Quinoa (Chenopodium quinoa Willd.) is a genetically diverse Andean crop that has earned special attention worldwide due to its nutritional and health benefits and its ability to adapt to contrasting environments, including nutrient-poor and saline soils and drought stressed marginal agroecosystems. Drought and salinity are the abiotic stresses most studied in quinoa; however, studies of other important stress factors, such as heat, cold, heavy metals, and UV-B light irradiance, are severely limited. In the last few decades, the incidence of abiotic stress has been accentuated by the increase in unpredictable weather patterns. Furthermore, stresses habitually occur as combinations of two or more. The goals of this review are to: (1) provide an in-depth description of the existing knowledge of quinoa’s tolerance to different abiotic stressors; (2) summarize quinoa’s physiological responses to these stressors; and (3) describe novel advances in molecular tools that can aid our understanding of the mechanisms underlying quinoa’s abiotic stress tolerance.

Pitseed goosefoot (Chenopodium berlandieri) is a free-living North American member of an allotetraploid complex that includes the Andean pseudocereal quinoa (C. quinoa). Like quinoa, pitseed goosefoot was domesticated, possibly independently, in eastern North America (subsp. jonesianum) and Mesoamerica (subsp. nuttaliae). To test the utility of C. berlandieri as a resource for quinoa breeding, we produced the whole-genome DNA sequence of PI 433,231, a huauzontle from Puebla, México. The 1.295 Gb genome was assembled into 18 pseudomolecules and annotated using RNAseq data from multiple tissues. Alignment with the v.2.0 genome of Chilean-origin C. quinoa cv. ‘QQ74’ revealed several inversions and a 4A-6B reciprocal translocation. Despite these rearrangements, some quinoa x pitseed goosefoot crosses produce highly fertile hybrids with faithful recombination, as evidenced by a high-density SNP linkage map constructed from a Bolivian quinoa ‘Real-1’ × BYU 937 (Texas coastal pitseed goosefoot) F₂ population. Recombination in that cross was comparable to a ‘Real-1’ × BYU 1101 (Argentine C. hircinum) F₂ population. Furthermore, SNP-based phylogenetic and population structure analyses of 90 accessions supported the hypothesis of multiple independent domestications and descent from a common 4 × ancestor, with a likely North American Center of Origin.