Integration of GWAS and Co-Expression Network Analysis Identified Main Genes Responsible for Nitrogen Uptake Traits...

Background/Objectives: Waxy corn has a unique taste and flavor that a majority of consumers love, and the market application prospect is broad. Nitrogen plays an important role in the growth and development of waxy corn. Exploring the key genes that affect nitrogen absorption can lay a foundation for improving the quality of waxy corn. Methods: In this study, a total of 534 local waxy corn inbred lines were used to perform genome-wide association studies (GWAS) to mine the significant Quantitative Trait Nucleotides (QTNs) for nitrogen content of waxy corn at seedling stage in two different environments. The Weighted Gene Co-Expression Network Analysis (WGCNA) nitrogen response co-expression network was also constructed to explore the differences of gene expression patterns and the co-expression relationship between transcription factors and functional genes to find candidate genes significantly associated with nitrogen uptake in waxy corn. Results: A total of 97 significant associations (LOD-value ≥ 3) were detected between SNPs and nitrate content traits under single and multi-environment conditions. Fifty-four candidate genes were identified around the significant SNPs in about a 20 Kb region. Combined with nitrogen response differential co-expression network analysis, 17 out of the 54 candidate genes were identified in the nitrogen response module, among which 4 main genes (Zm00001d029012, Zm00001d034035, Zm00001d007890, and Zm00001d045097) were repeatedly detected in multiple environments. Conclusions: This study jointly identified four stable and heritable candidate genes involved in the nitrogen metabolism process through GWAS and co-expression network analysis. The results of this study provide theoretical guidance for further elucidating the genetic mechanism of nitrogen efficiency in waxy corn and breeding new germplasm of waxy corn.