**7. The path to domestication: learning from transitional models**

Decreased genetic diversity in plants populations is often associated with increased cultivation [7, 129]. Less cultivated plant populations tend to have more genetic diversity or "wildness" than plants that have been domesticated [129]. Wild characteristics broaden genetic responses and are valuable for maintaining phenotypic plasticity [129–131]. Leveraging broad genetic responses to enhance plasticity is especially important for the survival of plant species in unpredictable and changing climates [74, 75].

Since the dawn of agriculture, farmers have used selective breeding techniques for cultivating and domesticating wild plants for food [132]. Seeds from wild plant populations are smaller, an adaptation thought to enhance dispersal [132]. From an agricultural perspective, increased domestication is useful for reliable germination, uniform emergence, uniform stand establishment, larger seed size, increased yield, and improved nutrition [132]. Domestication of wild maize, soybean, and barley has resulted in significant increases in seed size [86]. However, there has also been a negative cost associated with domestication [86]. In maize, soybean, and rice, domestication and intensive cultivation have resulted in the elimination of genetic loci in modern crop cultivars [86, 133–136]. Breeding strategies that do not address adaptation and plasticity decrease trait diversity and may limit the development of new crop varieties with the ability to adapt to insects and extreme environmental fluctuations [133–136].

A reduction in heritability of favorable traits within breeding populations has been one of the main reasons plant breeders have explored the possibility of integrating genetic diversity from wild populations (landraces) back into selective breeding programs [133–137]. Two wild plant models that have been very instrumental in the effort to introduce diversity back into breeding population are: (1) barley (*Hordeum vulgare*); a standard model for monocots, and (2) quinoa (*Chenopodium quinoa* Wild); a model for dicots [137–145]. These two models are very powerful because they highlight a clear transition from wild populations to domesticated cultivars. They also provide tools for understanding plasticity by comparing characteristics that have remained constant, changed, or been lost through a history of domestication [137–145].

Barley was domesticated very early in history from the wild grass relative, *Hordeum spontaneum* [137]. Barley, along with einkorn (*T. monococcum*, genomes AmAm) and emmer (*T. turgidum* ssp. *dicoccoides*, genomes BBAA), marked the beginning of domestication in cereals [137]. Barley is often used as a model to improve crops like wheat (*Triticum aestivum*) [138]. Barley demonstrates a wide range of plasticity including superior growth in nutrient-limited environments, and adapted root architecture [139, 140]. Although there are evolutionary similarities between barley and other monocots like wheat, the orthologous genomic regions between the two species have a completely diverged [141–143]. However, genomic similarities between barley and wheat have enriched the comparative studies of plasticity and provide new information about horizontal gene transfer [141–143].

Quinoa, like barley, was recognized as a valuable food resource, and was domesticated very long ago [144]. Although quinoa has been highly domesticated, it retains vast genetic variability and plasticity with a wide range of resistance to many abiotic and biotic stresses [144, 145]. Quinoa thrives in extreme environmental conditions including in regions with high salinity soils, areas of extremely low precipitation, and environments with extremely cold temperatures [105, 146]. Moreover, quinoa grain is resistant to starch degradation in environments susceptible to extreme temperature and moisture fluctuations [147]. The differences in plasticity discovered between wild and domesticated quinoa species illustrate the importance of continued studies identifying physiological and genetic mechanisms regulating plasticity [147]. These discoveries also highlight the feasibility and importance of selectively breeding for gene targets that improve adaptability and fitness [133–136]. Additionally, because quinoa is a polyploid, it is a rich resource for studying how complex genomes contribute new dimensions of genetic regulation to phenological plasticity [147]. Recent studies investigating modern cultivated varieties of quinoa show that cellular plasticity mechanisms, and more specifically ROS homeostasis, are dependent on both genotype and type of stress [123]. The emerging discoveries in quinoa are important because they provide a model for how plasticity mechanisms present in other polyploid crop species may be regulated [123].
