Transcriptome and WGCNA Reveal the Key Genes of Arbuscular Mycorrhizal Fungi in Regulating Sugarcane Growth and Nutrient Absorption

Lifang Mo; Ziqin Pang; Zhuowei Tan; Qiang Liu; Yixian Jia; Yijie Xiao; Zhaonian Yuan

doi:10.1002/fsn3.70508

Transcriptome and WGCNA Reveal the Key Genes of Arbuscular Mycorrhizal Fungi in Regulating Sugarcane Growth and Nutrient Absorption

Food Sci Nutr. 2025 Jul 3;13(7):e70508. doi: 10.1002/fsn3.70508. eCollection 2025 Jul.

Authors

Lifang Mo¹, Ziqin Pang^{1

2}, Zhuowei Tan³, Qiang Liu⁴, Yixian Jia¹, Yijie Xiao¹, Zhaonian Yuan¹

Affiliations

¹ National Engineering Research Center for Sugarcane Fujian Agriculture and Forestry University Fuzhou China.
² Xianghu Laboratory Hangzhou China.
³ Agricultural Products Quality and Safety Supervision and Management Station of Qintang District Guigang China.
⁴ College of Natural Resources and Environment Northwest A&F University Yangling China.

Abstract

Sugarcane is a major sugar crop with substantial economic importance worldwide. Arbuscular mycorrhizas (AM), which are capable of forming symbioses with the majority of terrestrial plants, play a pivotal role in plant productivity and soil nutrient cycling. The present study employed pot experiments using a randomized block design. Two treatments were applied: inoculation with AM fungi (A20) and non-inoculation (CK), each with nine replicates within each block. A comparative analysis was conducted on the phenotypic traits, rhizosphere soil nutrient contents, and transcriptomics of sugarcane during the elongation stage. The results demonstrated that AM fungal inoculation not only facilitated the accumulation of above- and belowground biomass in sugarcane but also significantly influenced the contents of soil organic matter, available nitrogen, available phosphorus, and total phosphorus in the rhizosphere. The utilization of RNA-seq and Weighted Gene Co-expression Network Analysis (WGCNA) enabled the identification of genes and modules associated with sugarcane growth and nutrient absorption during the elongation stage following AM fungal inoculation. In particular, the MEmoccasin and MElightpink3 modules were identified as being highly specific to nutrient phenotypes, including nitrogen and phosphorus, as well as belowground growth. In contrast, the MEhoneydew1 module was found to be specifically associated with aboveground phenotypic traits, such as plant height and stem diameter. It is noteworthy that CESA9, ANR, CYCP4, LHA1, SUS4, RPS15AE, and CNGC2 were identified as potential hub genes, exerting crucial regulatory functions in soil carbon cycling, nitrogen and phosphorus content, and sugarcane growth. This study provides insights into the effects of AM fungi on sugarcane growth and nutrient absorption, establishing a theoretical foundation for further understanding the molecular mechanisms underlying AM fungal influence on these processes in sugarcane.

Keywords: RNA‐seq; WGCNA; arbuscular mycorrhizal fungi; soil nutrients; sugarcane growth.