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Rice Gene Index:A comprehensive pan-genome database for comparative and functional genomics of Asian rice

Molecular Plant 2023年第5期16卷 798-801页

作者：于志超陈永明周勇张雨露李梦圆欧阳亦聃 Dmytro Chebotarov Ramil Mauleon 赵虎谢为博 kenneth l.mcnally Rod A.Wing 郭伟龙张建伟 National Key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China 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 Center for Desert Agriculture Biological and Environmental Sciences&Engineering Division(BESE)King Abdullah University of Science and Technology(KAUST)Thuwal 23955-6900Saudi Arabia International Rice Research Institute(IRRI) Los Ban˜osLaguna 4031Philippines Arizona Genomics Institute School of Plant SciencesUniversity of ArizonaTucsonAZ 85721USA

Dear Editor,Asian rice(Oryza sativa)is the staple food for half the world and is a model crop that has been extensively *** contributes20%of calories to the human diet(Stein et al.,2018).With the increase in global population and rapid changes in climate,rice breeders need to develop new and sustainable cultivars with higher yields,healthier grains,and reduced environmental footprints(Wing et al.,2018).Since the first gold-standard reference genome of rice variety Nipponbare was published(International Rice Genome Sequencing Project,2005),an increasing number of rice accessions have been sequenced,assembled,and annotated with global ***,a single reference genome is obviously insufficient to perform the genetic difference analysis for rice ***,the pan-genome has been proposed as a solution,which allows the discovery of more presence-absence variants compared with single-reference genome-based studies(Zhao et al.,2018).Over the past years,several databases,such as RAP-db(https://***),RGAP(http://***),and Gramene(https://***),have long-term served rice genomic research by providing information based on one or a series of individual reference *** integrate and utilize the genomic information of multiple accessions,we performed comparative analyses and established the user-friendly Rice Gene Index(RGI;https://***)*** is the first gene-based pan-genome database for rice.

关键词： sativa comprehensive cultivar

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A High-throughput Genomic Tool： Diversity Array Technology Complementary for Rice Genotyping

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Journal of Integrative Plant Biology 2006年第9期48卷 1069-1076页

作者： Yong Xie kenneth mcnally Cheng-Yun li Hei leung You-Yong Zhu National Center for Agro-biodiversity Yunnan Agricultural University Kunming 650201 China Genetic Resources Center International Rice Research Institute DAPO P.O. Box 7777 Metro Manila Philippines Entomology and Plant Pathology Division International Rice Research Institute DAPO P.O. Box 7777 Metro Manila Philippines

Diversity array technology （DART^TM） was a genotyping tool characterized gel-independent and high throughput. The main purpose of present study is to validate DArT for rice （Oryza sativa l.）genotyping in a high throughput manner. Technically, the main objective was to generate a rice general purpose gene pool, and optimize this genomic tool in order to evaluate rice germplasm genetic diversity. To achieve this, firstly, a generalpurpose DArT array was developed. Ten representatives from 24 varieties were hybridized with the general-purpose array to determine the informativeness of the clones printed on the array. The informative 1 152 clones were re-arrayed on a slide and used to fingerprint 17 of 24 germplasms. Hybridizing targets prepared from the germplasm to be assayed to the DNA array gave DNA fingerprints of germplasms. Raw data were normalized and transformed into binary data, which were then analyzed by using NTSYSpc （Numerical taxonomy system for cluster and ordination analysis, v. 2.02j） software package. The graphically displayed dendrogram derived from the array experimental data was matched with simple sequence repeats genotyping outline and varieties＇ pedigree deviation of the different varieties. Considering DArT is a sequence-independent genotyping approach, it will be applied in studies of the genetic diversity and the gene mapping of diverse of organisms, especially for those crops with less-developed molecular markers.

关键词： amplified fragment length polymorphisms diversity array technology genome complexity reduction microarray rice genotyping

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The Genomic Variation of 3,000 diverse Rice (Oryza sativa l.)Accessions:Discoveries And Applications In Rice Improvement

The Genomic Variation of 3,000 diverse Rice (Oryza sativa L....

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2018中国作物学会学术年会

作者：黎志康 Fan Zhang Whensheng Wang Ramil Mauleon Zhiqiang Hu Dmytro Chebotarov Shuaishuai Tai Zhichao Min li Tianqing Zheng Roven Rommel Fuentes locedie Mansueto Dario Copetti Millicent Sanciangco Kevin Christian Palis Jianlong Xu Chen Sun Hongliang Zhang Binying Fu Yongming Gao Xiuqin Zhao Fei Shen Xiao Cui Hong Yu Zichao li Miaolin Chen Jeffery Detras Yongli Zhou Xinyuan Zhang Yue Zhao Dave Kudrna Chunchao Wang Rui li Ben Jia Jinyuan lu Xianchang He Zhaotong Dong Jiabao Xu Yanhong li Miao Wang Jianxin Shi Jing li Dabing Zhang Seunhee lee Wushu Hu Alexander Poliakov Inna Dubchak Victor Jun Ulat Frances Nikki Borja John Robert Mendoza Jauhar Ali Ming Yang Yongchao Niu Zhen Yue Ma.Elizabeth B.Naredo Jayson Talag Xueqiang Wang Jinjie li Xiaodong Fang Ye Yin Jean-Christophe Glaszmann Jianwei Zhang Jiayang li Ruaraidh Sackville Hamilton Rod A.Wing Chaochun Wei Jue Ruan Gengyun Zhang kenneth l.mcnally Nickolai Alexandrov Hei leung Hei Institute of Crop Sciences Chinese Academy of Agricultural Sciences Shenzhen Institute for Innovative Breeding Chinese Academy of Agricultural Sciences International Rice Research Institute School of life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai Center for Bioinformation Technology BGI Genomics BGI-Shenzhen Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Anhui Agricultural University Arizona Genomics Institute School of Plant SciencesUniversity of Arizona China Agricultural University Institute of Genetics and Developmental Biology Chinese Academy of Sciences lawrence Berkeley National laboratory

Asian cultivated rice(Oryza sativa l.) is the staple food for the half world population with rich within species *** analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within ***,over 42 million SNPs and >3 million small InDels were discovered against five reference ***,we discovered more than 90,000 structural(>100 bps) variations(SVs) when compared with the Geng reference genome,consisting primarily of small-sized deletions and translocations,plus many duplications and *** SVs accounted for significant portion of the rice genome and involved most(～80%) rice ***,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference *** rice pan genome consists of ～62%core genes/gene families that are present in all rice lines,and ～38%distributed genes that are present only some of rice ***,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was *** SNP,PG and SV variation clearly resolve the 3,010 rice accessions into two major subspecies,Xian(indica) and Geng(japonica),plus Aus and Aro groups and multiple subpopulations within Xian and *** reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes *** efforts have been taken to identify and mine genes/QTls/alleles associated with a wide range of important traits in rice using the 3 k materials and SNP *** demonstrate how the results of the 3 k RGP could be used in rice improvement,genomic constitutions of 476 BC F introgression lines(Ils) from our breeding program were constructed using high-quality reference genomes of their 9 parents and the 3 k RGP *** compared with their recurrent parent,Huang-hua-

关键词： Rice genome diversity population structure pan genomes genomics-based breeding by design

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Annual survival and site fidelity of free-ranging white-tailed deer (Odocoileus virginianus): comparative demography before (1983- 1992) and after (1993-2005) spatial confinement

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Integrative Zoology 2014年第1期9卷 24-33页

作者： Stephen l.WEBB kenneth l.GEE The Samuel Roberts Noble Foundation ArdmoreOklahoma USA

Survival and movement are important demographic variables influencing the dynamics of large herbivores with implications for management and evolution of life-history *** practices such as spatial con-finement and harvest regulation attempt to control survival and movement for the sustainability of harvested deer populations,but a paucity of long-term data exists on these management *** examined annual survival and site fidelity of free-ranging white-tailed deer(Odocoileus virginianus)over 10 years(1983-1992)to compare demographic parameters after spatial confinement(1993-2005).We used capture records(n=174;104 females,70 males),marked deer recaptures(n=42),and dead recoveries(n=68)to estimate sex-specif-ic,age-specific and time-specific *** found that annual female survival was 50%from 1983-1987 during a period of intense harvest,but increased to 93.7%after intense harvesting was *** to spa-tial confinement,annual survival of marked male deer averaged 36.7%-42.5%.After spatial confinement,annu-al survival increased on average for males(58%-99%)and females(77%-98%).Females showed high levels of site fidelity(>99%)prior to spatial confinement,whereas males showed much less site fidelity(≤4.5%for the 2 top-ranking models).During spatial confinement,the semi-impermeable fence effectively increased site fidelity of males(≥56%).These results stem from long-term study(23 years)of a large herbivore experiencing changes to life-history,resulting from changes in management that were applied to the population and aimed at altering population demographics,for sustainability of a harvestable population of deer.

关键词： conservation deer fidelity mortality Odocoileus virginianus population dynamics

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OTX2 signaling in retinal dysfunction,degeneration and regeneration

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Neural Regeneration Research 2021年第10期16卷 2002-2003页

作者： kenneth.l.Moya Raoul Torero Ibad Centre for Interdisciplinary Research in Biology(CIRB) Collège de FranceCNRS UMR 7241INSERM U1050Labex MemoLifePSL Research UniversityParisFrance(Moya KLIbad RT)Univ.LilleCNRSUMR 8523-PhLAM-Physique des Lasers Atomes et MoléculesF-59000 LilleFrance(Ibad RT)

The protein OTX2 in the retina is necessary for the maintenance of normal physiologic processes,and may be a promising therapeutic agent for some ophthalmic *** this Perspective,we first shortly introduce the organization of the retina and the importance of OTX2 *** then present an example of reduced OTX2 activity in the developed retina associated with structural and functional *** next show that homeoproteins can have neuroprotective *** finally review several clear examples of OTX2 non-cell autonomous activity in the retina and the effects of diminishing or providing extracellular OTX2.

关键词： expression. functions. agent

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Dendritic cells in cancer immunology

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Cellular & Molecular Immunology 2022年第1期19卷 3-13页

作者： Theresa l.Murphy kenneth M.Murphy Department of Pathology and Immunology Washington University in St.LouisSchool of MedicineSt.LouisMO 63110USA

The clinical success of immune checkpoint therapy(ICT)has produced explosive growth in tumor immunology research because ICT was discovered through basic studies of immune *** of the current translational efforts are aimed at enhancing ICT by identifying therapeutic targets that synergize with CTlA4 or PD1/PD-l1 blockade and are solidly developed on the basis of currently accepted *** these principles through continuous basic research may help broaden translational *** this mindset,we focused this review on three threads of basic research directly relating to mechanisms underlying ***,this review covers three aspects of dendritic cell(DC)biology connected with antitumor immune responses but are not specifically oriented toward therapeutic ***,we review recent advances in the development of the cDC1 subset of DCs,identifying important features distinguishing these cells from other types of ***,we review the antigen-processing pathway called cross-presentation,which was discovered in the mid-1970s and remains an *** pathway serves an essential in vivo function unique to cDC1s and may be both a physiologic bottleneck and therapeutic ***,we review the longstanding field of helper cells and the related area of DC licensing,in which CD4 T cells influence the strength or quality of CD8 T cell *** topic is connected with ICT in some manner but is also a fundamental aspect of cell-mediated immunity directed toward intracellular pathogens.

关键词： Dendritic cells transcription factors cross-presentation tumor rejection CD4 help

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Technology advancing the study of animalcognition： using virtual reality to presentvirtually simulated environments to investigatenonhuman primate spatial cognition

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Current Zoology 2017年第1期63卷 97-108页

作者： Francine l. DOlINS kenneth SCHWEllER Scott MIlNE Department of Behavioral Sciences University of Michigan-Dearborn Dearborn MI 48128 USA Ape Cognition and Conservation Initiative Des Moines IA USA Impact Madagascar Nanisana Antananarivo 101Madagascar Africa

Virtual simulated environments provide multiple ways of testing cognitive function and evaluatingproblem solving with humans （e.g., Woollett et al. 2009）. The use of such interactive technologyhas increasingly become an essential part of modern life （e.g., autonomously driving vehicles, glo-bal positioning systems （GPS）, and touchscreen computers; Chinn and Fairlie 2007; Brown 2011）.While many nonhuman animals have their own forms of technology, such as chimpanzees whocreate and use tools, in captive animal environments the opportunity to actively participate withinteractive technology is not often made available. Exceptions can be found in some state-of-the-art zoos and laboratory facilities （e.g., Mallavarapu and Kuhar 2005）. When interactive technologyis available, captive animals often selectively choose to engage with it. This enhances the animal＇ssense of control over their immediate surroundings （e.g., Clay et al. 2011; Ackerman 2012）. Suchself-efficacy may help to fulfill basic requirements in a species＇ daily activities using problem solv-ing that can involve foraging and other goal-oriented behaviors. It also assists in fulfilling thestrong underlying motivation for contrafreeloading and exploration expressed behaviorally bymany species in captivity （Young 1999）. Moreover, being able to present nonhuman primates vir-tual reality environments under experimental conditions provides the opportunity to gain insightinto their navigational abilities and spatial cognition. It allows for insight into the generation andapplication of internal mental representations of landmarks and environments under multiple con-ditions （e.g., small- and large-scale space） and subsequent spatial behavior. This paper reviewsmethods using virtual reality developed to investigate the spatial cognitive abilities of nonhumanprimates, and great apes in particular, in comparison with that of humans of multiple age *** make recommendations about training, best practices, and also pi

关键词： animal cognition, apes, bonobos, chimpanzees, nonhuman primates, spatial cognition, virtual reality.

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Development of a Core Set from a large Rice Collection using a Modified Heuristic Algorithm to Retain Maximum Diversity

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Journal of Integrative Plant Biology 2009年第12期51卷 1116-1125页

作者： Hun-Ki Chung Kyu-Won Kim Jong-Wook Chung Jung-Ro lee Sok-Young lee Anupam Dixit Hee-Kyoung Kang Weiguo Zhao kenneth l. mcnally Ruraidh S. Hamilton Jae-Gyun Gwag Yong-Jin Park National Agrobiodiversity Center National Academy of Agricultural Science Suwon 441-707 Korea Department of Plant Resources College of Industrial Sciences Kongju National University Yesan 340-802 Korea Rice DNA and Quality Testing laboratory Basmati Export Development Foundation SVBP University of Agriculture and Technology Meerut 250110 India Department of Horticultural Science College of Industrial Science Kongju National University Yesan 340-802 Korea jiangsu University of Science and Technology Seficultural Research Institute Chinese Academy of Agricultural Sciences Zhenjiang 212018 China Genetic Resources Center International Rice Research Institute Metro Manila 1301 Philippines

A new heuristic approach was undertaken for the establishment of a core set for the diversity research of rice. As a result, 107 entries were selected from the 10 368 characterized accessions. The core set derived using this new approach provided a good representation of the characterized accessions present in the entire collection. No significant differences for the mean, range, standard deviation and coefficient of variation of each trait were observed between the core and existing collections. We also compared the diversity of core sets established using this Heuristic Core Collection （HCC） approach with those of core sets established using the conventional clustering methods. This modified heuristic algorithm can also be used to select genotype data with allelic richness and reduced redundancy, and to facilitate management and use of large collections of plant genetic resources in a more efficient way.

关键词： core collection genetic diversity heuristic core collection Oryza sativa sampling strategy.

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Evolutionary Genomics of Weedy Rice in the USA

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Journal of Integrative Plant Biology 2007年第6期49卷 811-816页

作者： kenneth M. Olsen Ana l. Caicedo Yulin Jia Department of Biology Washington University St Louis MO 63130 USA Department of Biology University of Massachusetts Amherst MA 01003 USA USDA-ARS Dale Bumpers National Rice Research Center Stuttgart AR 72160 USA

Red rice Is an Interfertlle, weedy form of cultivated rice （Oryza sativa l.） that competes aggressively with the crop In the southern US, reducing yields and contaminating harvests. No wild Oryza species occur In North America and the weed has been proposed to have evolved through multiple mechanisms, Including ＂de-domestication＂ of US crop cultlvars, accidental introduction of Asian weeds, and hybridization between US crops and Asian wild/weedy Oryza strains. The phenotype of US red rice ranges from ＂crop mimics＂, which share some domestication traits with the crop, to strains closely resembling Asian wild Oryza species. Assessments of genetic diversity have Indicated that many weed strains are closely related to Asian taxa （Including indica and aus rice varieties, which have never been cultivated In the US, and the Asian crop progenitor O. ruflpogon）, whereas others show genetic similarity to the tropical Japonica varieties cultivated In the southern US. Herein, we review what Is known about the evolutionary origins and genetic diversity of US red rice and describe an ongoing research project to further characterize the evolutionary genomlcs of this aggressive weed.

关键词： crop-weed introgression de-domestication Oryza sativa weed evolution weedy rice.

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Diagnosing gastrointestinal illnesses using fecal headspacevolatile organic compounds

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World Journal of Gastroenterology 2016年第4期22卷 1639-1649页

作者： Daniel K Chan Cadman l leggett kenneth K Wang Division of Gastroenterology and Hepatology Mayo ClinicRochesterMN 55905United States

Volatile organic compounds(VOCs) emitted from stool are the components of the smell of stool representing the end products of microbial activity and metabolism that can be used to diagnose disease. Despite the abundance of hydrogen, carbon dioxide, and methane that have already been identified in human flatus, the small portion of trace gases making up the VOCs emitted from stool include organic acids, alcohols, esters, heterocyclic compounds, aldehydes, ketones, and alkanes, among others. These are the gases that vary among individuals in sickness and in health, in dietary changes, and in gut microbial activity. Electronic nose devices are analytical and pattern recognition platforms that can utilize mass spectrometry or electrochemical sensors to detect these VOCs in gas samples. When paired with machine-learning and pattern recognition algorithms, this can identify patterns of VOCs, and thus patterns of smell, that can be used to identify disease states. In this review, we provide a clinical background of VOC identification, electronic nose development, and review gastroenterology applications toward diagnosing disease by the volatile headspace analysis of stool.

关键词： Electronic nose Volatile organic compounds Feces Mass spectrometry Odors

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