Genome-wide identification of the MADS-box gene family and SEP1 target genes regulating young embryo development in hazel (Corylus spp.) via ChIP sequencing

Abstract

Hazel (Corylus spp.) is a nut-producing species with important cultivation value. The purpose of this study was to identify important MADS genes involved in the ovule and embryo development of hazel and explore the possible mechanism of MADS regulation on embryo development. After identifying all MADS-box gene members and differentially expressed genes in the hazel genome, we further verified the expression characteristics of important differentially expressed genes (DEGs) using in situ hybridization, and verified the interaction between important proteins using yeast two-hybrid analyses. Finally, ChIP-Seq analysis of ChSEP1 was conducted to identify its target genes. In total, 59 ChMADSs were identified across all 11 chromosomes, and protein length was predicted to vary between 89 and 524 amino acids. All ChMADSs were divided into Type I and Type II MADS-box genes with 14 subgroups. Most ChMADSs showed low expression, and 11 Type II ChMADSs were highly and differentially expressed in the ovule. Of these, floral quartet model genes, both ChMADS11 (AG-like) and ChMADS37 (SEP1) were highly expressed in young embryos at the rapid ovule growth stage and interacted with each other, indicating that they might coordinate embryo development through protein-protein interactions. In total, 4,143 ChSEP1 differential target genes were identified through ChIP-Seq. Important ChSEP1 target genes included ChSEP1/3, ChAG, ChSHP, and ChSTK as well as ChAGL6, ChAP1, ChFUL1, and ChTT16–2, indicating that ChSEP1 might regulate ovule development by cooperating with and mediating ChMADSs. Overall, our study provides new insights into the molecular mechanisms of hazel ovule development.