Author
Jianping Wang
Other affiliations: Chinese Ministry of Education, University of Illinois at Urbana–Champaign, Fujian Agriculture and Forestry University
Bio: Jianping Wang is an academic researcher from University of Florida. The author has contributed to research in topics: Population & Genome. The author has an hindex of 23, co-authored 85 publications receiving 1800 citations. Previous affiliations of Jianping Wang include Chinese Ministry of Education & University of Illinois at Urbana–Champaign.
Papers
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Fujian Agriculture and Forestry University1, University of Illinois at Urbana–Champaign2, Chinese Academy of Sciences3, University of Georgia4, Michigan State University5, University of Ottawa6, University of Tennessee7, CAS-MPG Partner Institute for Computational Biology8, University of Missouri9, University of Florida10, Texas A&M University System11, Johns Hopkins University12, Microsoft13, University of São Paulo14
TL;DR: In this article, a haplotype of S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined.
Abstract: Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.
383 citations
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Fujian Agriculture and Forestry University1, University of Florida2, International Crops Research Institute for the Semi-Arid Tropics3, National Cheng Kung University4, North China University of Science and Technology5, University of Western Australia6, Agricultural Research Service7, Crops Research Institute8, Zhongkai University of Agriculture and Engineering9, Tsinghua University10, Shenzhen University11, Tuskegee University12, Osmania University13, National Tsing Hua University14, Plant Genome Mapping Laboratory15, University of Illinois at Urbana–Champaign16
TL;DR: High-quality genome sequence of cultivated peanut provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut, providing a cornerstone for functional genomics and peanut improvement.
Abstract: High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.
320 citations
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International Crops Research Institute for the Semi-Arid Tropics1, Institut de recherche pour le développement2, University of Georgia3, Leibniz Association4, Fort Valley State University5, Cornell University6, University of Florida7, Junagadh Agricultural University8, United States Department of Agriculture9, Amity University10, University of Vienna11, University of Arizona12, Indian Council of Agricultural Research13, University of Montpellier14, University of Lyon15, Oklahoma State University–Stillwater16, DuPont Pioneer17, Aberystwyth University18, Visva-Bharati University19, Agricultural Research Service20
TL;DR: This work resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication, and establishes marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance.
Abstract: Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
285 citations
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TL;DR: A combination of emerging technologies is rapidly enhancing understanding of key points in cell wall biosynthesis and the capacity to shift C-flux between sucrose, cell wall polymers, or other C-sinks.
Abstract: Focus has centered on C-partitioning in stems of sugarcane (Saccharum sp.) due to their high-sucrose accumulation features, relevance to other grasses, and rising economic value. Here we review how sugarcane balances between sucrose storage, respiration, and cell wall biosynthesis. The specific topics involve 1) accumulation of exceptionally high sucrose levels (up to over 500 mM), 2) a potential, turgor-sensitive system for partitioning sucrose between storage inside (cytosol and vacuole) and outside cells, 3) mechanisms to prevent back-flow of extracellular sucrose to xylem or phloem, 4) apparent roles of sucrose-P-synthase in fructose retrieval and sucrose re-synthesis, 5) enhanced importance of invertases, and 6) control of C-flux at key points in cell-wall biosynthesis (UDP-glucose dehydrogenase) and respiration (ATP- and pyrophosphate-dependent phospho-fructokinases). A combination of emerging technologies is rapidly enhancing our understanding of these points and our capacity to shift C-flux between sucrose, cell-wall polymers, or other C-sinks.
122 citations
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TL;DR: One major QTL (more than 10% PVE) was identified in both the populations for oil content with source alleles from NC94022 and GT-C20 parental genotypes.
Abstract: Peanut is one of the major source for human consumption worldwide and its seed contain approximately 50% oil. Improvement of oil content and quality traits (high oleic and low linoleic acid) in peanut could be accelerated by exploiting linked markers through molecular breeding. The objective of this study was to identify QTLs associated with oil content, and estimate relative contribution of FAD2 genes (ahFAD2A and ahFAD2B) to oil quality traits in two recombinant inbred line (RIL) populations. Improved genetic linkage maps were developed for S-population (SunOleic 97R × NC94022) with 206 (1780.6 cM) and T-population (Tifrunner × GT-C20) with 378 (2487.4 cM) marker loci. A total of 6 and 9 QTLs controlling oil content were identified in the S- and T-population, respectively. The contribution of each QTL towards oil content variation ranged from 3.07 to 10.23% in the S-population and from 3.93 to 14.07% in the T-population. The mapping positions for ahFAD2A (A sub-genome) and ahFAD2B (B sub-genome) genes were assigned on a09 and b09 linkage groups. The ahFAD2B gene (26.54%, 25.59% and 41.02% PVE) had higher phenotypic effect on oleic acid (C18:1), linoleic acid (C18:2), and oleic/linoleic acid ratio (O/L ratio) than ahFAD2A gene (8.08%, 6.86% and 3.78% PVE). The FAD2 genes had no effect on oil content. This study identified a total of 78 main-effect QTLs (M-QTLs) with up to 42.33% phenotypic variation (PVE) and 10 epistatic QTLs (E-QTLs) up to 3.31% PVE for oil content and quality traits. A total of 78 main-effect QTLs (M-QTLs) and 10 E-QTLs have been detected for oil content and oil quality traits. One major QTL (more than 10% PVE) was identified in both the populations for oil content with source alleles from NC94022 and GT-C20 parental genotypes. FAD2 genes showed high effect for oleic acid (C18:1), linoleic acid (C18:2), and O/L ratio while no effect on total oil content. The information on phenotypic effect of FAD2 genes for oleic acid, linoleic acid and O/L ratio, and oil content will be applied in breeding selection.
98 citations
Cited by
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
10,124 citations
01 Aug 2000
TL;DR: Assessment of medical technology in the context of commercialization with Bioentrepreneur course, which addresses many issues unique to biomedical products.
Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.
4,833 citations
10 Dec 2007
TL;DR: The experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
1,528 citations
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TL;DR: This review aims to capture the most exciting developments in this area by evaluating the roles of key sucrose metabolic enzymes in development, abiotic stress responses, and plant-microbe interactions and the coupling between sucrose metabolism and sugar signaling from extra- to intracellular spaces.
Abstract: Sucrose metabolism plays pivotal roles in development, stress response, and yield formation, mainly by generating a range of sugars as metabolites to fuel growth and synthesize essential compounds (including protein, cellulose, and starch) and as signals to regulate expression of microRNAs, transcription factors, and other genes and for crosstalk with hormonal, oxidative, and defense signaling. This review aims to capture the most exciting developments in this area by evaluating (a) the roles of key sucrose metabolic enzymes in development, abiotic stress responses, and plant–microbe interactions; (b) the coupling between sucrose metabolism and sugar signaling from extra- to intracellular spaces; (c) the different mechanisms by which sucrose metabolic enzymes could perform their signaling roles; and (d ) progress on engineering sugar metabolism and transport for high yield and disease resistance. Finally, the review outlines future directions for research on sugar metabolism and signaling to better understand and improve plant performance.
878 citations