Weighted Gene Correlation Network Analysis Reveals Key Regulatory Genes Influencing Selenium Enrichment and Yield with Exogenous Selenite in Tartary Buckwheat

Abstract

Selenium (Se) is an essential trace element for human health, and dietary Se intake is an effective supplement. Rich in nutrients and functional components with potential for Se enrichment, Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) is a Se-biofortified cereal. To determine the optimal Se treatment concentration and fully understand its effects on Tartary buckwheat, sodium selenite (Na₂SeO₃) in different concentrations was sprayed onto leaves of Tartary buckwheat at the initial flowering stage. Agronomic and yield-related traits and Se enrichment were analyzed between CK and treatments. The results showed that Na₂SeO₃ concentrations of 3.0 and 6.0 mg/L significantly increased the contents of Se and starch in the grains, the 1000-grain weight, the number of grains per plant, and the yield. The 6.0 mg/L treatment had the best effect. Transcriptome and weighted gene co-expression network analyses showed that selenite promoted chlorophyll synthesis and photoelectron transport by upregulating chlorophyll synthase (CHLG) and protein CURVATURE THYLAKOID 1B (CURT1B) levels, improving photosynthesis, increasing sucrose synthesis and transport in leaves and starch synthesis and accumulation in grains, and promoting grain-filling and yield. These changes were regulated by genes related to photosynthesis, sucrose, and starch metabolism-related genes, including CAB3C, HPR3, SUS5, BAM9, SS3, SWEET1, and SWEET12. Selenite absorption in Tartary buckwheat was regulated by aquaporin genes NIP1-1 and PIP1-5. Selenite transport was regulated by the inorganic phosphate transporter gene PHT1-1, and organic Se transport was controlled by the proton-dependent oligopeptide transporters NPF3.1 and NPF4.6. Methionine gamma-lyase (MGL) was involved in selenocompound metabolism. This study identified the best spraying scheme for enhancing Se content in the grains. It also revealed the regulatory genes responding to selenite absorption, transport, and metabolism and the regulatory pathways promoting yield in Tartary buckwheat. These results provide technical guidance and theoretical support for producing high-yielding and Se-enriched Tartary buckwheat.

Keywords: Fagopyrum tataricum (L.) Gaertn.; absorption and transport of selenite; differentially expressed genes; regulation model; transcriptome.

Figure 1

Changes in chlorophyll a, b, total chlorophyll, and carotenoid contents in Tartary buckwheat on days 10, 20, and 30 following selenite treatment. Different lowercase letters above the bars indicate significant differences between the means according to Duncan’s test (p ≤ 0.05). CK, Se1.5, Se3.0, and Se6.0 indicate the Na₂SeO₃ concentrations 0, 1.5, 3.0, and 6.0 mg/L.

Figure 2

Changes in the sucrose and starch contents and GPx activity of Tartary buckwheat on days 10, 20, and 30 following selenite treatment. The three bar graphs above show the sucrose and starch contents and GPx activity in leaves, and the graphs below show the sucrose and starch contents and GPx activity in grains. Different lowercase letters above the bars indicate significant differences between the means according to Duncan’s test (p ≤ 0.05). GPx, glutathione peroxidase. CK, Se1.5, Se3.0, and Se6.0 indicate the Na₂SeO₃ concentrations 0, 1.5, 3.0, and 6.0 mg/L.

Figure 3

Agronomic, yield-related, quality traits, and Se enrichment of Tartary buckwheat between control and selenite treatments. Different lowercase letters above the bars indicate significant differences between the means according to Duncan’s test (p ≤ 0.05). CK, Se1.5, Se3.0, and Se6.0 indicate the Na₂SeO₃ concentrations 0, 1.5, 3.0, and 6.0 mg/L.

Figure 4

Histogram, Venn diagram, and KEGG enrichment analysis of the differentially expressed genes (DEGs) between the control and selenite treatments. (A) Histogram of the DEG counts. (B) Venn diagram of the DEGs. (C) KEGG enrichment analysis of DEGs in grains. (D) KEGG enrichment analysis of DEGs in the leaves. KEGG, Kyoto encyclopedia of genes and genomes; GCK, control of grains; GSe, grains with Se6.0 treatment; LCK, control of leaves; LSe, leaves with Se6.0 treatment; 10th day, 20th day, and 30th day indicate the days after selenite treatments.

Figure 5

Weighted gene co-expression network analysis of physiological index in leaves and grains during the filling stage. (A) Gene cluster dendrograms and module detection. (B) Gene number for each module. (C) Heat map of module–trait correlation. The first three columns represent the traits in grains, while the subsequent seven columns correspond to the leaves. The different colors indicate different modules. The values in the brackets indicate the correlation coefficient (p-value) with a legend on the right. GPx, glutathione peroxidase; Chl, chlorophyll.

Figure 6

Comparison of relative gene expression of candidate genes based on RNA-seq and real-time quantitative PCR (qRT-PCR). CK and Se6.0 indicate the Na₂SeO₃ concentrations 0 and 6.0 mg/L.

Figure 7

A hypothetical regulation model of the genes responding to Na₂SeO₃ in Tartary buckwheat. The left side of the figure illustrates the key regulatory genes and pathways involved in selenite absorption, translocation, and metabolism in leaves and grains. The right side of the figure shows the key regulatory genes and pathways that promote photosynthesis, grain filling, and increased yield under selenite treatments. The yellow arrows indicate the transformation between substances, the blue arrows indicate substance transport, and the red arrow indicates a result.