Genome wide identification and characterization of strictosidine synthase-like (SSL) genes in wheat (Triticum aestivum L.)

Introduction
Wheat (Triticum aestivum L.) is globally recognized as a crucial food crop. Due to the significant increase in human population in recent years, there is a need for food production to match population growth, especially for primary crops like wheat. Given the decline in wheat cultivation and yield caused by biotic and abiotic stresses, the cultivation of stress-resistant varieties is a cost-effective and fundamental strategy to mitigate their adverse impacts. Identifying resistance genes is essential for developing new resistant varieties using breeding programs. Strictosidine synthase-like (SSL) genes with a length of approximately 400 amino acids, play a role in plant immunity regulation and possess an extracellular structural domain resembling animal hemomyosin. Previous studies have shown that all categories of AtSSL genes exhibit a response to various biotic and abiotic stressors. At present, our major understanding of the SSL gene family in plants is primarily based on research conducted on Arabidopsis thaliana. In this study, bioinformatics tools were used to explore the evolutionary relationships and functional roles of the SSL gene family in wheat.
Materials and methods
In the first step, the sequence of SSL proteins from rice and Arabidopsis was used to identify genes encoding wheat SSL in the Ensembl Plants database by the PlastP algorithm. Next, phylogenetic relationships were analyzed by MEGA7, the exon-intron structure and intron phase using the Gene Structure view in TBtools-II, and conserved motifs with Multiple Em for Motif Elicitation. Additionally, cis-regulatory elements in the promoter region, gene duplication events, and selection pressure were investigated through PlantCare and the Simple Ka/Ks Calculator in TBtools-II. The expression profiles of TaSSL genes in response to abiotic stresses were analyzed using the expVIP server. All analyses were conducted using default parameters of the software and servers.
Research findings
This study identified 69 SSL genes in the wheat genome, exhibiting a non-unifom distribution across chromosomes. The evolutionary study of this family revealed two main phylogenetic groups in the SSLs of different organisms: The first group (I), encompassing exclusively wheat and rice SSLs genes, and the second group (II), containing genes from diverse organisms. Further subdivision of group II into three subgroups (A, B, and C) highlighted potential functional divergence among members. The analysis of conserved motifs, gene structure, and intron phase indicated a high degree of conservation for these genes. Furthermore, segmental duplication emerged as the primary driver of wheat SLL gene expansion, and these duplicated genes experiencing strong negative selection pressure. The presence of cis-regulatory elements responsive to hormones and stresses suggests intricate regulation of TaSSL gene expression. Consistent with this notion, RNA-seq data revealed the inducible expression of TaSSL genes in response to abiotic stresses, including cold, heat, drought, and PEG.
Conclusion
The presence of a distinct evolutionary cluster of wheat SSL genes, characterized by features typically associated with stress-responsive genes such as a low number of introns, the application of negative selection pressure, the presence of regulatory elements responsive to stresses and hormones, as well as the expression patterns of TaSSL genes in response to abiotic stresses indicated their significant role in wheat's stress response mechanisms. Consequently, the findings of this study can provide valuable insights into the functions of TaSSL genes, facilitating the identification of potential candidates for producing stress-resistant wheat varieties in future breeding programs.