Comprehensive analysis of physiological characteristic and global transcriptional profiling to unravel the mechanism of wheat yield increase in intercropping

Introduction Wheat ( Triticum aestivum L.) is a major staple crop for billions of people. Intercropping can increase wheat grain yield and contribute to food security. However, the physiological characteristics and molecular basis underlying yield increases in intercropped wheat remain insufficiently understood. Methods This study integrated physiological measurements with global transcriptional profiling of wheat leaves and roots to investigate responses associated with wheat yield increase under intercropping relative to sole cropping. Results Intercropping increased wheat grain yield by 19.12% and 14.94% and spike number per unit area by 27.4% and 25.3% in 2020 and 2021, respectively, whereas grain number per spike and thousand-grain weight were not significantly affected. Intercropping also increased relative chlorophyll content (SPAD value), net photosynthetic rate (Pn), leaf soluble protein content, peroxidase (POD) activity, and sucrose-phosphate synthase (SPS) activity, while decreasing malondialdehyde (MDA) content in wheat leaves. RNA sequencing (RNA-seq) analysis identified 1993 differentially expressed genes (DEGs) in leaves, including 1005 upregulated and 988 downregulated genes, and 17866 DEGs in roots, including 10782 upregulated and 7084 downregulated genes. Upregulated DEGs were mainly enriched in protein processing in the endoplasmic reticulum, plant–pathogen interaction, and photosynthesis–antenna proteins in leaves, and in phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism in roots. The expression trends of 15 of the 16 selected DEGs were consistent between RNA-seq and quantitative reverse-transcription PCR (qRT-PCR) analyses. Discussion Taken together, the increased biomass accumulation and grain yield of intercropped wheat may be associated with coordinated changes in secondary-metabolite-related pathways, plant–pathogen interactions, protein synthesis and processing, and photosynthesis-related processes. These findings advance our understanding of the physiological and transcriptional responses of wheat to intercropping, identify candidate processes and pathways associated with its yield advantage, and provide a basis for further functional validation and breeding research in intercropping systems.