Abstract The domestication of crops is associated with the genome-wide loss of nucleotide diversity caused by selection and genetic drift. Here we investigated 32 genotypes representing key stages in the domestication of tetraploid wheat, i.e. wild emmer, emmer and durum wheat. RNA-Seq analysis was combined with estimates of evolvability, heritability and Q ST to characterize the plasticity of gene expression and its adaptive role in primary and secondary domestication under different nitrogen growth conditions. We confirmed the loss of nucleotide diversity and found that primary and secondary domestication affected gene expression diversity in different ways, influenced by nitrogen availability. We found that nitrogen starvation induced the expression of a larger number of genes in durum wheat compared to emmer and wild emmer. Q ST distributions and Q ST –F ST comparisons revealed distinct selection signatures at each domestication stage. While primary domestication affected the expression of genes involved in biotic interactions, secondary domestication was associated with changes in expression of genes involved in metabolism of amino acids, particularly lysine. Our combined results revealed genes specifically involved in nitrogen metabolism, such as glutamate dehydrogenase , with important role in early development, underwent selection during secondary domestication. Therefore, our findings show that nitrogen availability had a pivotal role during the domestication and adaptive responses of one of our major food crops, with varying effects across different traits.

Nitrogen availability during domestication shaped the divergence of tetraploid wheat