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Title: Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz)
Authors: Wirulda Pootakham
Jeremy R. Shearman
Panthita Ruang-areerate
Chutima Sonthirod
Duangjai Sangsrakru
Nukoon Jomchai
Thippawan Yoocha
Kanokporn Triwitayakorn
Somvong Tragoonrung
Sithichoke Tangphatsornruang
Mahidol University. Institute of Molecular Biosciences
Keywords: Large-Scale SNP;Discovery through RNA;Cassava;SNP Genotyping;Targeted Enrichment Sequencing;Manihot esculenta Crantz;Open Access article
Issue Date: 2014
Citation: Plos One. Vol.9, No.12 (2014), e116028
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.
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