Gene Expression Analysis of Different Organs and Identification of AP2 Transcription Factors in Flax (Linum usitatissimum L.)

Abstract

Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops.

Keywords: AP2; gene expression; organ; transcription factor.

Figure 1

Analysis of whole-genome gene expression profiles in different tissue organs of Longya10 flax. (a) Heatmaps were generated to illustrate gene expression levels in different flax tissues. The abbreviations LyR, LyL, LyS, LyP, and LyF represent Longya10 flax roots, leaves, stamens, pistils, and fruits, respectively. Yellow indicates gene expression levels (read counts per million with log2 value). (b) Venn diagrams were created to depict common and unique gene expression patterns observed in roots, leaves, stamens, pistils, and fruits of Longya10 flax plants. (c) Gene Ontology (GO) classification and enrichment analysis of Longya10 flax pistil-specific expressed genes. (d) Longya10 flax leaf-specific expressed gene GO classification and enrichment analysis. (e) GO classification and enrichment analysis of Longya10 flax fruit-specific expression genes. (f) GO classification and enrichment analysis of Longya10 flax root-specific expressed genes. (g) GO classification and enrichment analysis of Longya10 flax stamen-specific expressed genes.

Figure 2

(a) Venn diagram representing common and specific gene expression under comparison of different organs of Longya10 flax. (b) Volcano plot of differentially expressed gene profiles under different organ comparisons of Longya10 flax. Up-regulated DEGs are marked with red dots and down-regulated DEGs are marked with blue dots. The abbreviations LyR, LyL, LyS, LyP, and LyF represent Longya10 flax roots, leaves, stamens, pistils, and fruits, respectively.

Figure 3

Venn diagrams representing the gene expression of common and specific DEGs in different organs of Longya10 flax after a two-by-two comparison. The abbreviations LyR, LyL, LyS, LyP, and LyF represent the root, leaf, stamen, pistil, and fruit of Longya10 flax, respectively.

Figure 4

GO classification and enrichment analysis of Differentially Expressed Genes (DEGs) among Longya10 roots, leaves, stamens, pistils, and fruits. The acronyms LyR, LyL, LyS, LyP, and LyF represent Longya10 flax roots, leaves, stamens, pistils, and fruits, respectively.

Figure 5

(a) Phylogenetic tree clustering of AP2 family genes from Arabidopsis and Longya10. (b) Heatmap of 96 AP2 family genes in different tissues and comparison groups of Longya10. (c) Screening 24 genes with greater than 7 groups as DEGs in different tissue comparison groups of Longya10 and making a correlation coefficient chord plot. The acronyms LyR, LyL, LyS, LyP, and LyF represent Longya10 flax roots, leaves, stamens, pistils, and fruits, respectively. The yellow color represents the expression levels of genes (in log2-transformed read counts per million), while the white color indicates the fold change (log2 value) of the DEGs. Statistical significance is denoted by asterisks (*) with p < 0.05.

Figure 6

(a) The results of qRT-PCR to amplify the expression of ten genes. (b) The comparison results of RNA-seq and qRT-PCR. The acronyms LyR, LyL, LyS, LyP, and LyF are root, leaf, stamen, pistil, and fruit of Longya10 flax, respectively. Statistical significance is denoted by asterisks (*) with p < 0.05.