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. 2021 Nov 22:12:760379.
doi: 10.3389/fpls.2021.760379. eCollection 2021.

Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

Yuxi Chen  1   2 , Rijin Zhou  2 , Qiong Hu  2 , Wenliang Wei  1 , Jia Liu  2
Affiliations

Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

Yuxi Chen et al. Front Plant Sci. .

Abstract

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.

Keywords: Brassica napus; CONSTANS-LIKE (COL) genes; expression pattern; genome-wide analysis; photoperiod.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Chromosomal localization of BnaCOL genes in B. napus. The chromosomes with different sizes are represented by the yellow vertical bars with different lengths. The locations of genes are shown from top to bottom.
FIGURE 2
FIGURE 2
Phylogenetic analysis and number statistics of COL homologs in different species. (A) Phylogenetic tree using 137 COL proteins from 7 species, including rice, maize, Arabidopsis, B. napus, B. oleracea, B. rapa, and radish. The clades of group 1, 2, and 3 are marked in red, blue, and purple, respectively. Among them, BnaCOLs are represented by red five-pointed stars. The abbreviations represent the species as follows: Os, Oryza sativa; Zma, Zea mays; At, Arabidopsis thaliana; Bna, Brassica napus; Bol, Brassica oleracea; Bra, Brassica rapa; Cru, Capsella rubella, and Rsa, Raphanus sativus. (B) Statistics of the number of COL genes in each group. The ordinate is the number of genes and the abscissa is the COL genes of each species.
FIGURE 3
FIGURE 3
Comparative analysis for conserved domain and gene structure between AtCOL genes and BnaCOL genes. (A) The phylogenetic analysis of 17 AtCOL genes and 33 BnaCOL genes divided them into three groups: 1, 2, and 3. (B) The conserved domains of AtCOL and BnaCOL proteins. Schematic representation of the 10 conserved motifs in BnaCOL proteins, different colored boxes represent different motifs. (C) The gene structure of AtCOL and BnaCOL genes. The green box represents exons, the yellow box represents UTR and the black line represents introns.
FIGURE 4
FIGURE 4
Collinearity analysis of the AC subgenome of COL genes in B. napus. Among them, the gray line represents the replication event of all genes in B. napus and the red line represents tandem repeat events within the BnaCOL genes.
FIGURE 5
FIGURE 5
Syntenic relationship of COL genes in B. napus and three ancestral plant species. The figure shows the collinearity between Arabidopsis (A. thaliana), Brassica rape (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus).
FIGURE 6
FIGURE 6
Cis-acting element analysis of COL gene family in B. napus. The boxes with different colors on the black line represent different cis elements.
FIGURE 7
FIGURE 7
The heat map shows the expression profile of BnaCOL genes in different tissues. The transcriptome data origins from the online website (BnTIR: Brassica napus transcriptome information resource).
FIGURE 8
FIGURE 8
The expression pattern of BnaCOL genes under LD conditions. Under LD (16 h dark/8 h), the third true leaf was collected every 4 h. The error column represents the standard deviation of the three biological replicates.
FIGURE 9
FIGURE 9
The expression pattern of BnaCOL genes under SD conditions. Under SD (8 h light/16 h dark), the third true leaf was collected every 4 h. The error column represents the standard deviation of the three biological replicates.
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