Genome-Wide Association Mapping of Low-Nitrogen Tolerance in Hexaploid Oat Identifies a Suggestive Candidate Locus near P5CDH Associated with Root Dry Weight.
- 1College of Grassland Science, Inner Mongolia Agricultural University, Hohhot 010011, China.
Abstract
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.
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BibTeX
@article{ling2026genomewide,
title = {{Genome-Wide Association Mapping of Low-Nitrogen Tolerance in Hexaploid Oat Identifies a Suggestive Candidate Locus near P5CDH Associated with Root Dry Weight.}},
author = {Yu Ling and Ziyang Wang and Shuhao Yu and Zihao Zhang and Haizhou Yang and Lihui Zhang},
journal = {Genes},
year = {2026},
month = oct,
doi = {10.3390/genes17101314},
url = {https://europepmc.org/article/MED/42938430},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genome-Wide Association Mapping of Low-Nitrogen Tolerance in Hexaploid Oat Identifies a Suggestive Candidate Locus near P5CDH Associated with Root Dry Weight.
AU - Yu Ling
AU - Ziyang Wang
AU - Shuhao Yu
AU - Zihao Zhang
AU - Haizhou Yang
AU - Lihui Zhang
PY - 2026
DA - 2026/10/21
JO - Genes
DO - 10.3390/genes17101314
UR - https://europepmc.org/article/MED/42938430
AB - 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.
SN - 2073-4425
ER -