Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea (Vigna unguiculata L.) during the Early Vegetative Stage

Abstract

Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs.

Transcriptomic analysis reveals candidate genes associated with salinity stress tolerance during the early vegetative stage in fababean genotype, Hassawi-2

“…Similarly increasing pattern of down-regulated genes were observed except 24 h salt exposure, where down-regulated genes were less than 12 h of salt stress. These findings are in line with other studies on transcriptional responses in leaf tissues of several plant species under abiotic stressors 34 , 35 . The large number of genes that are downregulated in leaves exposed to high salinity may be a result of the leaves ability to conserve energy and resources by suppressing the transcription of genes primarily linked to oxidative processes and cell wall compartments.…”

“…S2 . These salt-induced pathways have been previously identified for Cowpea 35 , Cenostigma pyramidale 40 , and rape seed 41 .…”

Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery

“…The pipeline has been used within the field of cancer research ( 22–27 ) and beyond, such as the identification of rare variants in tinnitus patients ( 28 ), finding SNPs in driver genes related to stress-response in cowpeas ( 29 ), the genomic profiling of wild and commercial bumble bee populations ( 30 ), or the Personal Genome Project-UK ( 31 ).…”