Large-scale SNP discovery in cassava via transcriptome sequencing

Cassava 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.

Researchers 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 F1progeny 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 viscosity was identified and shown to coincide with the QTL previously reported for this trait. This work represents the first effort to perform capture-based targeted enrichment sequencing in cassava and illustrates the attractiveness of this approach for genotyping SNPs in predetermined genomic regions.

This study was a collaborative effort of researchers from Mahidol University and BIOTEC Genome Technology Research Unit

Full article can be accessed here.


Ref.: Pootakham, W., Shearman, J.R., Ruang-Areerate, P., Sonthirod, C., Sangsrakru, D., Jomchai, N., Yoocha, T., Triwitayakorn, K., Tragoonrung, S. and Tangphatsornruang, S. (2014). Large-scale SNP discovery through RNA sequencing and SNP genotyping by targeted enrichment sequencing in cassava (Manihot esculenta Crantz). PLOS ONE. 9(12):e116028. doi: 10.1371/journal.pone.0116028.

Posted on 19 August  2015