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Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.)

dc.contributor.authorNarina, S.S.
dc.contributor.authorBuyyarapu, R.
dc.contributor.authorKottapalli, K.R.
dc.contributor.authorSartie, A.M.
dc.contributor.authorAli, M.I.
dc.contributor.authorAsiedu, Robert
dc.contributor.authorHodeba, M.
dc.contributor.authorSayre, B.L.
dc.contributor.authorScheffler, B.E.
dc.date.accessioned2019-12-04T11:10:23Z
dc.date.available2019-12-04T11:10:23Z
dc.date.issued2011-02
dc.identifier.citationNarina, S.S., Buyyarapu, R., Kottapalli, K.R., Sartie, A.M., Ali, M.I., Asiedu, R., ... & Scheffler, B.E. (2011). Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.). BMC genomics, 12(1), 100.
dc.identifier.issn1471-2164
dc.identifier.urihttps://hdl.handle.net/20.500.12478/2118
dc.description.abstractBackground: Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology. Results: A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences. Conclusion: We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.
dc.description.sponsorshipUnited States Agency for International Development
dc.format.extent1-10.
dc.language.isoen
dc.publisherSpringer
dc.subjectYams
dc.subjectColletotrichum Gloeosporioides
dc.subjectGene Expression
dc.titleGeneration and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.)
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.crpRoots, Tubers and Bananas
cg.contributor.affiliationUnited States Department of Agriculture
cg.contributor.affiliationDow AgroSciences
cg.contributor.affiliationTexas Tech University
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.contributor.affiliationAfrican Agricultural Technology Foundation
cg.contributor.affiliationVirginia State University
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.isijournalISI Journal
cg.authorship.typesCGIAR and developing country institute
cg.iitasubjectYam
cg.journalBMC Genomics
cg.howpublishedFormally Published
cg.accessibilitystatusOpen Access
local.dspaceid90647
cg.identifier.doihttp://dx.doi.org/10.1186/1471-2164-12-100


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