Background Fatty acid desaturases (FADs) play crucial roles in plant growth and development. Fragaria nilgerrensis Schlecht., a wild diploid strawberry species, is characterized by a distinctive peach-like aroma. Objective To comprehensively characterize the FAD gene family in F. nilgerrensis and investigate the specific roles of FnFAD3s in peach-like aroma formation, thereby providing insights for breeding utilization. Methods A genome-wide identification of the FAD gene family was performed using bioinformatics approaches, including phylogenetic analysis, gene structure analysis, conserved motif prediction, chromosomal localization, collinearity analysis, and cis-acting regulatory element prediction. Additionally, expression patterns and subcellular localization of FnFAD3s were investigated. Results A total of 26 FnFAD genes were identified from the F. nilgerrensis genome and phylogenetically classified into five clades: FAB2, FAD3, FAD5, DES-1, and SLD. These genes were unevenly distributed across seven chromosomes, except for FnFAD5.2 and FnFAD5.3, which were not mapped to any specific chromosome. Both tandem and segmental duplication events contributed to the expansion of the FnFAD gene family. Members within the same subfamily exhibited relatively conserved exon-intron structures and motif compositions. Promoter analysis revealed various cis-acting elements related to hormones, stress responses, and growth and development, suggesting complex transcriptional regulatory mechanisms. Expression pattern analysis showed that FnFAD3.3 expression followed a bell-shaped curve during fruit development, peaking at the ripening stage. Notably, FnFAD3.5, which localizes to chloroplasts, was expressed at significantly higher levels in F. nilgerrensis (FN, with peach-like aroma) compared to an interspecific hybrid (IH, without peach-like aroma). Conclusions This study provides a genome-wide characterization of the FAD gene family in F. nilgerrensis and reveals the distinct roles of FnFAD3.3 and FnFAD3.5 in peach-like aroma formation, offering insights into the molecular mechanisms underlying strawberry fruit flavor for breeding improvement.

Genome-wide identification of the FAD gene family in Fragaria nilgerrensis reveals distinct roles of two FnFAD3 genes in peach-like aroma formation

期刊论文
发表日期：

2026年3月23日

查看全文

Ai-Hua Wang,
Yi-Xuan Wang,
Xiao-Cui Liu,
Chao Ma,
Jun Guo

摘要

Background

Fatty acid desaturases (FADs) play crucial roles in plant growth and development. Fragaria nilgerrensis Schlecht., a wild diploid strawberry species, is characterized by a distinctive peach-like aroma.

Objective

To comprehensively characterize the FAD gene family in F. nilgerrensis and investigate the specific roles of FnFAD3s in peach-like aroma formation, thereby providing insights for breeding utilization.

Methods

A genome-wide identification of the FAD gene family was performed using bioinformatics approaches, including phylogenetic analysis, gene structure analysis, conserved motif prediction, chromosomal localization, collinearity analysis, and cis-acting regulatory element prediction. Additionally, expression patterns and subcellular localization of FnFAD3s were investigated.

Results

A total of 26 FnFAD genes were identified from the F. nilgerrensis genome and phylogenetically classified into five clades: FAB2, FAD3, FAD5, DES-1, and SLD. These genes were unevenly distributed across seven chromosomes, except for FnFAD5.2 and FnFAD5.3, which were not mapped to any specific chromosome. Both tandem and segmental duplication events contributed to the expansion of the FnFAD gene family. Members within the same subfamily exhibited relatively conserved exon-intron structures and motif compositions. Promoter analysis revealed various cis-acting elements related to hormones, stress responses, and growth and development, suggesting complex transcriptional regulatory mechanisms. Expression pattern analysis showed that FnFAD3.3 expression followed a bell-shaped curve during fruit development, peaking at the ripening stage. Notably, FnFAD3.5, which localizes to chloroplasts, was expressed at significantly higher levels in F. nilgerrensis (FN, with peach-like aroma) compared to an interspecific hybrid (IH, without peach-like aroma).

Conclusions

This study provides a genome-wide characterization of the FAD gene family in F. nilgerrensis and reveals the distinct roles of FnFAD3.3 and FnFAD3.5 in peach-like aroma formation, offering insights into the molecular mechanisms underlying strawberry fruit flavor for breeding improvement.