SUMMARY: Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication‐related questions to understand the biological and cultural bases of the domestication process. We employed restriction site‐associated DNA sequencing (RAD‐seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well‐diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so‐called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

Societal Impact Statement: Underutilized species (also known as orphan crops) present opportunities to increase crop diversity and food security. Such crops lack modern genetic tools and knowledge to facilitate efficient modern breeding approaches. A wide collection of tef (Eragrostis tef (Zucc.) Trotter) genotypes was used to identify genomic regions associated with productivity, lodging, and morpho‐physiological traits under contrasting water availabilities. The obtained results are expected to enhance modern breeding and improve tef productivity under traditional and modern cropping systems, thus improving farmers' livelihood and food security.Summary: Tef (E. tef (Zucc.) Trotter) is an allotetraploid (2n = 4x = 40) C4 cereal crop, endemic to Ethiopia and mainly cultivated in the Horn of Africa. Tef is characterized by high grain and feed nutritional qualities and resilience to abiotic and biotic stresses; thus, it holds great potential to sustain food and nutrition security in Africa and other parts of the world. The objective of this study was to identify genomic regions associated with responses to contrasting water regimes, as a basis for future improvement. A tef diversity panel was genotyped with 28,837 single nucleotide polymorphisms (SNPs) and phenotyped for productivity, lodging, and morpho‐physiological traits along two seasons (2020 and 2021) under well‐watered and water‐limited treatments. A genome‐wide association study was performed to identify genomic regions associated with key traits for tef breeding. A total of 107 SNPs were associated with one or more of the studied traits, resulting in 138 marker–trait associations (MTAs) detected under both water treatments. Of these, 22 SNPs were associated with more than one trait, showing either multiple trait (pleiotropic) or multiple environment associations or both. A particularly strong association was found between grain yield, lodging, and time to heading. These findings open new avenues to further research on the genetic basis and physiological mechanisms underlying major traits in tef, as well as to marker‐assisted breeding of drought‐resilient tef cultivars.