Publication:
Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz)

dc.contributor.authorWirulda Pootakhamen_US
dc.contributor.authorJeremy R. Shearmanen_US
dc.contributor.authorPanthita Ruang-areerateen_US
dc.contributor.authorChutima Sonthiroden_US
dc.contributor.authorDuangjai Sangsrakruen_US
dc.contributor.authorNukoon Jomchaien_US
dc.contributor.authorThippawan Yoochaen_US
dc.contributor.authorKanokporn Triwitayakornen_US
dc.contributor.authorSomvong Tragoonrungen_US
dc.contributor.authorSithichoke Tangphatsornruangen_US
dc.contributor.otherMahidol University. Institute of Molecular Biosciencesen_US
dc.date.accessioned2016-04-12T02:18:24Z
dc.date.accessioned2017-04-25T03:40:57Z
dc.date.available2016-04-12T02:18:24Z
dc.date.available2017-04-25T03:40:57Z
dc.date.created2016-04-12
dc.date.issued2014
dc.description.abstractCassava (Manihot esculenta Crantz) is one of the most important crop species being the main source of dietary energy in several countries. Marker-assisted selection has become an essential tool in plant breeding. Single nucleotide polymorphism (SNP) discovery via transcriptome sequencing is an attractive strategy for genome complexity reduction in organisms with large genomes. We sequenced the transcriptome of 16 cassava accessions using the Illumina HiSeq platform and identified 675,559 EST-derived SNP markers. A subset of those markers was subsequently genotyped by capture-based targeted enrichment sequencing in 100 F1 progeny segregating for starch viscosity phenotypes. A total of 2,110 non-redundant SNP markers were used to construct a genetic map. This map encompasses 1,785 cM and consists of 19 linkage groups. A major quantitative trait locus (QTL) controlling starch pasting properties was identified and shown to coincide with the QTL previously reported for this trait. With a high-density SNP-based linkage map presented here, we also uncovered a novel QTL associated with starch pasting time on LG 10.en_US
dc.identifier.citationPlos One. Vol.9, No.12 (2014), e116028en_US
dc.identifier.doi10.1371/journal.pone.0116028
dc.identifier.urihttps://repository.li.mahidol.ac.th/handle/20.500.14594/1841
dc.language.isoengen_US
dc.rightsMahidol Universityen_US
dc.subjectLarge-Scale SNPen_US
dc.subjectDiscovery through RNAen_US
dc.subjectCassavaen_US
dc.subjectSNP Genotypingen_US
dc.subjectTargeted Enrichment Sequencingen_US
dc.subjectManihot esculenta Crantzen_US
dc.subjectOpen Access articleen_US
dc.titleLarge-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz)en_US
dc.typeResearch Articleen_US
dcterms.dateAccepted2014-11-30
dspace.entity.typePublication
mods.location.urlhttp://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0116028.PDF

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