Allelic Diversity of Candidate Genes Underlying Nitrogen Use Efficiency in Potato

Abstract Potato is a globally important food crop, but its production faces major challenges related to inefficient nitrogen fertilizer use. Excessive nitrogen application, particularly in intensive agricultural systems, compromises sustainability and increases environmental and health risks. Improving nitrogen use efficiency (NUE), defined as the capacity of plants for nitrogen uptake and assimilation, is therefore essential to optimize fertilization practices and enhance sustainable crop production. In this study, we analyzed candidate genes associated with NUE in a diploid potato diversity panel (Solanum tuberosum Group Phureja) by evaluating morphological, physiological, and biochemical variables under contrasting nitrogen levels. Association analyses were performed between these variables and genetic polymorphisms within NUE-related genes. Single nucleotide polymorphisms (SNPs) were identified in three candidate genes: AMT1.1 (ammonium transporter), 2OGDD (2-oxoglutarate-dependent dioxygenase), and PPR (pentatricopeptide repeat protein gene). These variants explained 8–20% of the phenotypic variation in traits such as relative chlorophyll content, aerial biomass, and NUE. Notably, a missense variant (Lys → Glu) in 2OGDD was associated with a 30.5% reduction in NUE under low nitrogen conditions, suggesting distinct adaptive strategies. Specific SNPs were associated with NUE-related traits, representing candidate variants for future functional validation and marker-assisted breeding.