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genomics approaches to unlock the high yield potential of cassava,a tropical model plant

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Frontiers of Agricultural Science and Engineering 2014年第4期1卷 259-266页

作者： Shengkui ZHANG Ping’an MA Haiyan WANG Cheng LU Xin CHEN Zhiqiang XIA Meiling ZOU Xinchen ZHOU Wenquan WANG Institute of Tropical Biosciences&Biotechnology Chinese Academy of Tropical Agricultural SciencesHaikou 571101China Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture Haikou 571101China

Cassava,a tropical food,feed and biofuel crop,has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition,which makes it highly suitable as a model plant for tropical ***,the understanding of the metabolism and genomics of this important crop is *** recent breakthroughs in the genomics of cassava,including whole-genome sequencing and transcriptome analysis,as well as advances in the biology of photosynthesis,starch biosynthesis,adaptation to drought and high temperature,and resistance to virus and bacterial diseases,are reviewed *** of the new developments have come from comparative analyses between a wild ancestor and existing ***,the current challenges and future potential of cassava as a model plant are discussed.

关键词： cassava genomics yield potential adaptability tropical model

The Past, Present, and Future of Maize Improvement: Domestication, genomics, and Functional Genomic Routes toward Crop Enhancement

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Plant Communications 2020年第1期1卷 38-56页

作者： Jie Liu Alisdair R.Fernie Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Department of Molecular Physiology Max-Planck-Institute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany

After being domesticated from teosinte,cultivated maize(Zea mays ***)spread worldwide and now is one of the most important staple *** to its tremendous phenotypic and genotypic diversity,maize also becomes to be one of the most widely used model plant species for fundamental research,with many important discoveries reported by maize ***,we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits,review the currently available resources for functional genomics studies in maize,and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop ***,we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.

关键词： maize domestication genomics functional genomics improvement

Research progress in genomics of environmental and industrial microorganisms

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Science China(Life Sciences) 2009年第1期52卷 64-73页

作者： WANG Lei1,2,LIU Bin1,2 & ZHOU ZheMin1,2 1 TEDA School of Biological Sciences and Biotechnology,Nankai University,Tianjin 300457,China 2 Tianjin Research Center for Functional genomics and Biochip,Tianjin 300457,China TEDA School of Biological Sciences and Biotechnology Nankai University Tianjin China Tianjin Research Center for Functional genomics and Biochip Tianjin China

Microbes contribute to geochemical cycles in the *** also play important roles in biodegradation and bioremediation of contaminated environments,and have great potential in energy conversion and *** to date,at least 150 genomes of non-pathogenic microbes have been sequenced,of which,the majority are bacteria from various environments or of industrial *** emerging field 'metagenomics' in combination with the high-throughput sequencing technology offers opportunities to discover new functions of microbes in the environment on a large scale,and has become the 'hot spot' in the field of environmental *** genomes of bacteria from various extreme environments,including high temperature,high and low pressure,and extreme acidic regions,have been sequenced by researchers in China,leading to the discovery of metabolic pathways,genetic functions and new enzymes,which are related to the niches those bacteria *** results were published in Nature,PNAS,Genome Research and other top international *** the meantime,several groups in China have started 'metagenomics' *** outcomes of these researches are expected to generate a considerable number of novel findings,taking Chinese researchers to the frontier of genomics for environmental and industrial microorganisms.

关键词： genomics microbiology and metagenomics

Integrating pathomics with radiomics and genomics for cancer prognosis:A brief review

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Chinese Journal of Cancer Research 2021年第5期33卷 563-573页

作者： Cheng Lu Rakesh Shiradkar Zaiyi Liu Biomedical Engineering Department Case Western Reserve UniversityCleveland 44106OHUSA Department of Radiology Guangzhou First People’s HospitalSchool of MedicineSouth China University of TechnologyGuangzhou 510080China

In the last decade,the focus of computational pathology research community has shifted from replicating the pathological examination for diagnosis done by pathologists to unlocking and discovering"sub-visual"prognostic image cues from the histopathological *** we are getting more knowledge and experience in digital pathology,the emerging goal is to integrate other-omics or modalities that will contribute for building a better prognostic *** this paper,we provide a brief review of representative works that focus on integrating pathomics with radiomics and genomics for cancer *** includes:correlation of pathomics and genomics;fusion of pathomics and genomics;fusion of pathomics and *** also present challenges,potential opportunities,and avenues for future work.

关键词： Radiomics pathomics genomics prognosis digital pathology

Evolutionary genomics of Plant Gametophytic Selection

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Plant Communications 2020年第6期1卷 18-33页

作者： Felix E.G.Beaudry Joanna L.Rifkin Spencer C.H.Barrett Stephen I.Wright Department of Ecology and Evolutionary Biology The University of Toronto25 Willcocks StreetTorontoON M5S 3B2Canada These authors contributed equally to this article

It has long been recognized that natural selection during the haploid gametophytic phase of the plant life cycle may have widespread importance for rates of evolution and the maintenance of genetic *** theoretical advances have further highlighted the significance of gametophytic selection for diverse evolutionary *** approaches offer exciting opportunities to address key questions about the extent and effects of gametophytic selection on plant evolution and ***,we review the progress and prospects for integrating functional and evolutionary genomics to test theoretical predictions,and to examine the importance of gametophytic selection on genetic diversity and rates of *** is growing evidence that selection during the gametophyte phase of the plant life cycle has important effects on both gene and genome evolution and is likely to have important pleiotropic effects on the *** discuss the opportunities to integrate comparative population genomics,genome-wide association studies,and experimental approaches to further distinguish how differential selection in the two phases of the plant life cycle contributes to genetic diversity and adaptive evolution.

关键词： gametophyte pollen ovule evolution genomics selection

Human sperm chromatin epigenetic potential： genomics, proteomics, and male infertility

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Asian Journal of Andrology 2015年第4期17卷 601-609页

作者： ludit Castillo Josep Maria Estanyol Josep Lluis Ballesca Rafael Oliva Human Genetics Research Group IDIBAPS Faculty of Medicine University of Barcelona Casanova 143 08036 Barcelona Spain Biochemistry and Molecular GeneticsService Biomedical Diagnostic Centre Hospital Clinic Villarroel 170 08036 Barcelona Spain Proteomics Unit Scientific and Technological Centres of the Universityof Barcelona (CCiTUB) Casanova 143 08036 Barcelona Spain Clinic Institute of Gynaecology Obstetrics and Neonatology Hospital Clinic Villarroel 170 08036Barcelona Spain.

The classical idea about the function of the mammalian sperm chromatin is that it serves to transmit a highly protected and transcriptionally inactive paternal genome, largely condensed by protamines, to the next generation. In addition, recent sperm chromatin genome-wide dissection studies indicate the presence of a differential distribution of the genes and repetitive sequences in the protamine-condensed and histone-condensed sperm chromatin domains, which could be potentially involved in regulatory roles after fertilization. Interestingly, recent proteomic studies have shown that sperm chromatin contains many additional proteins, in addition to the abundant histones and protamines, with specific modifications and chromatin affinity features which are also delivered to the oocyte. Both gene and protein signatures seem to be altered in infertile patients and, as such, are consistent with the potential involvement of the sperm chromatin landscape in early embryo development. This present work reviews the available information on the composition of the human sperm chromatin and its epigenetic potential, with a particular focus on recent results derived from high-throughput genomic and proteomic studies. As a complement, we provide experimental evidence for the detection of phosphorylations and acetylations in human protamine 1 using a mass spectrometry approach. The available data indicate that the sperm chromatin is much more complex than what it was previously thought, raising the possibility that it could also serve to transmit crucial paternal epigenetic information to the embryo.

关键词： genomics male infertility proteomics sperm chromatin sperm epigenetics

Toward A New Paradigm of genomics Research——Celebration of the 20th Anniversary of Beijing Institute of genomics

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genomics, Proteomics & Bioinformatics 2023年第5期21卷 904-909页

作者： Zhang Zhang Songnian Hu Jun Yu National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Twenty years after the completion and forty years after the proposal of the Human Genome Project(HGP),genomics,together with its twin field-bioinformatics,has entered a new paradigm,where its bioscience-related,discipline-centric applications have been creating many new research *** Institute of genomics(BIG),now also known as China National Center for Bioinformation(CNCB),will play key roles in supporting and participating in these frontier research *** the 20th anniversary of the establishment of BIG,we provide a brief retrospective of its historic events and ascertain strategic research directions with a broader vision for future genomics,where digital genome,digital medicine,and digital health are so structured to meet the needs of human life and healthcare,as well as their related metaverses.

关键词： genomics Bioinformatics BIG CNCB NGDC

Leap forward with insect genomics

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Insect Science 2016年第3期23卷 332-334页

作者： Bin Chen Xian-Hui Wang Zhijian Tu Yong-Ping Huang Institute of Entomology and Molecular Biology Chongqing Normal University Chongqing China State Key Laboratory of IntegratedManagement of Pest Insects & Rodents Institute of Zoology Chinese Academy of Sciences Beijing China Department of Biochemistry Fralin Life Science Institute and Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg Virginia USAand Key Laboratory of Insect Development and Evolutionary Biology Institute of Plant Physiology and Ecology Shanghai Institutes forBiological Sciences Chinese Academy of Sciences Shanghal China

Insects comprise the largest animal group in the world. More than a million insect species have been identified, leaving possibly two to three times more to be discovered. Systematic understanding of the genetic content of an insect species began more than 15 years ago when the genome sequence of the fruit fly, Drosophila melanogaster was reported （Adams et al., 2000）. For the first time, scientists were able to glean unprecedented insights into the genetic blueprint of a model insect, presenting its 13 600 protein coding genes. Such fundamental information opened a floodgate for comparative and functional analysis of these genes and enabled systems approaches to comparative, evolutionary and population genomic studies. In recent years, next-generation and third-generation sequencing platforms brought genome sequencing to more than a hundred insect species, reach- ing far beyond the few well-studied model organisms. The international consortium for insect genomes is work- ing toward an ambitious goal to sequence 5000 species of insects.

关键词： Leap genomics species

Maize biology: From functional genomics to breeding application

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Journal of Integrative Plant Biology 2019年第6期61卷 654-657页

作者： Jianbing Yan Bao-Cai Tan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University(HZAU) School of Life Sciences Shandong University

Maize (Zea mays L.) is one of the most important crops globally for food, feed, and fuel. Maize grain production has increased more than eight-fold in the past century to a current annual global production of one billion tons (http://***/). By 2050, it will require 70% more food than today's consumma-tion since the population size will increase to 9 billions. It is estimated that maize will contribute more than half of the increased demand for cereals in the future. Thus, there is a tremendous innovation stream for maize breeders to utilize in their attempts to substantially increase maize productivity in an en-vironmentally sensitive way (FAO 2009).

关键词： Maize biology functional genomics breeding application^FA