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Background  Mitogen-activated protein kinase (MAPK) cascades play a crucial role in plant growth and development as well as biotic and abiotic stress responses. Knowledge about the MAPK gene family in cotton is limited, and systematic investigation of MAPK family proteins has not been reported.    Results  By performing a bioinformatics homology search, we identified 28 putative MAPK genes in the  Gossypium raimondii  genome. These MAPK members were anchored onto 11 chromosomes in  G. raimondii , with uneven distribution. Phylogenetic analysis showed that the MAPK candidates could be classified into the four known A, B, C and D groups, with more MAPKs containing the TEY phosphorylation site (18 members) than the TDY motif (10 members). Furthermore, 21 cDNA sequences of MAPKs with complete open reading frames (ORFs) were identified in  G. hirsutum  via PCR-based approaches, including 13 novel MAPKs and eight with homologs reported previously in tetraploid cotton. The expression patterns of 23 MAPK genes reveal their important roles in diverse functions in cotton, in both various developmental stages of vegetative and reproductive growth and in the stress response. Using a reverse genetics approach based on tobacco rattle virus-induced gene silencing (TRV-VIGS), we further verified that  MPK9 ,  MPK13  and  MPK25  confer resistance to defoliating isolates of  Verticillium dahliae  in cotton. Silencing of  MPK9 ,  MPK13  and  MPK25  can significantly enhance cotton susceptibility to this pathogen.    Conclusions  This study presents a comprehensive identification of 28 mitogen-activated protein kinase genes in  G. raimondii . Their phylogenetic relationships, transcript expression patterns and responses to various stressors were verified. This study provides the first systematic analysis of MAPKs in cotton, improving our understanding of defense responses in general and laying the foundation for future crop improvement using MAPKs.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-014-0345-9) contains supplementary material, which is available to authorized users.

bmc plant biology

Genome-wide identification of mitogen-activated protein kinase gene family in Gossypium raimondii and the function of their corresponding orthologs in tetraploid cultivated cotton