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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #429820

Research Project: RNAseq to Accelerate Oat Breeding for Nutritional Quality

Location: Plant, Soil and Nutrition Research

Project Number: 8062-21000-045-02-A
Project Type: Cooperative Agreement

Start Date: Sep 20, 2015
End Date: Sep 19, 2019

Objective:
Obtain and analyze gene expression data using RNA sequencing on a series of oat lines that have been characterized for nutritional quality and have been assayed using high-throughput metabolomics of mature grain. These lines have also been genotyped by sequencing reduced representations of their genomes. Differential gene expression and correlation between gene expression, metabolomics profiles, and nutritional quality will be used to identify loci harboring genetic variation that affects nutritional quality. These data will also enable prediction of nutritional quality for newly developed oat lines.

Approach:
Funds available are sufficient to implement RNA extraction and sequencing on 384 oat lines. These lines will be grown in the field, planted in spring 2016. Careful monitoring of flowering will take place to be able to sample oat florets at 20 days after anthesis. Florets will be sampled and frozen in liquid nitrogen. RNA will be extracted from developing oat grains excised from the florets, prepared for sequencing, and sequenced in libraries with 16 samples per lane of sequence to obtain on average 15M reads per sample. Correlation and clustering analysis between expression levels of different genes will be performed. Expression levels will be treated as a phenotype and loci associated with expression level identified. Expression levels will be correlated with metabolomics data treated in similar ways. Finally, expression levels will be used as predictors to train models predicting oat nutritional quality.