Characterization of drought stress-responsive root transcriptome of faba bean (Vicia faba L.) using RNA sequencing

Abstract

Drought and salinity are the major factors that limit the faba bean (Vicia faba L.) production worldwide. The aim of this study is to identify the water stress differentially expressed genes (DEGs) through the root transcriptome analyses of the droughttolerant Hassawi 2 genotype at vegetative and flowering stages. A total of 624.8 M high-quality Illumina reads were generated and assembled into 198,155 all-unigenes with a mean length of 738 bp and an N50 length of 1347 bp. Among all-unigenes, 78,262 were assigned to non-redundant (Nr), 66,254 to nucleotide (Nt), 54,034 to KEGG, and 43,913 to gene ontology (GO) annotations. A total of 36,834 and 35,510 unigenes were differentially expressed at the vegetative and flowering stages of Hassawi 2 under drought stress, respectively. The majority of unigenes were down-regulated at both developmental stages. However, the number of genes up-regulated (15,366) at the flowering stage exceeded the number of those up-regulated (14,097) at the vegetative stage, and the number of genes down-regulated (20,144) at the flowering stage was smaller than the number of those down-regulated (22,737) at the vegetative stage. The drought stress-responsive differentially expressed unigenes coded for various regulatory proteins, including protein kinases and phosphatases, transcription factors and plant hormones and functional proteins including enzymes for osmoprotectant, detoxification and transporters were differentially expressed, most of which were largely up-regulated. Moreover, a substantial proportion of the DEGs identified in this study were novel, most exhibited a significant change in their expression levels under water stress, making them an unexploited resource that might control specific responses to drought stress in the faba bean. Finally, qRT-PCR results were found almost consistent with the results of next-generation sequencing. Our data will help in understanding the drought tolerance mechanisms in plants and will provide resources for functional genomics.

Characterization of Drought-Responsive Transcriptome During Seed Germination in Adzuki Bean (Vigna angularis L.) by PacBio SMRT and Illumina Sequencing

“…RNA sequencing (RNA-Seq) makes it possible to capture these genes (Cheng et al, 2017). In recent years, fundamental changes happened for the sequencing technology (Alghamdi et al, 2018). The second generation sequencing (NGS) technology deeply enhanced the efficiency and speed in gene discovery (Mortazavi et al, 2008;Asmann et al, 2009;Hershkovitz et al, 2013).…”

Recent Advances in Faba Bean Genetic and Genomic Tools for Crop Improvement

“…Next-generation sequencing (NGS) platforms, especially high-throughput RNA sequencing (RNA-seq) technology, one of the most powerful tools currently available for transcriptome profiling, has enhanced the efficiency and speed of gene discovery in faba bean (Table 3). For example, the identification and characterization of differential gene expression from tissues subjected to drought (Alghamdi et al, 2018;Wu et al, 2020), vernalization (Gao et al, 2020), and salinity stress (Yang et al, 2020) have benefited greatly. These findings will help in understanding the stress tolerance mechanisms in the crop and will provide resources for functional genomics.…”

Legume genomics and transcriptomics: From classic breeding to modern technologies

“…Identified DEGs were novel and showed substantial change at expression level under drought stress conditions. Consequently, the qRT-PCR results were coinciding with sequencing, which could help for functional genomics and tolerance mechanisms in crop plants (Alghamdi et al, 2018).…”

“…Moreover, proteomics plays a significant part in the study of differences at cellular, subcellular, and plant levels under abiotic stress conditions (Hossain and Komatsu, 2014). Alghamdi et al (2018) studied seven cowpea genotypes about solubility-based protein analysis; their results revealed that water-soluble proteins were dominant in cowpea seeds when compared to total proteins. Moreover, gel patterns revealed molecular diversity, total protein complement, and the presence of different protein fractions.…”