Identification and expression analysis of the SPL transcription factor family in rye (Secale cereale L.) in response to abiotic stresses

Abstract

Abstract Background Squamous promoter binding protein-like (SPL) gene family, a typical class of plant transcription factors, plays an essential role in plant growth and developmental stages, signal transduction, and response to biotic and abiotic stresses. Given the rapid development of whole genome sequencing, the SPL gene family has been identified and characterized in many species. However, the identification or systematic analysis of SPL gene family in rye has not been reported yet. Results In this study, 21 SPL genes were identified for the first time, which were unevenly distributed on seven rye chromosomes. After analyzing the number of conserved structural domains and gene structure based on homology in Arabidopsis thaliana, these 21 genes were classified into seven subfamilies. To better understand the developmental mechanisms of the ScSPL gene family during evolution, six species closely related to rye were selected as comparative homology maps. These results revealed that fragment replication events regulated the expansion of the ScSPL gene family. In addition, the identification of promoters containing many hormone- and stress-responsive cis-acting elements suggested that the regulation of ScSPLs expression is complex. Most ScSPL genes might be involved in the MeJA and ABA responses with a potential abiotic function through ERF regulation. Finally, RT-qPCR evaluated the expression patterns of the 21 genes in different tissues, fruit developmental stages, three hormones and six different abiotic stresses. Conclusions To our knowledge, this is the first study to identify and characterize SPL genes in rye. This study demonstrated that ScSPL genes, especially ScSPL1, played a critical role in rye development and its response to various abiotic stresses.