Genome-wide identification and comparative analysis of Alfin-like transcription factors in maize

Members of the Alfin-like (AL) transcription factor family, which contain a highly conserved DUF3594 domain and a PHD-finger motif, play important roles in the responses of plants to abiotic stress during various metabolic and physiological processes. To date, no systematic, comprehensive study of this family has been reported in maize. In this study, we identified 18 nonredundant ZmAL genes and classified them into four groups. These genes are unevenly distributed among all ten maize chromosomes except chromosome 9. Our results suggest that segmental duplication has played an important role in the expansion of the AL family in maize. Ka/Ks ratio analysis showed that most duplicated ZmALs have undergone large-scale purifying selection in the maize genome. We detected interspecies microsynteny among three graminaceous species, suggesting that there were independent duplication events in addition to the whole-genome duplication of the maize genome. Furthermore, microarray analysis showed that most ZmALs are differentially expressed in diverse tissues and stages. We also performed expression profiling of the ZmALs under salt, cold and drought stress conditions using quantitative reverse-transcription PCR (qRT-PCR). The results of this study provide useful clues for further functional analysis of the AL gene family in maize.