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ARS Home » Plains Area » Lincoln, Nebraska » Wheat, Sorghum and Forage Research » Research » Research Project #428051

Research Project: Exploiting natural diversity to identify alleles and mechanisms of cold adaption in switchgrass

Location: Wheat, Sorghum and Forage Research

Project Number: 3042-21000-032-04-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Oct 1, 2014
End Date: Aug 31, 2019

Our proposed research will identify alleles, transcripts, and regulatory RNAs associated with cold hardiness that will 1) substantially advance our understanding of the biochemical, physiological, and molecular mechanisms for cold adaptation in switchgrass and 2) provide molecular tools to improve switchgrass breeding efficiency.

To assess the frequency of alleles associated with cold hardiness, DNA from survivors and non-survivors will be pooled and used in exome capture sequencing using the NimbleGen SeqCap EZ Switchgrass Exome probe set and the Illumina platform. Captured reads will be cleaned, aligned to Release 1.1 of the switchgrass genome and variants (SNPs, Indels) identified. Allele frequencies will be estimated in each of the survivor/non-survivor pools. Genes with differential allele frequencies in survivors vs non-survivors will be annotated for gene function including biochemical pathway, gene ontology, and orthology to other Poaceae species and Arabidopsis thaliana to associate cold adaptation with physiological and biochemical mechanisms. Using RNA isolated from each individual in the populations described in Obj 1, we will pool RNA from the “survivor” and “non-survivor”” individuals and perform mRNA-seq sequencing using the Illumina platform. For mRNA-seq, cleaned reads will be aligned to the switchgrass genome, and expression abundances estimated for the non-survivor and the survivor bulked pools. In addition, allele specific expression will be determined and frequencies of expression for each allele will be determined and correlated with the genotypic allele frequency in the same pool.