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F-Box Genes in Brassica rapa: Genome-Wide Identification, Structural Characterization, Expressional Validation, and Comparative Analysis

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Abstract

The F-box genes form one of the largest functionally important, rapidly evolving plant gene families. The encoded proteins mainly function as part of the Skp1–Cullin–F-box complex involved in ubiquitinating and degrading proteins. The F-box proteins also regulate diverse functions, including embryogenesis, organ development, floral organ identity, self-incompatibility, senescence, homeostasis, signaling, and responses to biotic and abiotic stresses. We identified 571 Brassica rapa F-box genes (BrFBX) and mapped approximately 560 genes onto 10 chromosomes. We also classified the duplicated genes. A phylogenetic tree consisting of the B. rapa F-box genes and an analysis of conserved motif sequences enabled us to categorize the identified genes into 11 subgroups based on node support. Additionally, we determined the intron–exon structural characteristics, which helped detect differences among the BrFBX genes. Gene ontology predictions enabled the classification of 431 genes related to biological processes, 63 genes involved in molecular functions, and 40 genes associated with cellular localization. The 69 genes differentially expressed under abiotic stress conditions (i.e., cold, drought, and salt stresses) and 446 genes expressed in specific tissues (i.e., calli, roots, leaves, stems, flowers, and siliques) were further categorized into three groups based on their expression levels. These genes exhibited various spatiotemporal expression patterns during stress treatments and in specific tissues. Based on motif and expression analyses, we selected approximately 30 BrFBX genes for quantitative reverse transcription polymerase chain reaction analysis, which detected differences in expression among eight tissues during B. rapa (Chiifu) growth. The genome-wide study results reveal the relationships among the BrFBX genes regarding evolution, structural variability, potential functions, and these data can be further used as a resource for the gene characterization in relation to growth, development, and during different stress conditions for the development of Brassica rapa.

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Funding

This research was supported by Golden Seed Project (No. 213002-04-4-SB130), Ministry of Agriculture, Food and Rural Affairs (MAFRA), Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA) and Korea Forest Service (KFS).

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  1. Jana Jeevan Rameneni and Vignesh Dhandapani contributed equally to this work.

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  1. Molecular Genetics and Genomics Laboratory, Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, 34134, South Korea

    Jana Jeevan Rameneni, Vignesh Dhandapani, Parameswari Paul, Sangeeth Prasath Devaraj, Su Ryun Choi, So Young Yi, Seongmin Hong, Sang Heon Oh & Yong Pyo Lim

  2. Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, South Korea

    Man-Ho Oh

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  1. Jana Jeevan Rameneni
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Rameneni, J.J., Dhandapani, V., Paul, P. et al. F-Box Genes in Brassica rapa: Genome-Wide Identification, Structural Characterization, Expressional Validation, and Comparative Analysis. Plant Mol Biol Rep 36, 500–517 (2018). https://doi.org/10.1007/s11105-018-1083-1

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