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. 2023 Nov 8;24(1):673.
doi: 10.1186/s12864-023-09629-2.

Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development

Shengqun Chen #  1 , Yingfu Chen #  2 , Mei Liang  2 , Shuang Qu  1 , Lianwen Shen  1   3   4 , Yajun Zeng  5 , Na Hou  6
Affiliations

Genome-wide identification and molecular expression profile analysis of FHY3/FAR1 gene family in walnut (Juglans sigillata L.) development

Shengqun Chen et al. BMC Genomics. .

Abstract

Background: Juglans sigillata L. (walnut) has a high economic value for nuts and wood and has been widely grown and eaten around the world. Light plays an important role in regulating the development of the walnut embryo and promoting nucleolus enlargement, which is one of the factors affecting the yield and quality of walnut. However, little is known about the effect of light on the growth and quality of walnuts. Studies have shown that far red prolonged hypocotyl 3 (FHY3) and far red damaged response (FAR1) play important roles in plant growth, light response, and resistance. Therefore, FHY3/FAR1 genes were identified in walnuts on a genome-wide basis during their growth and development to reveal the potential regulation mechanisms involved in walnut kernel growth and development.

Results: In the present study, a total of 61 FHY3/FAR1 gene family members in walnuts have been identified, ranging in length from 117 aa to 895 aa. These gene family members have FHY3 or FAR1 conserved domains, which are unevenly distributed on the 15 chromosomes (Chr) of the walnut (except for the Chr16). All 61 FHY3/FAR1 genes were divided into five subclasses (I, II, III, IV, and V) by phylogenetic tree analysis. The results indicated that FHY3/FAR1 genes in the same subclasses with similar structures might be involved in regulating the growth and development of walnut. The gene expression profiles were analyzed in different walnut kernel varieties (Q, T, and F). The result showed that some FHY3/FAR1 genes might be involved in the regulation of walnut kernel ripening and seed coat color formation. Seven genes (OF07056-RA, OF09665-RA, OF24282-RA, OF26012-RA, OF28029-RA, OF28030-RA, and OF08124-RA) were predicted to be associated with flavonoid biosynthetic gene regulation cis-acting elements in promoter sequences. RT-PCR was used to verify the expression levels of candidate genes during the development and color change of walnut kernels. In addition, light responsiveness and MeJA responsiveness are important promoter regulatory elements in the FHY3/FAR1 gene family, which are potentially involved in the light response, growth, and development of walnut plants.

Conclusion: The results of this study provide a valuable reference for supplementing the genomic sequencing results of walnut, and pave the way for further research on the FHY3/FAR1 gene function of walnut.

Keywords: FAR1; FHY3; Gene family; Kernel; Walnut.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Location and distribution of FHY3/FAR1 gene family members in walnut chromosomes. The ruler on the left indicates the length (Mb) of the walnut chromosome. The yellow letters (Chr01 to Chr15) indicate the chromosome number of the walnut. The font marked in red indicates the ID number of the FHY3/FAR1 gene family in the walnut genome
Fig. 2
Fig. 2
Motif-domain analysis of FHY3/FAR1 family members in Walnut. The evolutionary tree of the FHY3/FAR1 gene family is shown on the left. On the right side of the figure are the schematic diagram of the Motif’s color blocks and the sequence of 10 Motifs of FHY3/FAR1 family members
Fig. 3
Fig. 3
Phylogenetic tree and cluster analysis of FHY3/FAR1 family members in Walnut. Different line colors and Roman numerals (I, II, III, IV, and V) in the figure indicate subcategories of FHY3/FAR1 family members
Fig. 4
Fig. 4
Phenotypes of Hongguo Wuren (Q), Songhe Wuren (T), and Sachijiwuren (F) in walnut kernels at different developmental stages. F1, Q1, and T1 represent 120 days post-anthesis (DPA), and F2, Q2, and T2 represent 165 DPA
Fig. 5
Fig. 5
Expression profiles of the FHY3/FAR1 gene family in Q, T, and F walnut kernels at different developmental stages. The color bar on the right, purple, indicates a significant increase in gene expression level. A sky-blue color indicates a low gene expression level. p < 0.05
Fig. 6
Fig. 6
RT-PCR verification of candidate genes of the FHY3/FAR1 gene family in walnuts. The uppercase letters in the horizontal coordinates are “Hongguo Wuren (Q), Songhe Wuren (T), and Sachijiwuren (F)”. The numbers (1 and 2) next to the letters in the horizontal coordinate represent two developmental stages (sampling periods) of different walnut varieties. The column in the figure represents the gene expression level detected by RT-PCR, and the broken line in the column figure represents the gene expression level (FPKM value) of the RNA-Seq profile. The scatterplot in the lower right corner showed the correlation analysis between RT-PCR and RNA-Seq results (p < 0.01). * in the bar chart indicates the significance of the difference comparison (*, p < 0.05; **, p < 0.01)
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