Identification and characterization of pathogen recognition genes families in Gastrodia elata: Insights into their roles in growth and disease resistance

Background Gastrodia elata Bl., a perennial herb of the Orchidaceae family whose dried tubers are used as medicine, requires symbiosis with at least two fungal species for growth and development. This study aims to identify disease-resistance gene families in the dark red G. elata genome and analyze their structural and expression characteristics, providing a theoretical basis for disease-resistance breeding and cultivation. Result We identified 68 pathogen recognition genes in G. elata ( GePRG s). This included phylogenetic analysis, classification, chromosomal distribution, protein motifs, gene structure organization, and gene duplication events, revealing substantial evolutionary diversity. The G. elata resistance gene family has undergone tandem and segmental duplications, with three identified tandem duplication events. Additionally, 55 GePRG genes show syntenic relationships with homologous genes in other plant species, suggesting that these genes have maintained functional stability throughout evolution. A total of 101 cis -regulatory elements (CREs) were identified in the 2,000 bp upstream region of the translation start codon (ATG) of GePRG s. These CREs include many environmental stress-related elements, such as MYB binding sites, dehydration-responsive element (DRE) core, and low-temperature responsive elements, indicating that these genes play critical roles in responding to abiotic stresses (such as drought, cold, and oxidative stress) and biotic stresses (such as pathogen defense). The expression analysis of GePRG genes at different developmental stages of G. elata showed that certain genes, such as GeLRR-RLK12 , GeLec-RLK15 , and GeLRR-RLK28 , are highly expressed in early developmental stages (eg. immature tuber, S1). From the S1 to capsules (S5) stages of dark red G. elata , the expression levels of genes GeLRR-RLK24 , GeLec-RLK3 , GeLec-RLK2 , and GeLec-RLK8 are generally upregulated, indicating their potential roles in tissue growth, maturation, and immune regulation. The G. elata f. viridis with light green stems(TMQG) genotype exhibited the highest expression levels among various G. elata genotypes. Specifically, GeLRR-RLK17 , GeLRR-RLK36 , GeLYK1 , and GeLec-RLK13 were highly expressed in TMQG, making them promising molecular markers for resistance breeding. Conclusion This study analyzes gene expression profiles and CREs in G. elata ’s disease resistance genes, highlighting the need for further experiments to confirm their roles in growth and disease resistance, and offering valuable genetic resources for breeding. These genes of GeLRR-RLK17 , GeLRR-RLK36 , GeLYK1 , and GeLec-RLK13 are likely to play essential roles in enhancing the disease resistance and promoting the growth and development of G. elata .