Genome-wide analysis of ARF gene family and miR160 in avocado (Persea americana Mill.) and their roles in somatic embryogenesis from zygotic embryos

The genome-wide analysis revealed that miRNA160 and PaARFs are involved in avocado somatic embryogenesis and play a role in the low efficiency of embryo induction and the ineffective conversion of embryos into plants. The auxin response transcription factors (ARFs) play a role in signaling the auxin phytohormone Indole-3-acetic Acid (IAA) and are involved in plant growth, development, abiotic stress responses and somatic embryogenesis (SE). In the Lauraceae family, particularly in avocado (Persea americana Mill.), propagation via SE remains challenging due to the low efficiency of embryo induction and ineffective conversion of embryos into plants. This study investigates the phylogenetic relationships and evolutionary history of avocado ARFs (PaARFs). This multigenic family consists of at least 20 members that evolved from a now-extinct common ancestor shared by bryophytes and angiosperms. The expression profile of these genes was analyzed in immature zygotic embryos and three SE stages: early globular, late globular and white-opaque. Additionally, we identified six genes that contributed to the formation of a 100% identical single mature miRNA, the miR160. Almost all PaARF genes were upregulated during the embryo-induction stage, while genes such as PaARF1a, PaARF1c, PaARF2a, PaARF2b, and PaARF17 were downregulated at the white-opaque stage. We observed that the expression of miRNA160 differed significantly between the zygotic embryos and the three subsequent development stages. Additionally, free IAA distributions were highly concentrated in immature zygotic embryos. Our results suggest that miR160 and PaARF-mediated auxin signaling play a role in avocado SE, potentially contributing to the low efficiency of SE. This study is the first report on the ARF gene family in avocado. Our findings provide a valuable reference for comparative and functional analyses of ARFs in the context of avocado somatic embryogenesis.