title: Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz).
abstract: Cassava (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.
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Wirulda
authors.initials: W
authors.lastname: Pootakham
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Shearman
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Panthita
authors.initials: P
authors.lastname: Ruang-Areerate
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Chutima
authors.initials: C
authors.lastname: Sonthirod
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Duangjai
authors.initials: D
authors.lastname: Sangsrakru
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Nukoon
authors.initials: N
authors.lastname: Jomchai
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Thippawan
authors.initials: T
authors.lastname: Yoocha
authors.affiliation: Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.
authors.forename: Kanokporn
authors.initials: K
authors.lastname: Triwitayakorn
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Somvong
authors.initials: S
authors.lastname: Tragoonrung
authors.affiliation: National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Pathum Thani, Thailand.
authors.forename: Sithichoke
authors.initials: S
authors.lastname: Tangphatsornruang
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D008040:Genetic Linkage / Q000235:genetics; D005819:Genetic Markers; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D060005:Genotyping Techniques; D002365:Manihot / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005819:Genetic Markers