Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerata L.) through transcriptome analysis

Abstract

Orchardgrass (Dactylis glomerata L.) is a long-lived, cool-season forage grass that is commonly used for hay production. Despite its economic importance, orchardgrass genome remains relatively unexplored. In this study, we used Illumina RNA sequencing to identify gene-associated molecular markers, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), as well as heat stress-induced differentially expressed genes (DEGs) in two orchardgrass genotypes, 'Baoxing' (heat resistant) and '01998' (heat susceptible). Approximately 163 million high-quality trimmed reads were generated from 207 million raw reads using the Illumina HiSeq 2000 platform. A total of 126,846 unigenes were obtained after de novo assembly of the trimmed reads, and 40,078 unigenes were identified as coding sequences (CDSs). Based on the assembled unigenes, 669,300 high-quality SNPs, including 416,099 transitions and 257,736 transversions, were contained in 75,875 unigenes. In addition, a total of 8475 microsatellites were detected in 7764 unigenes. When placed under heat stress, the total number of DEGs in 'Baoxing' (3527) was higher than in '01998' (2649), indicating that in comparison with heat-susceptible '01998', heat-resistant 'Baoxing' seems to have more unigenes that respond to heat stress. The high-throughput transcriptome sequencing of orchardgrass under heat stress provides useful information for gene identification and for the development of SNP and SSR molecular markers. The comparison of DEGs under different periods of heat stress allowed us to identify a wealth of candidate DEGs that can be further analysed in order to determine the genetic mechanisms underlying heat tolerance in orchardgrass.

Transcriptomic Identification of Drought-Related Genes and SSR Markers in Sudan Grass Based on RNA-Seq

“…Overall, Carbohydrate metabolism (1,071 unigenes, 8.4%) was the most among all pathways, while signal transduction (1,028 unigenes, 8.4%) contributed to Environmental Information Processing (Figure 8). Carbohydrate metabolism was heavily enriched in the KEGG analysis, in accordance with the results of Huang D. L. et al (2016), as well as a similar study in orchardgrass (Huang et al, 2015). …”

“…RNA-Seq has been successfully used in many plants such as Brachypodium sylvaticum (Fox et al, 2013), Sorghum sudanense (Li et al, 2016), sugarcane (Cardoso-Silva et al, 2014), pepper (Ashrafi et al, 2012), orchardgrass (Huang et al, 2015), Hemarthria (Huang X. et al, 2016), and annual ryegrass (Pan et al, 2016). Transcriptome data has been used in biological studies worldwide in order to better understand biological processes (Surget-Groba and Montoya-Burgos, 2010), and it has especially been applied to studying the responses of gene expression to various stresses (Kreps et al, 2002).…”

Comparative Analysis of the Complete Chloroplast Genome of Four Endangered Herbals of Notopterygium

“…Meanwhile, Illumina-based plastid sequencing has been proven to be a valid and cost-effective way to acquire the complete cp DNA. Many assembled cp DNA of non-model species also have been obtained and employed for the study of differential gene expression, genetic markers development [28], phylogenomics analysis [29], as well as for detecting selection and inferring adaptive evolution within and among angiosperm species [30,31]. …”

Transcriptome profiling of Elymus sibiricus, an important forage grass in Qinghai-Tibet plateau, reveals novel insights into candidate genes that potentially connected to seed shattering

“…Those data suggested genetic variation for seed shattering and provided a suitable population from which the molecular mechanisms of seed shattering may be investigated. Although transcriptome analysis based on next-generation sequencing (NGS) has allowed for the elucidation of complex genetic regulatory networks and provided functional data for many genes related to important agronomic traits [20,21], these tools and sequence resources for seed shattering in E. sibiricus are still lacking. This is the first step to investigate the mechanism of seed shattering for this species.…”