Feathers are an excellent model for studying the development and evolution of morphological traits because of having diverse forms with hierarchical branching patterns. Various types of morphological changes are allowed to occur by the complex structure of feathers. The genetic basis of the structural differences between different parts of a feather and between different types of feather is a fundamental question in the study of feather diversity, yet the actual genetic material responsible for feather diversity remains largely unresolved. Here, we performed high-throughput mRNA sequencing to investigate gene expression profiling and alternative splicing events. We present bioinformatics analysis of several morphotype-specific splice isoforms which can be related to gene functions in different morphotypes of feathers. This study laid the ground work for studying the evolutionary origin and diversification of feathers as abundant data were produced for the study of feather morphogenesis.