PeanutBase and Other Bioinformatic Resources for Peanut

Peanuts: Genetics, Processing, and Utilization

Volumn , Issue , 2016, Pages 241-252

  Dash, Sudhansu ^a   Cannon, Ethalinda K S ^b   Kalberer, Scott R ^c   Farmer, Andrew D ^a   Cannon, Steven B ^c  

^a NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^b Iowa State University   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

Bioinformatics; Breeder tool box; Gene markers; Genetic maps; Interactive dababases

Indexed keywords

EID: 84967164970     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-1-63067-038-2.00008-3     Document Type: Chapter

References (28)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
2. +: architecture and applications. BMC Bioinform. 2009, 10:421.
3. Campbell M.S., Law M., Holt C., Stein J.C., Moghe G.D., Hufnagel D.E., Lei J., Achawanantakun R., Jiao D., Lawrence C.J., et al. MAKER-p: A tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol. 2014, 64:513-524.
4. Chu Y., Wu C.L., Holbrook C.C., Tillman B.L., Person G., Ozias-Akins P. Marker-assisted selection to pyramid nematode resistance and the high oleic trait in peanut. Plant Genome 2011, 4:110-117.
5. Elsik C.G., Mackey A.J., Reese J.T., Milshina N.V., Roos D.S., Weinstock G.M. Creating a honey bee consensus gene set. Genome Biol. 2007, 8:R13.
6. Foncéka D., Tossim H.A., Rivallan R., Vignes H., Faye I., Ndoye O., Moretzsohn M.C., Bertioli D.J., Glaszmann J.C., Courtois B., et al. Fostered and left behind alleles in peanut: Interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding. BMC Plant Biol. 2012, 12:E26.
7. Gautami B., Foncéka D., Pandey M.K., Moretzsohn M.C., Sujay V., Qin H., Hong Y., Faye I., Chen X., BhanuPrakash A., et al. An international reference consensus genetic map with 897 marker loci based on 11 mapping populations for tetraploid groundnut (Arachis hypogaea L.). PLoS One 2012, 7:e41213.
8. Grant D., Nelson R.T., Cannon S.B., Shoemaker R.C. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010, 38:D843-D846.
9. Guo Y., Khanal S., Tang S., Bowers J.E., Heesacker A.F., Khalilian N., Nagy E.D., Zhang D., Taylor C.A., Stalker H.T., et al. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut. BMC Genom. 2012, 13:608.
10. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
11. Khedikar Y.P., Gowda M.V.C., Sarvamangala C., Patgar K.V., Upadhyaya H.D., Varshney R.K. A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor. Appl. Genet. 2010, 121:971-984.
12. Kochert G., Stalker H.T., Ginenes M., Galgaro L., Moore K. RFLP and cytogenetic evidence for the progenitor species of allotetraploid cultivated peanut, Arachis hypogaea, (Leguminosae). Am. J. Bot. 1996, 83:1282-1291.
13. Leal-Bertioli S.C.M., José A.C.V.F., Alves-Freitas D.M., Moretzsohn M.C., Guimarães P.M., Nielen S., Vidigal B.S., Pereira R.W., Pike J., Fávero A.P., et al. Identification of candidate genome regions controlling disease resistance in Arachis. BMC Plant Biol. 2009, 9:E112.
14. Moretzsohn M.C., Barbosa A.V., Alves-Freitas D.M., Teixeira C., Leal-Bertioli S.C., Guimarães P.M., Pereira R.W., Lopes C.R., Cavallari M.M., Valls J.F., Bertioli D.J., Gimenes M.A. A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol. 2009, 9:40.
15. Moretzsohn M.C., Gouvea E.G., Inglis P.W., Leal-Bertioli S.C., Valls J.F., Bertioli D.J. A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers. Ann. Bot. Lond. 2013, 111:113-126.
16. Mungall C.J., Emmert D.B., FlyBase C. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics 2007, 23:i337-346.
17. Nagy E., Guo Y., Khanal S., Taylor C., Knapp S., Ozias-Akins P., Stalker H.T., Nielsen N. Developing a high-density molecular map of the A-genome species A. duranensis. Am. Peanut Res. Educ. Soc. 2010, 42:25. (Abstract).
18. Nagy E.D., Guo Y., Tang S., Bowers J.E., Okashah R.A., Taylor C.A., Zhang D., Khanal S., Heesacker A.F., Khalilian N., et al. A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut. BMC Genom. 2012, 13:469.
19. Sanderson L.A., Ficklin S.P., Cheng C.H., Jung S., Feltus F.A., Bett K.E., Main D. Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. Database 2013, 2013:bat075.
20. Schmutz J., McClean P.E., Mamidi S., Wu G.A., Cannon S.B., Grimwood J., Jenkins J., Shu S., Song Q., Chavarro C., et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 2014, 46:707-713.
21. Schoof H. Automated Assignment of Human Readable Descriptions (AHRD) 2014, GitHub site for AHRD in Group Prof. Dr. Heiko Schoof, (accessed September 2014). https://github.com/groupschoof/AHRD.
22. Seijo G., Lavia G.I., Fernandez A., Krapovickas A., Ducasse D.A., Bertioli D.J., Moscone E.A. Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH. Am. J. Bot. 2007, 94:1963-1971.
23. Shirasawa K., Bertioli D.J., Varshney R.K., Moretzsohn M.C., Leal-Bertioli S.C., Thudi M., Pandey M.K., Rami J.F., Foncéka D., Gowda M.V.C., et al. Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res. 2013, 20:173-184.
24. Simpson C.E., Krapovickas A., Valls J.F.M. History of Arachis including evidence of A. hypogaea L. progenitors. Peanut Sci. 2001, 28:78-80.
25. Stein L.D. Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform. 2013, 14:162-171.
26. Yandell M., Ence D. A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 2012, 13:329-342.
27. Youens-Clark K., Faga B., Yap I.V., Stein L., Ware D. CMap 1.01: A comparative mapping application for the internet. Bioinformatics 2009, 25:3040-3042.
28. Young N.D., Debelle F., Oldroyd G.E., Geurts R., Cannon S.B., Udvardi M.K., Benedito V.A., Mayer K.F., Gouzy J., Schoof H., et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480:520-524.