Genome-wide characterization of AP2/ERF genes and their potential roles in bulb and bolt development in Allium sativum

Garlic is an essential flavoring and health vegetable. Its bulb and bolt, as important edible tissues, are targets to be improved in garlic breeding. AP2/ERF transcription factor plays crucial regulatory roles in multiple biological processes. Nevertheless, identification and characterization of AP2/ERFs are poorly elucidated in garlic. Here, 163 AsAP2 / ERFs were identified in garlic genome and categorized into four subfamilies including AP2 (23), ERF (131), RAV (7), and Soloist (2). Gene structural analysis showed that most AsERFs and all AsRAVs were intron-less, while majority of AsAP2s were intron-rich. Thirty-one pairs of gene duplications were classified as 14 tandem duplications and 17 segmental duplications that were underwent purification selection. Abundant cis -acting elements associated with development, hormone signaling and stress responses were detected in promoter regions. AsAP2/ERFs exhibited different tissue-specific expression profiles. Diverse expression patterns of AsAP2/ERFs at different stages during bulb expansion and bolting processes suggested that these genes played different and well-coordinated roles in bulb and bolt development. The co-expression network analysis showed that 11 AsAP2/ERFs had high connectivity values and might play roles in garlic bolting process along with their co-expression genes which were enriched in ‘reproductive shoot system development’, ‘reproductive process’, and ‘flower development’. These results provide valuable foundation for investigating the function of AsAP2/ERFs for genetic improvement of garlic.