Research Article: Transcriptome Assembly and Analysis of Tibetan Hulless Barley (Hordeum vulgare L. var. nudum) Developing Grains, with Emphasis on Quality Properties

Date Published: May 28, 2014

Publisher: Public Library of Science

Author(s): Xin Chen, Hai Long, Ping Gao, Guangbing Deng, Zhifen Pan, Junjun Liang, Yawei Tang, Nyima Tashi, Maoqun Yu, Mark Gijzen.

http://doi.org/10.1371/journal.pone.0098144

Abstract

Hulless barley is attracting increasing attention due to its unique nutritional value and potential health benefits. However, the molecular biology of the barley grain development and nutrient storage are not well understood. Furthermore, the genetic potential of hulless barley has not been fully tapped for breeding.

In the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina paired-end RNA-Sequencing, we generated two data sets of the developing grain transcriptomes from two hulless barley landraces. A total of 13.1 and 12.9 million paired-end reads with lengths of 90 bp were generated from the two varieties and were assembled to 48,863 and 45,788 unigenes, respectively. A combined dataset of 46,485 All-Unigenes were generated from two transcriptomes with an average length of 542 bp, and 36,278 among were annotated with gene descriptions, conserved protein domains or gene ontology terms. Furthermore, sequences and expression levels of genes related to the biosynthesis of storage reserve compounds (starch, protein, and β-glucan) were analyzed, and their temporal and spatial patterns were deduced from the transcriptome data of cultivated barley Morex.

We established a sequences and functional annotation integrated database and examined the expression profiles of the developing grains of Tibetan hulless barley. The characterization of genes encoding storage proteins and enzymes of starch synthesis and (1–3;1–4)-β-D-glucan synthesis provided an overview of changes in gene expression associated with grain nutrition and health properties. Furthermore, the characterization of these genes provides a gene reservoir, which helps in quality improvement of hulless barley.

Partial Text

Barley (Hordeum vulgare L.) is among the most ancient cereal crops [1] and currently ranks fourth in terms of harvested area and tonnage of the world cereal production (http://faostat.fao.org). However, barley is the least utilized cereal for human food consumption and is usually cultivated either in regions unsuitable for wheat growing, or where barley is preferred for cultural reasons [2]. It was also neglected by plant breeders in Europe during the period of intensive crop improvement in the 20th Century. However, it is currently gaining attention as a health food in Europe, North America and other non-traditional barley growing areas [3], [4]. Barley grains are rich in minerals; proteins and lysine and have a high β-glucan content, which inhibits cholesterol synthesis [5]–[7]. Hulless (naked) barley with caryopses that thresh free from the pales is preferred for human consumption [8]–[10]. Hulless barley also allows to omit a processing step, thus, providing an additional advantage for the food industry [11], [12]. Therefore, hulless barley is a potential resource for breeding new healthy food worldwide. The grain of barley is the major storage tissue. Different end uses require alternative quality characteristics of barley grain in terms of molecular composition of starch and proteins. So far, there has been limited research regarding metabolic profiling and gene expression patterns related to the metabolism of storage compounds during barley grain development.

Hulled cultivated barley has been used in the brewing industry worldwide, however, lesser attention was paid on the grain quality of the hulless barley, which is the staple food at some barren regions or highland. Hulless barley has gained significant attention in recent years because of its potential health benefits such as higher β-glucan content than the hulled barley. Comparing to a long growing history and rich diversity in the Qinghai-Tibet Plateau, very few hulless barley cultivars have been developed for the modern UK or European agricultural systems. Thus, exploitation of germplasm resources and revealing the formation mechanism of grain quality in hulless barley will aid in the development of better hulless cultivars with desirable dietary characteristics. Here, we used high-throughput deep sequencing technology to profile the grain transcriptome of two Tibetan hulless barley landraces Nimubai and XQ754. We assembled 48,863 and 45,788 unigenes in two samples and constructed a combined non-redundant data set of 46,485 All-Unigenes. A total of 36,278 All-Unigenes could be functionally annotated, and the CDS and directions of 38,229 All-Unigenes were predicted.

 

Source:

http://doi.org/10.1371/journal.pone.0098144