Integrative identification of regulatory genes for potato root development through GWAS, QTL mapping, and transcriptome analysis

• A genome-wide association study was performed using a natural population composed of 214 diploid potato germplasm resources, yielding a total of 137 significant SNP loci, among which 12 were repeatedly detected across two environments. • An F₂ segregating population was constructed using two homozygous, self-compatible genomic materials. A high-density genetic map containing 4646 Bin markers was subsequently developed via whole-genome resequencing. QTL mapping for root-related traits yielded 38 genetic loci. By cross-referencing GWAS and QTL mapping results, 8 loci that were co-localized in both analyses and repeatedly detected across environments were selected as reliable loci. • Transcriptome sequencing of the two parental lines revealed 139 differentially expressed genes within these reliable loci, among which genes associated with plant hormones, lignin biosynthesis, and WAKY transcription factors were highlighted as the most promising candidate genes. Well-developed root systems are crucial for ensuring high and stable crop yields. Potato ( Solanum tuberosum L.) is a typical shallow-rooted crop, making the improvement of root traits to enhance its production potential a significant research objective. This study employed a hydroponic system to investigate potato root phenotypes. Utilizing a natural population composed of 214 diploid potato germplasm resources, we conducted a genome-wide association study. This analysis identified 137 significant single nucleotide polymorphism (SNP) loci associated with root traits, among which 12 were consistently detected across two independent environments. Furthermore, to complement the GWAS, an F 2 mapping population consisting of 170 individuals was developed from a cross between two diploid lines, HD5 and M9, which exhibit contrasting root phenotypes and possess highly homozygous genomes. Whole-genome resequencing was performed on the parental lines and the F 2 population for genotyping. This enabled the construction of a high-density genetic linkage map comprising 4646 Bin markers. Subsequent quantitative trait locus (QTL) mapping using this map identified 38 genetic loci associated with root-related traits, with 16 loci detected in more than one analysis. Comparative analysis of the GWAS and QTL mapping results revealed 11 co-localized loci. To effectively prioritize candidate genes, we focused on 8 reliable loci that were both co-localized by GWAS and QTL mapping and consistently detected across environments. Transcriptome sequencing analysis of the two parental lines (HD5 and M9) identified 139 differentially expressed genes (DEGs) within these reliable loci. Among these DEGs, DM8C01G32920, DM8C02G29270, DM8C02G30060, DM8C03G31680, DM8C05G06230, DM8C09G02710, and DM8C09G21900 emerged as the most promising candidate genes potentially involved in potato root development.