Marker Associations with Nitrogen Use Efficiency Traits in Hard Winter Wheat.

Wheat genotypes that efficiently capture and convert soil N into grain protein are key to meeting global demand for grain protein.  Direct measurement of nitrogen use efficiency (NUE) traits is labor-intensive, and selection across a range of N levels increases the cost of cultivar development.  Therefore, this research sought to identify marker associations with NUE traits.  NUE traits were measured in a panel of 299 contemporary and historical winter wheat genotypes grown at two N levels in two years.  Traits included nitrogen harvest index, nitrogen uptake efficiency, post-anthesis nitrogen uptake, nitrogen utilization efficiency, total nitrogen yield, and grain nitrogen yield.  Contributions of genotype-by-environment interaction to genetic variances for NUE traits were substantial.  Association analysis was conducted with high-density single nucleotide polymorphism (SNP) markers from the wheat 92K iSelect assay.  Markers for the reduced height alleles at the Rht-B1 and Rht-D1 loci and markers for photoperiod insensitive alleles at the Ppd-A1, Ppd-B1, and Ppd-D1 loci were evaluated as fixed effects (covariates), along with principle components of the SNP marker data.  Model selection using the Bayesian Information Criteria retained the Rht markers as covariates for most traits in both years.  The Ppd-B1 and Ppd-D1 markers were retained as covariates for NUE traits, with the exception of nitrogen uptake efficiency and total nitrogen yield.  Effects of covariates often were substantial.  For example, the Rht and Ppd covariates explained over 40% of the variation in nitrogen harvest index in one environment.  Association analysis within the subset of 217 semi-dwarf genotypes identified genomic regions associated with NUE traits.  The most common associations identified were with markers on chromosomes 1B, 2B, 3B, and 5D.  QTL effects for markers other than Rht and Ppd generally were small, suggesting that genomic selection strategies may be more productive than targeted QTL breeding strategies for NUE traits.