Transcriptome sequencing and genome-wide association study of wheat stem traits

Stem traits in wheat are closely associated with lodging, and the identification of significantly linked gene loci and candidate genes provides a foundation for analyzing the genetic mechanism and molecular marker-assisted breeding of wheat stem traits. In this study, a panel of 192 wheat varieties from the southern Huang-Huai region was utilized to assess 14 stem traits across seven mature stage environments and four mid-filling stage environments. Genome-wide association analysis (GWAS) was conducted using wheat 660K SNP chips, and the differentially expressed genes related to the strength and diameter of the first two basal internodes were analyzed through RNA-seq. The results revealed a substantial difference between the mature stage and the mid-filling stage for all traits. In comparison to the mid-filling stage, the height of the gravity center significantly increased during the mature stage, while the length of the second and third internodes at the base showed an increase, and the other traits exhibited a decrease. GWAS detected a total of 163 stable SNPs (MTA), out of which 45 had gene or protein annotations. Combining GWAS and transcriptome analysis, three candidate genes associated with wheat stem traits were identified. The candidate gene TraesCS5A02G522100 may regulate photosynthesis by synthesizing isoglutaric acid compounds, thereby enhancing cell membrane stability and permeability through sterol production. This regulation, in turn, promotes stem development and improves stem characteristics. The candidate gene TraesCS1D02G390600 is directly involved in cell division and organ formation in the wheat stem, resulting in thicker and fuller stems. The candidate gene TraesCS7A02G481800 plays a role in cell-to-cell signaling, regulation of stem development, and stress response. The expression trends of these candidate genes were consistent with the results of transcriptome sequencing, as validated by qRT-PCR.