Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis

• Published in: BMC genomics Vol. 24; no. 1; p. 399
• Main Authors: Zhang, Shan, Liu, Jian, Shi, Lian, Wang, Qianchao, Zhang, Ping, Wang, Hongxin, Liu, Junna, Li, Hanxue, Li, Li, Li, Xinyi, Huang, Liubin, Qin, Peng
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 15.07.2023; BioMed Central; BMC
• Subjects: Agricultural research; Amino acids; Biological activity; Biosynthesis; Chenopodium quinoa - genetics; Chenopodium quinoa - metabolism; DNA binding proteins; Encyclopedias; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes; Genetic aspects; Genetic research; Genetic transcription; Genomes; Genomics; Metabolic pathways; Metabolism; Metabolites; Modules; Network analysis; Phosphorus; Phosphorus - metabolism; Phosphorus content; Phosphorus levels; Photosynthesis; Physiological aspects; Plant Breeding; Proteins; Quinoa; Seedlings; Seedlings - genetics; Seedlings - metabolism; Signal transduction; Soils; Sugarcane; Transcription factors; Transcriptomes; Weighted gene co-expression network analysis; China; Quinoa; Transcription factors; Phosphorus levels; Weighted gene co-expression network analysis
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09507-x

Quinoa is a highly nutritious and novel crop that is resistant to various abiotic stresses. However, its growth and development is restricted due to its limited utilization of soil phosphorus. Studies on the levels of phosphorus in quinoa seedlings are limited; therefore, we analyzed transcriptome data from quinoa seedlings treated with different concentrations of phosphorus. To identify core genes involved in responding to various phosphorus levels, the weighted gene co-expression network analysis method was applied. From the 12,085 expressed genes, an analysis of the gene co-expression network was done. dividing the expressed genes into a total of twenty-five different modules out of which two modules were strongly correlated with phosphorus levels. Subsequently we identified five core genes that correlated strongly either positively or negatively with the phosphorus levels. Gene ontology and assessments of the Kyoto Encyclopedia of Genes and Genomes have uncovered important biological processes and metabolic pathways that are involved in the phosphorus level response. We discovered crucial new core genes that encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which are crucial for abiotic stress resistance. This new library of candidate genes associated with the phosphorus level responses in quinoa seedlings will help in breeding varieties that are tolerant to phosphorus levels.