Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.)

Feng Yan,Huaizhu Li,Peng Zhao,Shuoxin Zhang,Ge Yang,Ming Yue,Huijuan Zhou

doi:10.3390/f10030275

Abstract

The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.

Highlights

The ubiquitin–proteasome pathway, which involves the F-box protein, is one of the most important biological regulatory systems
In the reproductive tissues and vegetative tissues, a total of 13 members (Jure_07950.t1, Jure_21178.t1, Jure_07156.t1, Jure_07788.t1, Jure_14341.t1, Jure_21675.t1, Jure_06725.t1, Jure_19792.t1, Jure_06252.t1, Jure_02219.t1, Jure_05249.t1, Jure_26563.t1) of the F-box gene family were highly expressed in reproductive tissues, while those in other vegetative tissues were low in expression, and three F-box genes (Jure_29522.t1, Jure_10126.t1, Jure_30338.t1) were higher in reproductive tissues than in nutritive tissues (Figure 4)
Most of the common walnut F-box genes grouped into Group A were highly expressed in female and male flowers, while Group C members were lowly expressed in leaf and hull tissues

Summary

Introduction

The ubiquitin–proteasome pathway, which involves the F-box protein, is one of the most important biological regulatory systems. Recent studies indicated that the F-box gene is an important factor in the regulation of plant growth and development and response to stress [5,6,7]. Based on the different types of conserved domains of the F-box gene family, F-box proteins could be involved in many biological development processes, such as leaf senescence and branching [9,10], flowering [11,12], circadian rhythms [13,14], self-incompatibility [15,16,17], phytochrome signaling [18], and responses to plant growth regulators [19,20] and abiotic [20,21] and biotic factors [22].

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Results

Discussion

Conclusion