Identification of genomic regions and candidate genes for tuber micronutrient accumulation in potato (Solanum tuberosum L.) through GBS-based GWAS

Micronutrient deficiencies, commonly referred to as hidden hunger, affect nearly two billion people worldwide and pose a major challenge to global nutritional security. Potato, the most widely consumed non-grain staple crop, offers strong potential for biofortification due to its high yield, short crop duration, wide adaptability, and consumer acceptance. In the present study, a panel of 288 highly diverse tetraploid potato accessions was evaluated for tuber micronutrient concentrations, including iron (Fe), zinc (Zn), copper (Cu), and manganese (Mn), over two years. Substantial phenotypic variation was observed for all micronutrients across the panel. Genotyping was performed using genotyping-by-sequencing (GBS), and sequence reads were aligned to the Solanum tuberosum reference genome, achieving a mapping rate of 94.0-98.1% with a mean error rate of 0.03%. A total of 132,766,447 SNPs were initially identified, from which 23,522 (75% threshold) and 5,470 (90% threshold) high-quality SNPs were retained for downstream analysis. Genome-wide association analysis using the GWASpoly package identified 16 significant marker-trait associations (MTAs) across additive and dominance models for micronutrient traits. Notably, a major locus associated with Mn content explained up to 20% of the phenotypic variance, indicating a relatively large-effect region. Several MTAs were co-localized with putative candidate genes encoding metal transporters, transcription factors, and regulatory proteins involved in nutrient homeostasis. These findings provide insights into the genetic architecture of tuber micronutrient accumulation and support the development of nutrient-enriched potato cultivars through molecular breeding approaches.