Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines

• Published in: BMC genomics 2024-12, Vol.25 (1), p.1231-17, Article 1231
• Main Authors: Huang, Liubin, Zhang, Lingyuan, Zhang, Ping, Liu, Junna, Li, Li, Li, Hanxue, Wang, Xuqin, Bai, Yutao, Jiang, Guofei, Qin, Peng
• Format: Article
• Language: English
• Subjects: Amylases; Analysis; Anopheles; Chenopodium quinoa - genetics; Chenopodium quinoa - growth & development; DNA binding proteins; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes; Genetic transcription; Germination; Germination - genetics; Metabolites; Natural disasters; Physiological properties; Plant Proteins - genetics; Plant Proteins - metabolism; Quinoa; Spike germination; Transcription factors; Transcriptome; WGCNA
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-11151-y

Quinoa, as a new food crop, has attracted extensive attention at home and abroad. However, the natural disaster of spike germination seriously threatens the quality and yield of quinoa. Currently, there are limited reports on the molecular mechanisms associated with spike germination in quinoa. In this study, we utilized transcriptome sequencing technology and successfully obtained 154.51 Gb of high-quality data with a comparison efficiency of more than 88%, which fully demonstrates the extremely high reliability of the sequencing results and lays a solid foundation for subsequent analysis. Using these data, we constructed a weighted gene co-expression network (WGCNA) related to starch, sucrose, α-amylase, and phenolic acid metabolites, and screened six co-expression modules closely related to spike germination traits. Two of the modules associated with physiological indicators were analyzed in depth, and nine core genes were finally predicted. Further functional annotation revealed four key transcription factors involved in the regulation of dormancy and germination processes: gene LOC110698065, gene LOC110696037, gene LOC110736224, and gene LOC110705759, belonging to the bHLH, NF-YA, MYB, and FAR1 gene families, respectively. These results provide clues to identify the core genes involved in quinoa spike germination. This will ultimately provide a theoretical basis for breeding new quinoa varieties with resistance.