Genome-Wide Association Mapping of Low-Nitrogen Tolerance in Hexaploid Oat Identifies a Suggestive Candidate Locus near P5CDH Associated with Root Dry Weight

Background/Objectives: Optimizing nitrogen fertilizer efficiency is crucial for sustainable agriculture, but the genetic basis of low-nitrogen (LN) tolerance in oat (Avena sativa L.), an important forage and grain crop, remains poorly characterized. Methods: This study investigated eleven LN tolerance phenotypes across 103 oat accessions using high-density resequencing markers, mixed-model association mapping (MLM), a FarmCPU sensitivity analysis, and Bayesian genetic architecture inference (BSLMM). Results: No locus achieved genome-wide Bonferroni significance, and Bayesian estimates indicated a low-to-moderate model-based PVE (0.10–0.23) with no clearly identified major-effect locus, suggesting that genomic selection represents a plausible future direction for LN tolerance in oat. At a suggestive threshold (p < 1 × 10−5), a cross-model intersection nominated a hypothesis-generating locus at 1D:349,799,042 associated with root dry weight. This locus showed haplotype-level phenotypic segregation (Wilcoxon p = 1.36 × 10−5) on the discovery panel and concordant signals between the two models (r = 0.92). The nearest nitrogen-metabolism-related gene, P5CDH (22.7 kb away), encodes Δ1-pyrroline-5-carboxylate dehydrogenase, which catalyses the terminal step of proline catabolism, and its wheat ortholog was significantly down-regulated under nitrogen deficiency. Conclusions: These findings provide a testable hypothesis linking proline catabolism to oat root plasticity under low nitrogen and a framework for validation in larger panels.