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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 studied.It 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 efforts.Nowadays,a single reference genome is obviously insufficient to perform the genetic difference analysis for rice accessions.Therefore,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://rapdb.***.affrc.***.jp),RGAP(http://rice.***.edu),and Gramene(https://***),have long-term served rice genomic research by providing information based on one or a series of individual reference genomes.To integrate and utilize the genomic information of multiple accessions,we performed comparative analyses and established the user-friendly Rice Gene Index(RGI;https://***)platform.RGI is the first gene-based pan-genome database for rice.

关键词： sativa comprehensive cultivar

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Well-Posedness of Stochastic Continuity Equations on Riemannian Manifolds

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Chinese Annals of Mathematics,Series B 2024年第1期45卷 81-122页

作者： luca GAlIMBERTI kenneth H.KARlSEN Department of Mathematical Sciences NTNU Norwegian University of Science and TechnologyN-7491 TrondheimNorway Department of mathematics University of OsloP.O.Box 1053BlindernN-0316 OsloNorway

The authors analyze continuity equations with Stratonovich stochasticity,■ρ+divh[ρo(u(t,x)+∑_(i=1)^(N)a_(i)(x)w_(i)(t))]=0defined on a smooth closed Riemannian manifold M with metric h.The velocity field u is perturbed by Gaussian noise terms Wi(t),:WN(t)driven by smooth spatially dependent vector fields a1(x),...,aN(x)on M.The velocity u belongs to l_(t)^(1)W_(x)^(1,2)with divh u bounded in lf,for p>d+2,where d is the dimension of M(they do not assume div_(h) u∈l_(t,x)^(∞)).For carefully chosen noise vector fields ai(and the number N of them),they show that the initial-value problem is well-posed in the class of weak l^(2) solutions,although the problem can be ill-posed in the deterministic case because of concentration effects.The proof of this“regularization by noise”result is based on a l^(2) estimate,which is obtained by a duality method,and a weak compactness argument.

关键词： Stochastic continuity equation Riemannian manifold Hyperbolic equa-tion Non-smooth velocity field Weak solution Existence Uniqueness

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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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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 diversity.Comprehensive analyses of the genome resequencing data of a core collection of 3,010 rice accessions revealed four important aspects of the genomic diversity within O.sativa.First,over 42 million SNPs and >3 million small InDels were discovered against five reference genomes.Secondly,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 inversions.These SVs accounted for significant portion of the rice genome and involved most(～80%) rice genes.Thirdly,we discovered >12,000 full-length novel protein-coding genes plus 9000+ novel genes of partial sequences that are absent in the Nipponbare reference genome.The 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 accessions.Fourthly,using large-effect SNPs and InDels of all loci in the PG,a rice functional haplotype database was constructed.The 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 Geng.Significantly reduced diversity was found in genomic regions where over 1,000 agronomically important and domestication-related genes locate.Tremendous 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 data.To 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 databases.When compared with their recurrent parent,Huang-hua-zhan(HHZ),all these Ils had improved tolerances

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

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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 regulation.Much 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 principles.Expanding these principles through continuous basic research may help broaden translational efforts.With this mindset,we focused this review on three threads of basic research directly relating to mechanisms underlying ICT.Specifically,this review covers three aspects of dendritic cell(DC)biology connected with antitumor immune responses but are not specifically oriented toward therapeutic use.First,we review recent advances in the development of the cDC1 subset of DCs,identifying important features distinguishing these cells from other types of DCs.Second,we review the antigen-processing pathway called cross-presentation,which was discovered in the mid-1970s and remains an enigma.This pathway serves an essential in vivo function unique to cDC1s and may be both a physiologic bottleneck and therapeutic target.Finally,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 responses.Each 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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OTX2 stimulates adult retinal ganglion cell regeneration

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Neural Regeneration Research 2022年第3期17卷 690-696页

作者： Raoul Torero Ibad Nicole Quenech’du Alain Prochiantz kenneth l.Moya Centre for Interdisciplinary Research in Biology(CIRB) Collége de FranceCNRS UMR 7241INSERM U1050Labex MemoLifeParis Sciences et Lettres Research UniversityParisFrance

Retinal ganglion cell(RGC) axons provide the only link between the light sensitive and photon transducing neural retina and visual centers of the brain.RGC axon degeneration occurs in a number of blinding diseases and the ability to stimulate axon regeneration from surviving ganglion cells could provide the anatomic substrate for restoration of vision.OTX2 is a homeoprotein transcription factor expressed in the retina and previous studies showed that,in response to stress,exogenous OTX2 increases the in vitro and in vivo survival of RGCs.Here we examined and quantified the effects of OTX2 on adult RGC axon regeneration in vitro and in vivo.The results show that exogenous OTX2 stimulates the regrowth of axons from RGCs in cultures of dissociated adult retinal cells and from explants of adult retinal tissue and that RGCs respond directly to OTX2 as regrowth is observed in cultures of purified adult rat RGCs.Importantly,after nerve crush in vivo,we observed a positive effect of OTX2 on the number of regenerating axons up to the optic chiasm within 14 days post crush and a very modest level of acuity absent in control mice.The effect of OTX2 on RGC survival and regeneration is of potential interest for degenerative diseases affecting this cell type.All animal procedures were approved by the local "Comié d'éιthique en expérimentation animale n°59" and authorization n° 00702.01 delivered March 28,2014 by the French "Ministére de l'enseignement supérieur et de la recherche".

关键词： axon regeneration dissociated retinal culture GAP-43 homeoprotein optic nerve crush OTX2 retinal explants retinal ganglion cell

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Toward implantable devices for angle-sensitive,lens-less,multifluorescent,single-photon lifetime imaging in the brain using Fabry-Perot and absorptive color filters

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light(Science & Applications) 2022年第2期11卷 197-211页

作者： Adriaan J.Taal Changhyuk lee Jaebin Choi Björn Hellenkamp kenneth l.Shepard Columbia University-Department of Electrical Engineering 500W.120th St.Mudd 1310New York 10027 NYUSA Korea Institute of Science and Technology-Brain Science Institute 5 Hwarang-ro 14-gilSeongbuk-guSeoul 02792Republic of Korea

Implantable image sensors have the potential to revolutionize neuroscience.Due to their small form factor requirements;however,conventional filters and optics cannot be implemented.These limitations obstruct highresolution imaging of large neural densities.Recent advances in angle-sensitive image sensors and single-photon avalanche diodes have provided a path toward ultrathin lens-less fluorescence imaging,enabling plenoptic sensing by extending sensing capabilities to include photon arrival time and incident angle,thereby providing the opportunity for separability of fluorescence point sources within the context of light-field microscopy(lFM).However,the addition of spectral sensitivity to angle-sensitive lFM reduces imager resolution because each wavelength requires a separate pixel subset.Here,we present a 1024-pixel,50μm thick implantable shank-based neural imager with color-filtergrating-based angle-sensitive pixels.This angular-spectral sensitive front end combines a metal–insulator–metal(MIM)Fabry–Perot color filter and diffractive optics to produce the measurement of orthogonal light-field information from two distinct colors within a single photodetector.The result is the ability to add independent color sensing to lFM while doubling the effective pixel density.The implantable imager combines angular-spectral and temporal information to demix and localize multispectral fluorescent targets.In this initial prototype,this is demonstrated with 45μm diameter fluorescently labeled beads in scattering medium.Fluorescent lifetime imaging is exploited to further aid source separation,in addition to detecting pH through lifetime changes in fluorescent dyes.While these initial fluorescent targets are considerably brighter than fluorescently labeled neurons,further improvements will allow the application of these techniques to in-vivo multifluorescent structural and functional neural imaging.

关键词： filters lifetime angle

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Adding Value to Crop Production Systems by Integrating Forage Cover Crop Grazing

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American Journal of Plant Sciences 2024年第3期15卷 180-192页

作者： Robert B. Mitchell Daren D. Redfearn kenneth P. Vogel Terry J. Klopfenstein Galen Erickson P. Stephen Baenziger Bruce E. Anderson Mary E. Drewnoski Jay Parsons Steven D. Masterson Marty R. Schmer Virginia l. Jin USDA-ARS Wheat Sorghum and Forage Research Unit University of Nebraska-Lincoln Lincoln NE USA Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln NE USA Department of Animal Science University of Nebraska-Lincoln Lincoln NE USA Department of Agricultural Economics University of Nebraska-Lincoln Lincoln NE USA USDA-ARS Agroecosystem Management Research Unit University of Nebraska-Lincoln Lincoln NE USA

In addition to their value as cereal grains, wheat (Triticum aestivum l.) and triticale (× Triticosecale Wittmack) are important cool-season annual forages and cover crops. Yearling steer (Bos taurus) performance was compared in the spring following autumn establishment as for age cover crops after soybean [Glycine max (l.) Merr.] grain harvest. Replicated pastures (0.4 ha) were no-till seeded in three consecutive years into soybean stubble in autumn, fertilized, and grazed the following spring near Ithaca, NE, USA. Each pasture (n = 3) was continuously stocked in spring with four yearling steers (380 ± 38 kg) for 17, 32, and 28 d in 2005, 2006, and 2007, respectively. In 2005, average daily gain (ADG) for steers grazing triticale exceeded the ADG for wheat by 0.31 kghd-1d-1. In 2006, wheat ADG exceeded that for triticale by 0.12 kghd-1d-1. In 2007, steers grazing wheat lost weight, while steers grazing triticale gained 0.20 kghd-1d-1. Based on the 3-year average animal gains valued at $1.32 kg-1, mean net return ($ ha-1 yr-1) was $62.15 for triticale and $22.55 for wheat. Since these grazed cover crops provide ecosystem services in addition to forage, grazing could be viewed as a mechanism for recovering costs and adds additional value to the system. Based on this 3-year grazing trial, triticale was superior to wheat and likely will provide the most stable beef yearling performance across years with variable weather for the western Cornbelt USA.

关键词： Cover crops Soybean Triticale Wheat

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Expanding beyond endoscopy: A review of non-invasive modalities in Barrett’s esophagus screening and surveillance

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World Journal of Gastroenterology 2022年第32期28卷 4516-4526页

作者： Dariush Shahsavari Praneeth Kudaravalli John Erikson l Yap kenneth J Vega Division of Gastroenterology and Hepatology Augusta University-Medical College of GeorgiaAugustaGA 30912United States

Barrett’s esophagus(BE)is a condition that results from replacement of the damaged normal squamous esophageal mucosa to intestinal columnar mucosa and is the most significant predisposing factor for development of esophageal adenocarcinoma.Current guidelines recommend endoscopic evaluation for screening and surveillance based on various risk factors which has limitations such as invasiveness,availability of a trained specialist,patient logistics and cost.Trans-nasal endoscopy is a less invasive modality but still has similar limitations such as limited availability of trained specialist and costs.Non-endoscopic modalities,in comparison,require minimal intervention,can be done in an office visit and has the potential to be a more ideal choice for mass public screening and surveillance,particularly in patents at low risk for BE.These include newer generations of esophageal capsule endoscopy which provides direct visualization of BE,and tethered capsule endomicroscopy which can obtain high-resolution images of the esophagus.Various cell collection devices coupled with biomarkers have been used for BE screening.Cytosponge,in combination with TFF3,as well as EsophaCap and EsoCheck have shown promising results in various studies when used with various biomarkers.Other modalities including circulatory microRNAs and volatile organic compounds that have demonstrated favorable outcomes.Use of these cell collection methods for BE surveillance is a potential area of future research.

关键词： Barrett’s esophagus Screening Surveillance Non-endoscopic Cytosponge Esophacap Esocheck

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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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