Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Abstract

Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family

“…There are various platforms that can be applied for transcriptional profiling, including PCR-based differential display PCR (DDRT-PCR) [ 110 ], cDNA-amplified fragment length polymorphism (cDNA-AFLP) [ 111 ], cDNA and suppression subtractive hybridization (SSH) [ 112 ], cDNA and oligonucleotide microarrays [ 113 ], and digital expression analysis based on EST counts [ 114 ]. Super-serial analysis of gene expression (super-SAGE) is another technique that can be successfully used in different crops under stress conditions [ 115 ].…”

Molecular Breeding Strategy and Challenges Towards Improvement of Blast Disease Resistance in Rice Crop

“…Molecular markers have played an increasing role in rice breeding for cultivar improvement, screening, selection and germplasm collections ( Wang et al, 2007 ). The new sequencing tools provide valuable informations for the discovery, validation and assessment of genetic markers in populations ( Sahebi et al, 2015 ). For instance, the analysis of next generation sequencing (NGS) data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers ( Perez-de-Castro et al, 2012 ).…”

OMICS Technologies and Applications in Sugar Beet

“…SSH is a technique used to identify differentially expressed genes in cells important for growth and differentiation (Lukyanov et al, 2007 ). This method has often been used to study molecular mechanisms of plants in biotic and abiotic stresses (Sahebi et al, 2015 ). The response to insect pests in the root of sugar beet is an interesting area of plant defense research.…”