CerealsDB 3.0: Expansion of resources and data integration

BMC Bioinformatics

Volumn 17, Issue 1, 2016, Pages

  Wilkinson, Paul A ^a   Winfield, Mark O ^a   Barker, Gary L A ^a   Tyrrell, Simon ^b   Bian, Xingdong ^b   Allen, Alexandra M ^a   Burridge, Amanda ^a   Coghill, Jane A ^a   Waterfall, Christy ^a   Caccamo, Mario ^c   Davey, Robert P ^b   Edwards, Keith J ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b EARLHAM INSTITUTE   (United Kingdom)

^c NATIONAL INSTITUTE OF AGRICULTURAL BOTANY   (United Kingdom)

Author keywords

CerealsDB; Database; Genomic selection; Single nucleotide polymorphisms; SNPs; Wheat

Indexed keywords

AGRICULTURE; DATABASE SYSTEMS; FOOD SUPPLY; GENES; WEB SERVICES; WEBSITES;

CEREALSDB; GENOMIC SELECTION; SINGLE NUCLEOTIDE POLYMORPHISMS; SNPS; WHEAT;

DATA INTEGRATION;

AGRONOMIC TRAIT; BREEDING; CLIMATE; CROP; DATA BASE; DIET; FOOD SECURITY; GENETIC MARKER; GENOTYPE; HUMAN; LIVESTOCK; PROTEIN FUNCTION; SCIENTIST; SINGLE NUCLEOTIDE POLYMORPHISM; TRITICUM AESTIVUM; VALIDATION PROCESS; COMPUTER INTERFACE; DATABASE MANAGEMENT SYSTEM; GENETICS; GENOMICS; GENOTYPING TECHNIQUE; INTERNET; WHEAT;

BREEDING; CROPS, AGRICULTURAL; DATABASE MANAGEMENT SYSTEMS; GENOMICS; GENOTYPING TECHNIQUES; HUMANS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; TRITICUM; USER-COMPUTER INTERFACE;

EID: 84975757553     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1139-x     Document Type: Article

References (22)

1. 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. A transcriptomics resource for wheat functional genomics. Plant Biotechnol J. 2004;2:495-506.
2. Wilkinson PA, Winfield MO, Barker GLA, Allen AM, Burridge A, Coghill JA, Edwards KJ. CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinformatics. 2012;13:219.
3. 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. High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J. 2015;14:1195-206.
4. The Wheat Initiative [ http://www.wheatinitiative.org/ ]. Accessed on date 13 Jun 2016.
5. International Wheat Information System [ http://wheatis.org/ ]. Accessed on date 13 Jun 2016.
6. Cuppen E. Genotyping by allele-specific amplification (KASPar). Cold Spring Harb Protocols. 2007. pp 172-173.
7. Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, IWGSC, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnol J. 2014;12:787-96.
8. Allen AM, Barker GL, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D'Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J. 2011;9:1086-99.
9. Allen AM, Barker GLA, Wilkinson PA, Burridge AJ, Winfield MO, Coghill JA, Uauy C, Griffiths S, Jack P, Berry S, Werner P, Melichar J, McDougall J, Gwilliam R, Robinson P, Edwards KJ. Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). Plant Biotechnology J. 2012;11:279-95.
10. Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, Staines DM. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 2016;44:D574-80.
11. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403-10.
12. Brenchley R, Spannagl M, Pfeiffer M, Barker GLA, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill, B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer MFX, Hall N, Edwards KJ, Bevan MW, Hall N. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491:705-10.
13. Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N and Rokhsar D.S. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol. 2015;16:26.
14. Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WTB, Flavell AJ and Marshall D. Flapjack - graphical genotype visualization. Bioinformatics. 2010;26:3133-4.
15. Grassroots Infrastructure project [ https://wheatis.tgac.ac.uk ] Accessed on date 13 Jun 2016.
16. Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, Day, INM and Gaunt, TR. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using Hidden Markov Models. Hum Mutat. 2013;34:57-65.
17. The UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015;43:D204-12.
18. Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, et al. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2014;42:D546-52.
19. The Wheat Portal [ http://wheat-urgi.versailles.inra.fr/ ]. Accessed on date 13 Jun 2016.
20. Matthews D, Carollo VL, Lazo GR, Anderson OD. GrainGenes, the genome database for small-grain crops. Nucl Acids Res. 2003;31:183-6.
21. The International Wheat Genome Sequencing Consortium, Mayer KFX, Rogers J, Doležel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, et al. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345:1251788.
22. Jordan KW, Wang S, Lun Y, Gardiner L-J, MacLachlan R, Hucl P, Wiebe K, Wong D, Forrest KL, Sharpe AG, et al. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biol. 2015;16:48.