Abstract
Cultivated oat (Avena sativa L.) is an important cereal crop that has captured interest worldwide due to its nutritional properties and associated health benefits. Despite this interest, oat has lagged behind other cereal crops in genome studies and the development of DNA markers due to its large and complex genome. RNA-Seq technology has been widely used for transcriptome analysis, functional gene study, and DNA marker development. In this study, we performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina platform for the development of DNA markers. In total, 31,187,392~41,304,176 trimmed reads (an average of 34,322,925) were generated from 10 oat varieties. All of the trimmed reads of these varieties were assembled and generated, yielding a total of 128,244 assembled unigenes with an average length of 1071.7 bp and N50 of 1752 bp. According to gene ontology (GO) analysis, 30.7% of unigenes were assigned to the “catalytic activity” of the parent term in the molecular function category. Of the 1273 dCAPS markers developed using 491 genotype-specific SNPs, 30 markers exhibiting polymorphism in 28 oat varieties were finally selected. The transcriptome data of oat varieties could be used for functional studies about the seedling stage of oat and information about sequence variations in DNA marker development. These 30 dCAPS markers will be utilized for oat genetic analysis, cultivar identification, and breeders’ rights protection.
Highlights
Cultivated oat (Avena sativa L.) is an important cereal crop for human food and livestock feed worldwide
We identified a total of 6634 single-nucleotide polymorphisms (SNPs) after mapping reads of each of the 10 oat varieties on all assembled unigene sets as the reference sequence
We performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina sequencing platform in order to identify the sequence variations
Summary
Cultivated oat (Avena sativa L.) is an important cereal crop for human food and livestock feed worldwide. Oat ranks sixth in world grain production, following corn, wheat, barley, sorghum, and millet [1]. Compared to other cereal crops, oat is more suitable for cultivation under harsh environmental conditions, such as cool–wet climates and lowfertility soil [2]. Interest in oats as human food has increased due to their nutritional properties and associated health benefits [5]. Oat contains 12–20% high-quality protein and low fat content (
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