Near-infrared phenomic and genomic prediction for seed protein in winter legume white lupin (Lupinus albus L.): A utility comparison

Abstract

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 (R2 = 0.81). Under common cross-validation, phenomic predictive ability was 0.93 and genomic was 0.12. The low genomic value was consistent with moderate heritability (H2 = 0.33) 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 Plain Language SummarySoybean meal is the main protein source for livestock and fish farms in the United States. Because soybean is a summer crop, many Southeastern fields sit idle or grow low-value cover crops in winter. White lupin, a cool-season legume whose seeds are as protein-rich as soybean meal, makes a good complementary winter crop: it yields high-protein grain while serving as a cover crop that fixes nitrogen and frees up soil phosphorus for later crops. In our early-stage lupin breeding program, measuring seed protein by standard lab methods is slow and costly. We built a calibration that lets a handheld scanner estimate protein from light, and compared it with predicting protein from the plants DNA. The scanner gave accurate, low-cost protein screening from only about 40-60 lab tests, while DNA-based prediction remains suited to guiding parent selection. Used together, these tools offer breeders a practical path to develop high-protein white lupin. Core ideasO_LIHandheld NIRS provides screening-grade prediction of white lupin seed crude protein. C_LIO_LISpectra carried more usable protein signal than markers by measuring seed chemistry directly. C_LIO_LINIRS and genomic prediction serve different stages of a white lupin breeding program. C_LIO_LIAbout 40 to 60 reference assays sufficed to calibrate NIRS to near-full accuracy. C_LI