ARS | Publication request: Next generation transcriptome sequencing of the high oleic peanut Cultivar OLin and Identification of SNPs between cultivars.

Submitted to: American Peanut Research and Education Society Proceedings
Publication Type: Proceedings
Publication Acceptance Date: July 11, 2011
Publication Date: July 11, 2011
Citation: Burow, G.B., Xin, Z., Chopra, R., Swaroop, S., Burow, M. 2011. Next generation transcriptome sequencing of the high oleic peanut Cultivar OLin and Identification of SNPs between cultivars.. American Peanut Research and Education Society Proceedings, July 11-14, 2011, San Antonio, Texas. p. 51.

Technical Abstract: Total RNA was extracted from leaf, root and immature pod (yellow stage of development) tissue of greenhouse grown plants of the high oleic Texas AgriLife cultivar OLin and analyzed by next generation DNA sequencing. Illumina (Solexa) sequencing of the complete transcriptome of OLin provided 28.8 million short reads of which 21.3 million were aligned to the UGa Tifrunner reference set. Reads of OLin were assembled into 36,201contigs (putative genes) by comparing it to the 37,917 contigs from Tifrunner. A total of 72,586 polymorphisms were identified in 19,000 genes using a minimum quality score cutoff of =20. Initial bioinformatic analysis revealed that a number of contigs with homology to genes induced under water deficit stress contains single nucleotide polymorphisms (SNPs) that can aid in distinguishing OLin and Tifrunner. We expect that transcriptome sequencing and SNP identification would help to not only differentiate between the cultivars but will also prove useful in marker assisted selection, association mapping and eQTL analysis of biotic and biotic stress responses of peanut. Further studies are underway to validate the putative SNP variation discovered and to determine the significance of these polymorphism with physiological response and traits.