Genome-Wide Association Study and Identification of Core Candidate Genes for Shoot and Root Length in Wheat During Germination

To address the core breeding demand for greater seedling vigor in bread wheat (Triticum aestivum L.) varieties adapted to the uniform sowing system in China’s Huang-Huai Wheat Region, we aimed to dissect the genetic architecture and identify core candidate genes for shoot length (SL) and root length (RL) at the germination stage. A natural population consisting of 204 wheat accessions was genotyped using the 660K SNP array, and a genome-wide association study (GWAS) integrated with transcriptomic, metabolomic, and proteomic analyses of extreme phenotypic accessions was performed. Both SL and RL were typical quantitative traits with an extremely significant positive correlation. A total of 111 and 176 significant SNPs were associated with SL and RL, respectively, including 56 shared loci. Glutathione metabolism was identified as the conserved core pathway for both tissues, while photosynthesis–antenna proteins and phenylpropanoid biosynthesis were identified as tissue-specific pathways in shoots and roots, respectively. Finally, we identified 7 core candidate genes for SL and 13 for RL, including three pleiotropic genes regulating both traits. This study provides valuable genetic resources and key targets for the molecular breeding of wheat varieties specialized for uniform sowing.