ARS | Publication request: Comparative Next-Generation Sequencing for Transcriptome Definition and SNP Development in Gossypium hirsutum

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: October 9, 2009
Publication Date: January 9, 2010
Citation: Van Deynze, A., Matvienko, M., Kozik, A., Manchali, S., Wang, F., Yang, S.H., Jones, D.C., Chen, Z.J., Town, C., Cheung, F., Stelly, D. 2010. Comparative Next-Generation Sequencing for Transcriptome Definition and SNP Development in Gossypium hirsutum [abstract]. XVIII Plant and Animal Genome Conference Proceedings, January 9-13, 2010, San Diego, California. Abstract W317.

Technical Abstract: Current databases for cotton include 269,657 ESTs for Gossypium hirsutum representing 98,420 unigenes with a large proportion representing singletons. However, few lines are sequenced, each at a limited depth. Consequently, mining ESTs for single nucleotide polymorphisms (SNPs) results in a high rate of false positives. We aimed at developing informative SNPs for breeding and expanding current genomic resources for functional genomics in cotton. Using Illumina technology, we sequenced the transcriptome of five breeding lines including TM-1. Illumina sequences can be efficiently assembled de novo and combined with Sanger sequences for SNP and gene discovery. We will present the variation and importantly the complementary nature of this data to currently available Sanger assemblies.