Haplotype Diversity at a Grain Protein Content QTL Identified in Elite Six-Row and Two-Row Barley Germplasm.

Rising CO₂ concentrations inhibit nitrate assimilation in plants, reducing their productivity and protein levels. Growing crop varieties with improved nitrogen use efficiency (NUE) could counteract this hindrance and decrease fertilizer input costs for producers. We evaluated NUE-related traits in two association mapping (AM) panels—one consisting of 250 spring two-row barley (Hordeum vulgare) lines and one consisting of 250 spring six-row barley lines. Each panel was genotyped with 3,072 SNP markers and was assessed in nitrogen-limiting and non-limiting treatments in four environments. Stress indices calculated for relevant traits were used to compare lines’ performance under the different treatments. Our objectives were to: 1) define the genetic architecture of NUE and 2) investigate marker haplotypes for associated loci. Grain yield, grain protein content, and two stress indices—geometric mean (GM) and stress tolerance index (STI)—for these two traits consistently showed significant genetic variation in the AM panels. Using AM with a K model to correct for relatedness among lines, we identified markers associated with grain protein content and the GM and STI indices of grain protein at a region on chromosome 6H. Some of these markers map to a region previously associated with grain protein concentration referred to as Gpc-1. Based on markers in this region, we identified four haplotypes in each AM panel. Three of these haplotypes have significantly different grain protein values, corresponding to low, medium, and high protein alleles that have been previously isolated in six-row barley near isogenic lines. Though grain yield and grain protein content are often negatively correlated, the different haplotype classes did not have significantly different yields in the six-row AM panel. In addition to the available genetic variation, markers linked to loci for these traits should be useful in breeding efforts to improve barley for NUE.