Genome-Wide Identification and Expression Analysis of the TGA Gene Family in Banana (Musa nana Lour.) Under Various Nitrogen Conditions

Abstract

The TGA (TGACG motif-binding factor) transcription factors are integral to root growth and development, and are pivotal in mediating plant responses to abiotic stresses. Nonetheless, their role in the nutrient absorption processes of banana plants has not been extensively investigated. This research conducted a comprehensive analysis of the MaTGA gene family, emphasizing their physicochemical characteristics, phylogenetic relationships, gene duplication events, promoter cis-regulatory elements and protein interaction networks. Furthermore, this study investigated the expression patterns of MaTGA family members under varying nitrogen conditions. A total of 18 MaTGA members were identified within the banana genome, each encoding proteins characterized by the presence of bZIP and DOG domains. These genes exhibited an uneven distribution across eight chromosomes. Phylogenetic analysis further classified the MaTGA family into four distinct subgroups (I-IV), consisting of three, seven, three, and five members, respectively. An analysis of promoter cis-elements indicated that over 50% of the MaTGA gene family members contain hormone-responsive elements associated with abscisic acid (ABRE), ethylene (ERE), and salicylic acid (SARE), in addition to stress-responsive elements related to drought (MBS) and low temperature (LTR). Regarding gene expression, MaTGA7, MaTGA8, and MaTGA15 exhibited significantly elevated expression levels in the leaves and roots relative to other tissues. Under varying nitrogen conditions, 13 members, including MaTGA7 and MaTGA8, demonstrated the highest expression levels under reduced nitrogen (70%) treatment, followed by low nitrogen (20%) conditions, and the lowest expression levels were observed under nitrogen-deficient conditions. These findings imply that MaTGA genes may play crucial roles in enhancing nitrogen use efficiency. Protein interaction predictions suggest that MaTGA7, MaTGA8, and MaTGA15 may interact with nitrogen-related proteins, including Nitrate Transporter 2 (NRT2.1 and NRT2.2), NIN-Like Protein 7 (NLP7), and Nitrate Transporter 1.1 (NPF6.3). In summary, MaTGA7, MaTGA8, and MaTGA15 are likely involved in the processes of nitrogen absorption and utilization in bananas. The present findings establish a basis for subsequent investigations into the functional roles of MaTGA genes in augmenting nutrient use efficiency and mediating responses to abiotic stresses in banana plants.

Keywords: TGA transcription factors; banana; gene expression; nutrient utilization.

Figure 1

Distribution of the 18 MaTGA genes on the chromosomes of the banana. Chr: chromosome. The left scale indicates chromosome length in megabytes (Mb).

Figure 2

Phylogenetic relationship of the MaTGA family genes. The four groups (I to IV) are represented by different colors, and MaTGA members are represented by stars.

Figure 3

Conserved domains and motifs of the MaTGA members. (A) Phylogenetic tree; (B) Conserved domain; (C) Conserved motif.

Figure 4

Intergenomic and collinear relationships of the MaTGA family. (A) The diagram illustrates, from the innermost to the outermost layer, gene chromosome localization, GC skew, GC ratio, and gene density. (B) The interspecific collinearity analysis is presented for rice (O. sativa), soybean (G. max), Arabidopsis (A. thaliana), and tomato (S. lycopersicum), arranged from top to bottom. The gray line represents the collinearity of all the genes in the banana, and the red line represents the collinearity of the MaTGA genes.

Figure 5

Analysis of the MaTGA promoter cis-acting elements. (A) Phylogenetic tree; (B) Statistical histogram of the four types of responsive elements; (C) Heat map of the number of promoter cis-acting elements.

Figure 6

Gene expression profiles of the MaTGA family in the different tissue (root, stem, leaf, flower, fruit) parts of the banana. Statistical significance was defined as p < 0.05. The notation “a and a” signifies that the difference is not statistically significant, whereas “a and b” denotes a statistically significant difference.

Figure 7

Gene expression profiles of the MaTGA family, in response to different nitrogen levels (3 days: 0 N, 20% N, 70% N, 100% N). BX3D-0: No nitrogen treatment for 3 days, BX3D-20: 20% nitrogen treatment for 3 days, BX3D-70: 70% nitrogen treatment for 3 days, BX3D-100: 100% nitrogen treatment for 3 days. Statistical significance was defined as p < 0.05. The notation “a and a” signifies that the difference is not statistically significant, whereas “a and b” denotes a statistically significant difference.

Figure 8

MaTGA7/8/15 protein interaction prediction. The gray lines represent possible interactions between the protein. Yellow circles represent MaTGA proteins, blue circles represent nitrogen-related proteins that interact with MaTGA, and cyan circles represent other proteins that interact with MaTGA.