Characterizing the Oat Transcriptome for Seed Nutrition Improvement
Plant Science Research
Project Number: 5062-21000-031-01
Specific Cooperative Agreement
Start Date: Apr 28, 2014
End Date: Jun 30, 2016
Compared to wheat and barley, oats have modest genome resources that can be exploited for acccelerated crop improvement. Given the well-established healthy promoting properties of oats, it is essential that a full toolbox of genomics tools be developed for this crop. One promising area that remains largely unexplored is the molecular dynamics of oat seed development. Since the regulation of gene expression in oats ultimately controls the accumulation of health-promoting compounds in oat seeds, it is critical to gain an understanding of global gene expression and its modulation during the course of seed development. The objectives of this research include 1) develop a high quality transcript assembly for developing oat seeds by a novel bioinformatic approach that merges information from two distinctly different next-generation sequencing platforms; 2) obtain information on the potential role of particular alleles of biosynthetic genes in determining the synthesis and accumulation of health-promoting compounds in oat seeds; 3) develop allele-specific markers for oat genes; and 4) make the oat transcriptome assembly and related information publically available to the oat research community.
A high quality transcript assembly was developed previously by ARS researchers using short sequence reads. To deconvolute highly similar allele sequences and thus refine the transcript assembly, longer high-quality 454 reads will be merged with the existing transcript assembly to assign polymorphisms in the assembly to distinct alleles and paralogs. The 454 and sequence reads will then be integrated in a hybrid analysis to develop a superior transcript assembly in which alleles will be differentiated based on the additional information obtained from 454 reads. The assembly will be used to evaluate the expression of genes encompassing the tocol biosynthetic pathway and genes potentially involved in beta-glucan synthesis over the course of seed development (4 separate timepoints, 3 biological replicates) to identify candidate genes and likely metabolic control points that control the accumulation of these compounds.