Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica).

Yanjie Qu,Jun Zhu,Hongmin Hou,Yugang Zhang,Yaping Wang

doi:10.3390/plants10010016

Abstract

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

Highlights

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.Transcription factors (TFs) control the transcription or expression of downstream target genes by interacting with cis-elements through covalent binding to the DNA binding domain
Following the removal of redundant sequences, we initially identified 11 MdNFYAs, 26 MdNF-YBs, and 12 MdNF-YCs through Hidden Markov Model (HMM) analysis of the M. domestica genome
Four putative MdNF-YBs (MD03G1280100, MD06G1209300, MD11G1164600, and MD14G1219800) and two putative MdNF-YCs (MD02G1273400 and MD07G1042300) did not contain the core structure of the Nuclear factor Y (NF-Y) domain, so we removed them from further analysis

Summary

Introduction

Transcription factors (TFs) control the transcription or expression of downstream target genes by interacting with cis-elements through covalent binding to the DNA binding domain. In plants, each NF-Y subunit has evolutionarily formed relatively large gene families expressed from multiple NF-Y genes. The three subunits each possess conserved DNA-binding domains and mutual interaction domains to form heterotrimeric complexes. The dimer complex combines with NF-YA to form a mature heterotrimeric NF-Y complex transcription factor that binds to CCAAT boxes in the promoters of target genes [4,5]. AtNF-YC9 is a positive regulator involved in abscisic acid (ABA) signaling by interacting with ABA-responsive bZIP transcription factor ABA-INSENSITIVE5(ABI5) [7,8]. The AtNF-YC4 gene interacts with the Qua-Quine Starch (QQS) orphan gene to regulate carbon and nitrogen allocation and reduce susceptibility to pathogens and pests [9,10]

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Results

Conclusion