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Background  Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development. However, the molecular mechanisms underlying soybean cotyledon development are largely unexplored.    Results  In this study, we characterised a soybean   c   urled-   co   tyledon  ( cco ) mutant. Compared with wild-type (WT), anatomical analysis revealed that the  cco  cotyledons at the torpedo stage became more slender and grew outward. The entire embryos of  cco  mutant resembled the “ tail of swallow ”. In addition,  cco  seeds displayed reduced germination rate and gibberellic acid (GA 3 ) level, whereas the abscisic acid (ABA) and auxin (IAA) levels were increased. RNA-seq identified 1,093 differentially expressed genes (DEGs) between WT and the  cco  mutant. The KEGG pathway analysis showed many DEGs were mapped to the hormone biosynthesis and signal transduction pathways. Consistent with assays of hormones in seeds, the results of RNA-seq indicated auxin and ABA biosynthesis and signal transduction in  cco  were more active than in WT, while an early step in GA biosynthesis was blocked, as well as conversion rate of inactive GAs to bioactive GAs in GA signaling. Furthermore, genes participated in other hormone biosynthesis and signalling pathways such as cytokinin (CK), ethylene (ET), brassinosteroid (BR), and jasmonate acid (JA) were also affected in the  cco  mutant.    Conclusions  Our data suggest that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in  cco , and changes in these pathways may partially contribute to the  cco  mutant phenotype, suggesting the involvement of multiple hormones in the coordination of soybean cotyledon development.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-510) contains supplementary material, which is available to authorized users.

bmc genomics

RNA-Seq analysis reveals that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in curled-cotyledons mutant of soybean [Glycine max (L.) Merr.]