Identification and Analysis of NaHCO3 Stress Responsive Genes in Wild Soybean (Glycine soja) Roots by RNA-seq

Abstract

Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed “phenylpropanoid biosynthesis” and “phenylalanine metabolism” pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity.

GsSLAH3, a Glycine soja slow type anion channel homolog, positively modulates plant bicarbonate stress tolerance

“…Plenty of alkali responsive genes were isolated and characterized (DuanMu et al ). Of these genes, a slow‐type anion channel homolog 3 gene, GsSLAH3 , was found to be upregulated after NaHCO 3 stimulation, which was in line with later RNA‐sequencing data of wild soybean roots (Zhang et al ).…”

“…S1). In a more recent study, 449 differentially expressed genes were isolated by RNA‐sequencing of wild soybean roots under 90 mM NaHCO 3 stress, including upregulated ABC transporter, nitrate transporter and zinc/iron transporter (Zhang et al ). The S‐type anion channel GsSLAH3 was included as well.…”

Diversity of Bacterial Microbiota of Coastal Halophyte Limonium sinense and Amelioration of Salinity Stress Damage by Symbiotic Plant Growth-Promoting Actinobacterium Glutamicibacter halophytocola KLBMP 5180

“…We used magnetic beads with oligo(dT) to enrich mRNA from total RNA. We then synthesized cDNA, performed end repair, and added single A (adenine) nucleotides at the 3= ends as described by Zhang et al (98). Sequencing of the 12 cDNA libraries was performed with an Illumina HiSeq 2500 platform by Biomarker Technology Co. (Beijing, China).…”

Connection the Rhizomicrobiome and Plant MAPK Gene Expression Response to Pathogenic Fusarium oxysporum in Wild and Cultivated Soybean

“…2). Wild soybean is a source of genetic diversity to identify novel genes underlying responses to biotic and abiotic stresses (Kim et al, 2011; Zhang et al, 2016). In our study, the RNA-seq results revealed more DEGs in the W + F vs. W comparison than in the C + F vs. C comparison, which implied that wild soybean exhibited a stronger response to F. oxysporum infection (Fig.…”