CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.

Genome, Plant Genomics Polymorphism, Single Nucleotide Triticum / genetics

Database Phylogeny QTL SNPs Single nucleotide polymorphisms Wheat

Journal

Methods in molecular biology (Clifton, N.J.)

ISSN: 1940-6029

Titre abrégé: Methods Mol Biol

Pays: United States

ID NLM: 9214969

Informations de publication

Date de publication:
2022

Historique:

entrez: 17 1 2022

pubmed: 18 1 2022

medline: 1 4 2022

Statut: ppublish

Résumé

The CerealsDB website, created by members of the Functional Genomics Group at the University of Bristol, provides access to a database containing SNP and genotyping data for hexaploid wheat and, to a lesser extent, its progenitors and several of its relatives. The site is principally aimed at plant breeders and research scientists who wish to obtain information regarding SNP markers; for example, obtain primers used for their identification or the sequences upon which they are based. The database underpinning the website contains circa one million putative varietal SNPs of which several hundreds of thousands have been experimentally validated on a range of common genotyping platforms. For each SNP marker, the site also hosts the allelic scores for thousands of elite wheat varieties, landrace cultivars, and wheat relatives. Tools are available to help negotiate and visualize the datasets. The website has been designed to be simple and straightforward to use and is completely open access.

Identifiants

DOI: 10.1007/978-1-0716-2067-0_6 PMID: 35037203

pubmed: 35037203

doi: 10.1007/978-1-0716-2067-0_6

doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

133-146

Subventions

Organisme : Biotechnology and Biological Sciences Research Council

ID : BBS/E/C/000I0210

Pays : United Kingdom

Organisme : Biotechnology and Biological Sciences Research Council

ID : BBS/E/C/000I0280

Pays : United Kingdom

Organisme : Biotechnology and Biological Sciences Research Council

ID : BBS/E/J/000PR9782

Pays : United Kingdom

Organisme : Biotechnology and Biological Sciences Research Council

ID : BBS/E/T/000PR9783

Pays : United Kingdom

Informations de copyright

Références

Lee TH, Guo H, Wang X, Kim C, Paterson AH (2014) SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data. BMC Genomics 15:162. https://doi.org/10.1186/1471-2164-15-162

doi: 10.1186/1471-2164-15-162 pubmed: 24571581 pmcid: 3945939

Xia W, Luo T, Zhang W, Mason AS, Huang D, Huang X, Tang W, Dou Y, Zhang C, Xiao Y (2019) Development of high-density SNP markers and their application in evaluating genetic diversity and population structure in Elaeis guineensis. Front Plant Sci 10:130. https://doi.org/10.3389/fpls.2019.00130

doi: 10.3389/fpls.2019.00130 pubmed: 30809240 pmcid: 6380268

Ren T, Hu Y, Tang Y, Li C, Yan B, Ren Z, Tan F, Tang Z, Fu S, Li Z (2018) Utilization of a wheat55K SNP array for mapping of major QTL for temporal expression of the tiller number. Front Plant Sci 9:333. https://doi.org/10.3389/fpls.2018.00333

doi: 10.3389/fpls.2018.00333 pubmed: 29599793 pmcid: 5862827

Gupta PK, Rustgi S, Mir RR (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101(1):5–18. https://doi.org/10.1038/hdy.2008.35

doi: 10.1038/hdy.2008.35 pubmed: 18461083

Voss-Fels K, Snowdon RJ (2016) Understanding and utilizing crop genome diversity via high-resolution genotyping. Plant Biotechnol J 14(4):1086–1094. https://doi.org/10.1111/pbi.12456

doi: 10.1111/pbi.12456 pubmed: 27003869

Allen AM, Barker GL, Wilkinson P, Burridge A, Winfield M, Coghill J, Uauy C, Griffiths S, Jack P, Berry S, Werner P, Melichar JP, McDougall J, Gwilliam R, Robinson P, Edwards KJ (2013) Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnol J 11(3):279–295. https://doi.org/10.1111/pbi.12009

doi: 10.1111/pbi.12009 pubmed: 23279710

Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GL, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, Griffiths S, Bentley AR, Alda M, Jack P, Phillips AL, Edwards KJ (2017) Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J 15(3):390–401. https://doi.org/10.1111/pbi.12635

doi: 10.1111/pbi.12635 pubmed: 27627182

Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, King J, West C, Griffiths S, King I, Bentley AR, Edwards KJ (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14(5):1195–1206. https://doi.org/10.1111/pbi.12485

doi: 10.1111/pbi.12485 pubmed: 26466852

Winfield MO, Wilkinson PA, Allen AM, Barker GL, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J 10(6):733–742. https://doi.org/10.1111/j.1467-7652.2012.00713.x

doi: 10.1111/j.1467-7652.2012.00713.x pubmed: 22703335

Wilson ID, Barker GL, Beswick RW, Shepherd SK, Lu C, Coghill JA, Edwards D, Owen P, Lyons R, Parker JS, Lenton JR, Holdsworth MJ, Shewry PR, Edwards KJ (2004) A transcriptomics resource for wheat functional genomics. Plant Biotechnol J 2(6):495–506. https://doi.org/10.1111/j.1467-7652.2004.00096.x

doi: 10.1111/j.1467-7652.2004.00096.x pubmed: 17147622

Winfield MO, Allen AM, Wilkinson PA, Burridge AJ, Barker GLA, Coghill J, Waterfall C, Wingen LU, Griffiths S, Edwards KJ (2018) High-density genotyping of the A.E. Watkins collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat. Plant Biotechnol J 16(1):165–175. https://doi.org/10.1111/pbi.12757

doi: 10.1111/pbi.12757 pubmed: 28500796

Wilkinson PA, Allen AM, Tyrrell S, Wingen LU, Bian X, Winfield MO, Burridge A, Shaw DS, Zaucha J, Griffiths S, Davey RP, Edwards KJ, Barker GLA (2020) CerealsDB—new tools for the analysis of the wheat genome: update 2020. Database 2020:baaa060. https://doi.org/10.1093/database/baaa060

doi: 10.1093/database/baaa060 pubmed: 32754757 pmcid: 7402920

Bian X, Tyrrell S, Davey RP (2107) The Grassroots life science data infrastucture. https://www.earlham.ac.uk/grassroots-genomics#Publications-3

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D’Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P (2016) Gramene database: navigating plant comparative genomics resources. Curr Plant Biol 7-8:10–15. https://doi.org/10.1016/j.cpb.2016.12.005

doi: 10.1016/j.cpb.2016.12.005 pubmed: 28713666 pmcid: 5509230

Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D (2018) Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res 46(D1):D1181–D1189. https://doi.org/10.1093/nar/gkx1111

doi: 10.1093/nar/gkx1111 pubmed: 29165610

Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ (2019) GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database 2019:baz065. https://doi.org/10.1093/database/baz065

doi: 10.1093/database/baz065 pubmed: 31210272 pmcid: 6580076

Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W et al (2020) Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res 48(D1):D689–D695. https://doi.org/10.1093/nar/gkz890

doi: 10.1093/nar/gkz890 pubmed: 31598706

The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Res 43:D204–D212

doi: 10.1093/nar/gku989

Wilkinson PA, Winfield MO, Barker GL, Allen AM, Burridge A, Coghill JA, Edwards KJ (2012) CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics 13:219. https://doi.org/10.1186/1471-2105-13-219

doi: 10.1186/1471-2105-13-219 pubmed: 22943283 pmcid: 3447715

Zamir D (2013) Where have all the crop phenotypes gone? PLoS Biol 11(6):e1001595. https://doi.org/10.1371/journal.pbio.1001595

doi: 10.1371/journal.pbio.1001595 pubmed: 23824246 pmcid: 3692434

International Wheat Genome Sequencing C (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361(6403):eaar7191. https://doi.org/10.1126/science.aar7191

doi: 10.1126/science.aar7191

Przewieslik-Allen AM, Burridge AJ, Wilkinson PA, Winfield MO, Shaw DS, McAusland L, King J, King IP, Edwards KJ, Barker GLA (2018) Developing a high-throughput SNP-based marker system to facilitate the introgression of traits from Aegilops species into bread wheat (Triticum aestivum). Front Plant Sci 9:1993. https://doi.org/10.3389/fpls.2018.01993

doi: 10.3389/fpls.2018.01993 pubmed: 30733728

Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR (2013) Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 34(1):57–65. https://doi.org/10.1002/humu.22225

doi: 10.1002/humu.22225

Moore G (2015) Strategic pre-breeding for wheat improvement. Nat Plants 1:15018. https://doi.org/10.1038/nplants.2015.18

doi: 10.1038/nplants.2015.18 pubmed: 27246885

Wingen LU, West C, Leverington-Waite M, Collier S, Orford S, Goram R, Yang CY, King J, Allen AM, Burridge A, Edwards KJ, Griffiths S (2017) Wheat landrace genome diversity. Genetics 205(4):1657–1676. https://doi.org/10.1534/genetics.116.194688

doi: 10.1534/genetics.116.194688 pubmed: 28213475 pmcid: 5378120

Shrestha R, Arnaud E, Mauleon R, Senger M, Davenport GF, Hancock D, Morrison N, Bruskiewich R, McLaren G (2010) Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants 2010:plq008. https://doi.org/10.1093/aobpla/plq008

doi: 10.1093/aobpla/plq008 pubmed: 22476066 pmcid: 3000699

Coordinators NR (2016) Database resources of the National Center for Biotechnology Information. Nucleic Acid Res 44(D1):D7–D19. https://doi.org/10.1093/nar/gkv1290

doi: 10.1093/nar/gkv1290

CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource.

Journal

Informations de publication

Résumé

Identifiants

Types de publication

Langues

Sous-ensembles de citation

Pagination

Subventions

Informations de copyright

Références

Auteurs

Mark Winfield (M)

Paul Wilkinson (P)

Amanda Burridge (A)

Alexandra Allen (A)

Jane Coghill (J)

Christy Waterfall (C)

Keith Edwards (K)

Gary Barker (G)

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