The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including
Arabidopsis thaliana
,
Oryza sativa
, and
Triticum aestivum
, but have not been identified in foxtail millet (
Setaria italica
). In this study, a total of 93 MAPK cascade genes, including 15
SiMAPKs
, 10
SiMAPKKs
and 68
SiMAPKKKs
genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the
SiMAPKs
and
SiMAPKKs
into four subgroups, respectively, and the
SiMAPKKKs
into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most
SiMAPKs
and
SiMAPKKs
were changed under both exogenous hormone and abiotic stress treatments, with
SiMAPK3
and
SiMAPKK4–2
being induced under almost all treatments, while the expression of
SiMAPKK5
was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (
Setaria italica
).
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