Laboratory of Rice Biology China National Rice Research Institute National Crop genebank Institute of Crop Science Chinese Academy of Agricultural Sciences

The critical node(CN) is an important stage during seed aging, which is related to effective genebank conservation. Previous studies have demonstrated that proteins undergo carbonylated modification at the CN in rice, indicating oxidative damage. However, the levels of reactive carbonyl species(RCS) and the associated scavenging system at the CN are largely unknown. In this study, we optimized methods for the extraction and analysis of RCS from dry rice embryos. In order to acquire seeds at the CN, rice seeds were subjected to natural conditions for 7, 9, 11 and 13 months, and the seed germination rates were reduced to 90%, 82%, 71% and 57%, respectively. We chose the stage with seed germination rate of 82% as the CN according to the rice seed vigor loss curve. The levels of crotonaldehyde and 4-hydroxy-(E)-2-nonenal(HNE) were significantly increased at the CN. In addition, genes encoding carbonyl-scavenging enzyme, including Os ALDHs and Os AKRs, were significantly down-regulated at the CN, and reductions in the expression of Os ALDH2-2, Os ALDH2-5, Os ALDH3-4, Os ALDH7, Os AKR1 and Os AKR2 in particular could be responsible for RCS accumulation. Thus, the accumulations of crotonaldehyde and HNE and down-regulation of genes encoding carbonyl-scavenging enzyme might be related to an accelerating loss of seed viability at the CN.

关键词： carbonyl-scavenging system reactive carbonyl species seed aging crotonaldehyde critical node rice storage

Sorghum germplasm from West and Gentral Africa maintained in the ICRISAT genebank: Status,gaps,and diversity

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The Crop Journal 2017年第6期5卷 518-532页

作者： Hari Deo Upadhyaya Kothapally Narsimha Reddy Mani Vetriventhan Mohammed Irshad Ahmed Gumma Murali Krishna Mulinti Thimma Reddy Shailesh Kumar Singh genebank International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 Telangana India Department of Agronomy Kansas State University Manhattan KS 66506 USA The UWA Institute of Agriculture The University of Western Australia Crawley WA 6009 Australia Remote Sensing and GIS Unit International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324Telangana India

The genebank at ICRISAT maintains 8020 accessions of sorghum from 16 West and Central African countries. Geographical gaps and diversity were assessed in the collection. Using the passport data of 3991 accessions for which georeferenced data were available, a total of386 districts(gaps) located in 11 West and Central African countries were identified as geographical gaps. Burkina Faso with 140 and Nigeria with 118 districts were identified as countries with major geographical gaps. The collection of 43 accessions of wild species represented only three species belonging to Sorghum bicolor ssp. drummondii and ssp.verticilliflorum, S. hevisonii, and S. macrochaeta, highlighting the need for collection missions aimed exclusively at enriching the collection of wild relatives. Accessions having characterization data(7630) were used to assess diversity. The first three principal components contributed to >60% of variation. Maximum diversity was observed in the collection from Nigeria for both qualitative and quantitative traits. Mean values indicated significant differences between basic and intermediate races for the traits studied. Among the races, accessions of guinea-caudatum for qualitative traits and those of caudatum for quantitative traits were highly diverse. The low intensity of the sorghum collection and the many geographical gaps in the collection underline the importance of launching collection missions to fill the gaps, particularly in regions of predominantly guinea sorghums.Genotyping of possible duplicate accessions is needed to identify duplicates in the collection. It is suggested that all passport information including georeferenced data of collection sites should be collected when samples are collected in gaps.

关键词： Collection Diversity Gaps Germplasm Landraces Sorghum

The first AsiaEvo conference, connecting Asian evolutionary biologists to the world

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National Science Review 2018年第5期5卷 614-616页

作者： Guojie Zhang Section for Ecology and Evolution Department of BiologyUniversity of Copenhagen China National genebank BGI-Shenzhen State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences

‘Nothing in biology makes sense except in the light of evolution.’ Theodosius Dobzhansky wrote this sentence 45 years ago to point out the pivotal role of evolutionary biology in understanding any question about living organisms. Since then, the evolutionary perspective based on Darwinian natural selection and particulate inheritance has become a major integrative force across the biological and medical sciences, and the field continues to achieve further theoretical and empirical advances.

关键词： The first AsiaEvo conference connecting Asian evolutionary biologists to the world