ZF-HD gene family in rapeseed (Brassica napus L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses

Abstract

Abstract Background The zinc finger-homeodomain (ZF-HD) transcription factor family is widely involved in regulating plant growth and fruit filling, as well as responding to various abiotic stress. Rapeseed (Brassica napus L.), the second largest oil-producing crop in the world, is an annual or biennial herb of Brassica in Cruciferae. However, there is currently no systematic study on the evolutionary relationship and stress response of ZF-HD transcription factors in rapeseed. Results In this study, 60 ZF-HD genes in B. napus (BnZHDs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these BnZHD genes were systematically analyzed. These 60 BnZHD members were divided into seven groups. According to the phylogenetic tree and repetitive events, subfamilies MIF, and V may have undergone stronger expansions during the evolutionary process. Interestingly, segmental duplications may have a more important contribution, which distinguishes them from other dicotyledon plants. To further investigate the evolutionary relationship of the ZF-HD family, we constructed eleven comparative genomic maps of homologous genes between rapeseed and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression pattern of 15 BnZHD genes from different subfamilies under different tissues, fruit developmental stages, and different abiotic stress were analyzed. The expression profile from real-time quantitative PCR analysis showed different expression patterns of BnZHD gene in B. napus. We found that certain BnZHD genes are preferentially expressed in specific tissues of B. napus, while most genes are expressed in multiple tissues. For example, BnZHD37, BnZHD53, and BnZHD55 may be sensitive to different hormones. Under different stresses, the expression of BnZHD3, BnZHD4, BnZHD7, BnZHD38, BnZD45, and BnZHD53 significantly increased in roots, stems, and leaves within 24 h. These genes may play important roles in the growth, development, and environmental adaptation of rapeseed. Conclusions These findings provide a basis for a comprehensive understanding of the ZF-HD family in rapeseed, which will provide information for further research on the functional characteristics of the BnZHD genes.

Keywords

• Brassica napus
• ZF-HD gene family
• Evolutionary relationship
• Genome-wide analysis
• Abiotic stress