Molecular evolution, diversification, and expression assessment of MADS gene family in Setaria italica, Setaria viridis, and Panicum virgatum

Key messageThis paper sheds light on the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 maybe involved in the ABA-dependent pathway of drought response.The MADS gene family is a key regulatory factor family that controls growth, reproduction, and response to abiotic stress in plants. However, the molecular evolution of this family is rarely reported. Here, a total of 265 MADS genes were identified in Setaria italica (foxtail millet), Setaria viridis (green millet), and Panicum virgatum (switchgrass) and analyzed by bioinformatics, including physicochemical characteristics, subcellular localization, chromosomal position and duplicate, motif distribution, genetic structure, genetic evolvement, and expression patterns. Phylogenetic analysis was used to categorize these genes into M and MIKC types. The distribution of motifs and gene structure were similar for the corresponding types. According to a collinearity study, the MADS genes have been mostly conserved during evolution. The principal cause of their expansion is segmental duplication. However, the MADS gene family tends to shrink in foxtail millet, green millet, and switchgrass. The MADS genes were subjected to purifying selection, but several positive selection sites were also identified in three species. And most of the promoters of MADS genes contain cis-elements related to stress and hormonal response. RNA-seq and quantitative Real-time PCR (qRT-PCR) analysis also were examined. SiMADS genes expression levels are considerably changed in reaction to various treatments, following qRT-PCR analysis. This sheds fresh light on the evolution and expansion of the MADS family in foxtail millet, green millet, and switchgrass, and lays the foundation for further research on their functions.

Automated summary

This study investigated the evolution and expression patterns of MADS genes in Setaria and Panicum virgatum. SiMADS51 and SiMADS64 may play a role in the ABA-dependent drought response pathway. The MADS gene family, which regulates plant growth, reproduction, and responses to abiotic stress, was analyzed in foxtail millet, green millet, and switchgrass using bioinformatics. Phylogenetic analysis categorized the genes into M and MIKC types, with similar motif distribution and gene structure. The expansion of this gene family was mainly due to segmental duplication, while a shrinking trend was observed in the three species. Purifying selection and positive selection sites were identified in the MADS genes, and many promoters contained stress and hormonal response-related cis-elements. RNA-seq and qRT-PCR analysis supported changes in SiMADS gene expression under various treatments. This study provides new insights into the evolution and expansion of the MADS family and lays the foundation for further research on their functions.