Abstract
<jats:p>White lupin (Lupinus albus L.) is a cool-season grain legume with seed crude protein of 33-47%, competitive with soybean (Glycine max L.) meal. It also fixes nitrogen and mobilizes soil phosphorus. Because soybean is a summer crop, white lupin can occupy Southeastern winter fields as a complementary protein source. Breeding for seed protein is limited by the cost and throughput of reference phenotyping. To determine how each is best deployed, we compared the utility of near-infrared spectroscopy (NIRS)-based phenomic selection with genomic selection based on 246,847 SNPs from low-pass, whole genome sequencing in a panel of Auburn University breeding lines and USDA National Plant Germplasm System germplasm. A handheld NIR calibration against Dumas reference protein reached screening-grade accuracy. Under common cross-validation, phenomic predictive ability was 0.93 and genomic was 0.12. The low genomic value was consistent with moderate heritability and strong genotype-by-year interaction. Beyond predictive ability, NIRS recovered superior accessions the strictest selection intensity, and 40 to 60 reference assays sufficed to calibrate the model. Handheld NIRS is a low-cost tool for protein calibration and early-generation screening, while genomic prediction remains suited to parental selection, together supporting a complementary strategy for legume breeding</jats:p>