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Robbie Waugh

Bio: Robbie Waugh is an academic researcher from James Hutton Institute. The author has contributed to research in topics: Hordeum vulgare & Population. The author has an hindex of 76, co-authored 268 publications receiving 24219 citations. Previous affiliations of Robbie Waugh include University of Sheffield & University of Dundee.
Topics: Hordeum vulgare, Population, Genome, Gene, Meiosis


Papers
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Journal ArticleDOI
Xun Xu1, Shengkai Pan1, Shifeng Cheng1, Bo Zhang1, Mu D1, Peixiang Ni1, Gengyun Zhang1, Shuang Yang1, Ruiqiang Li1, Jun Wang1, Gisella Orjeda2, Frank Guzman2, Torres M2, Roberto Lozano2, Olga Ponce2, Diana Martinez2, De la Cruz G3, Chakrabarti Sk3, Patil Vu3, Konstantin G. Skryabin4, Boris B. Kuznetsov4, Nikolai V. Ravin4, Tatjana V. Kolganova4, Alexey V. Beletsky4, Andrey V. Mardanov4, Di Genova A5, Dan Bolser5, David M. A. Martin5, Li G, Yang Y, Hanhui Kuang6, Hu Q6, Xiong X7, Gerard J. Bishop8, Boris Sagredo, Nilo Mejía, Zagorski W9, Robert Gromadka9, Jan Gawor9, Pawel Szczesny9, Sanwen Huang, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Youjun Zhang, Xie B, Du Y, Qu D, Merideth Bonierbale10, Marc Ghislain10, Herrera Mdel R, Giovanni Giuliano, Marco Pietrella, Gaetano Perrotta, Paolo Facella, O'Brien K11, Sergio Enrique Feingold, Barreiro Le, Massa Ga, Luis Aníbal Diambra12, Brett R Whitty13, Brieanne Vaillancourt13, Lin H13, Alicia N. Massa13, Geoffroy M13, Lundback S13, Dean DellaPenna13, Buell Cr14, Sanjeev Kumar Sharma14, David Marshall14, Robbie Waugh14, Glenn J. Bryan14, Destefanis M15, Istvan Nagy15, Dan Milbourne15, Susan Thomson16, Mark Fiers16, Jeanne M. E. Jacobs16, Kåre Lehmann Nielsen17, Mads Sønderkær17, Marina Iovene18, Giovana Augusta Torres18, Jiming Jiang18, Richard E. Veilleux19, Christian W. B. Bachem20, de Boer J20, Theo Borm20, Bjorn Kloosterman20, van Eck H20, Erwin Datema20, Hekkert Bt20, Aska Goverse20, van Ham Rc20, Richard G. F. Visser20 
10 Jul 2011-Nature
TL;DR: The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.
Abstract: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

1,813 citations

Journal ArticleDOI
Klaus F. X. Mayer, Jane Rogers, Jaroslav Doležel1, Curtis J. Pozniak2, Kellye Eversole, Catherine Feuillet3, Bikram S. Gill4, Bernd Friebe4, Adam J. Lukaszewski5, Pierre Sourdille6, Takashi R. Endo7, M. Kubaláková1, Jarmila Číhalíková1, Zdeňka Dubská1, Jan Vrána1, Romana Šperková1, Hana Šimková1, Melanie Febrer8, Leah Clissold, Kirsten McLay, Kuldeep Singh9, Parveen Chhuneja9, Nagendra K. Singh10, Jitendra P. Khurana11, Eduard Akhunov4, Frédéric Choulet6, Adriana Alberti, Valérie Barbe, Patrick Wincker, Hiroyuki Kanamori12, Fuminori Kobayashi12, Takeshi Itoh12, Takashi Matsumoto12, Hiroaki Sakai12, Tsuyoshi Tanaka12, Jianzhong Wu12, Yasunari Ogihara13, Hirokazu Handa12, P. Ron Maclachlan2, Andrew G. Sharpe14, Darrin Klassen14, David Edwards, Jacqueline Batley, Odd-Arne Olsen, Simen Rød Sandve15, Sigbjørn Lien15, Burkhard Steuernagel16, Brande B. H. Wulff16, Mario Caccamo, Sarah Ayling, Ricardo H. Ramirez-Gonzalez, Bernardo J. Clavijo, Jonathan M. Wright, Matthias Pfeifer, Manuel Spannagl, Mihaela Martis, Martin Mascher17, Jarrod Chapman18, Jesse Poland4, Uwe Scholz17, Kerrie Barry18, Robbie Waugh19, Daniel S. Rokhsar18, Gary J. Muehlbauer, Nils Stein17, Heidrun Gundlach, Matthias Zytnicki20, Véronique Jamilloux20, Hadi Quesneville20, Thomas Wicker21, Primetta Faccioli, Moreno Colaiacovo, Antonio Michele Stanca, Hikmet Budak22, Luigi Cattivelli, Natasha Glover6, Lise Pingault6, Etienne Paux6, Sapna Sharma, Rudi Appels23, Matthew I. Bellgard23, Brett Chapman23, Thomas Nussbaumer, Kai Christian Bader, Hélène Rimbert, Shichen Wang4, Ron Knox, Andrzej Kilian, Michael Alaux20, Françoise Alfama20, Loïc Couderc20, Nicolas Guilhot6, Claire Viseux20, Mikaël Loaec20, Beat Keller21, Sébastien Praud 
18 Jul 2014-Science
TL;DR: Insight into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

1,421 citations

Journal ArticleDOI
29 Nov 2012-Nature
TL;DR: An integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context and suggests that post-transcriptional processing forms an important regulatory layer.
Abstract: Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

1,347 citations

Journal ArticleDOI
27 Apr 2017-Nature
TL;DR: The importance of the barley reference sequence for breeding is demonstrated by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Abstract: Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.

1,105 citations

Journal ArticleDOI
01 Dec 2000-Genetics
TL;DR: The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations.
Abstract: A total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F(1) of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

657 citations


Cited by
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Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
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

Journal ArticleDOI
T. Kraft1, M. Hansen1, N.-O. Nilsson1
TL;DR: A low but significant level of linkage disequilibrium was found for unlinked markers and only for very tigthly linked (<3 cM) markers was this level substantially higher, implying that little is gained in utilising the map position of the markers in fingerprinting applications.
Abstract: It has been suggested that map information for molecular markers can be used to strengthen finterprinting analyses. The success of this strategy depends on the distribution of linkage disequilibrium over the genome. Using 451 mapped AFLP markers, we investigated the occurrence of linkage disequilibrium in nine sugar beet breeding lines. A low but significant level of linkage disequilibrium was found for unlinked markers. Only for very tigthly linked (<3 cM) markers was this level substantially higher. This implies that little is gained in utilising the map position of the markers in fingerprinting applications.

5,275 citations

Journal ArticleDOI
04 May 2011-PLOS ONE
TL;DR: A procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs) is reported, which is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches.
Abstract: Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restriction enzymes (REs). This approach is simple, quick, extremely specific, highly reproducible, and may reach important regions of the genome that are inaccessible to sequence capture approaches. By using methylation-sensitive REs, repetitive regions of genomes can be avoided and lower copy regions targeted with two to three fold higher efficiency. This tremendously simplifies computationally challenging alignment problems in species with high levels of genetic diversity. The GBS procedure is demonstrated with maize (IBM) and barley (Oregon Wolfe Barley) recombinant inbred populations where roughly 200,000 and 25,000 sequence tags were mapped, respectively. An advantage in species like barley that lack a complete genome sequence is that a reference map need only be developed around the restriction sites, and this can be done in the process of sample genotyping. In such cases, the consensus of the read clusters across the sequence tagged sites becomes the reference. Alternatively, for kinship analyses in the absence of a reference genome, the sequence tags can simply be treated as dominant markers. Future application of GBS to breeding, conservation, and global species and population surveys may allow plant breeders to conduct genomic selection on a novel germplasm or species without first having to develop any prior molecular tools, or conservation biologists to determine population structure without prior knowledge of the genome or diversity in the species.

5,163 citations

Journal ArticleDOI
TL;DR: Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.
Abstract: The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

3,728 citations

Journal ArticleDOI
TL;DR: The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses.
Abstract: MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.

3,388 citations