Distinct Effects of Domestication and Improvementon Genetic Load and Nitrogen-Response Variation inSorghum

Abstract

Crop domestication and subsequent improvement under modern agronomic conditions have altered the nitrogen (N) regimes experienced by crops, yet how selection has reshaped the genetic architecture of phenotypic responses to N availability remains poorly understood. Here, we integrated population genomic analyses of n = 289 sorghum accessions spanning multiple stages of domestication and improvement with N-response (NR) trait-associated variants identified through genome-wide association studies (GWAS) of phenotypic data collected under two contrasting N conditions in n = 347 diverse sorghum accessions. Unlike maize and sunflower, sorghum showed a reduced deleterious burden both genome-wide and within historically balanced and recently selected regions following domestication and improvement. Additionally, we identified 470 trait-associated loci (TALs), including 273 associated with NR traits. The effects of these NR-associated loci showed no apparent bias toward derived alleles, suggesting that selection on NR traits in sorghum has not been sufficiently strong or directional to consistently overcome genetic drift. Together, these results reveal distinct patterns of selection in sorghum and provide promising genetic targets for improving N-use efficiency in sustainable agricultural systems.