Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Abstract

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

“…Therefore, the de novo assembled transcriptome by Bridger (32 k-mer) was used for further analysis. The GC content of the reference transcriptome was 49.72%, which is in the range of previous studies in Festuca arundinacea (49.49%) and Arundo donax (49%) transcriptomes (both belongs to Poaceae family) 27,28 .…”

“…Each assembler was run with two k-mer sizes (25 and 32 base pair). While Trinity employs the De Bruijn method to perform assembly 25,26 , Bridger applies a rigorous mathematical model to construct splicing graphs 27 . Following, the four contig datasets, Trinity (25-mer), Trinity (32-mer), Bridger (25-mer) and Bridger (32-mer) reassembled by Cap3 tool 67 to perform a meta-assembly, reducing redundancy and generating more complete consensus sequences (cutoff 95%).…”

Differential gene expression in tall fescue tissues in response to water deficit

“…Transcriptome studies on tall fescue conducted by our groups and others so far have focused on de novo transcriptome assembly (Talukder et al., 2015; Dinkins et al., 2017), comparison between drought‐tolerant and susceptible tall fescue plants, comparison between endophyte‐infected and endophyte‐free tall fescue genotypes under unstressed condition (Dinkins et al., 2017), effects of presence or absence of endophyte on gene expression in pseudostem and reproductive tissues (Nagabhyru et al., 2019), under salinity stress (Amombo et al., 2018), under lead and cadmium stress (Li et al., 2017; Zhu et al., 2018), effects on responses to drought stress in pseudostem tissue in different host–endophyte genotypes comprising combinations of tall fescue plants with common toxic endophytes (CTEs) or nontoxic endophytes, so designated based on (respectively) whether or not they produce the ergot alkaloids that are toxic to livestock (Dinkins et al., 2019).…”

A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses

“…In order to understand how this resilience is manifested within temperate pasture grasses, a number of studies have looked at the contribution of differential gene expression, usually in leaves and sometimes in roots, in response to various aspects of stress within Lolium and Festuca spp. These studies have involved stresses such as cold-acclimation [ 3 ], xenobiotics [ 4 , 5 ], disease resistance [ 6 ], submergence [ 7 ], salinity [ 8 , 9 ], heavy metals [ 10 , 11 ], as well as water-stress [ 12 – 20 ]. Because of the resources required to conduct and analyse transcriptomics experiments, a common approach is to compare gene expression in pairs of tolerant and susceptible genotypes and then to frame observed differences in terms of how expression profiles may be contributing to the differing responses to stress—and this can provide valuable insights.…”