Genetic changes and demography of introduction of grain amaranth to India

The predicted climate change will impact worldwide crop yields, requiring shifts and adaptation of crop varieties. The recent global spread of crops across different continents represents an extreme case of expansion, serving as a model to study the factors and sources enabling adaptation to rapidly changing environments. One such spread is the introduction of the nutritious pseudocereal amaranth to India. Grain amaranth has been domesticated over 6,000 years ago in three different regions of the Americas and was only introduced to India approximately 400 years ago. Nowadays numerous local landraces grow throughout the country's wide climatic conditions. We investigate the introduction of grain amaranth to India to understand the factors allowing successful establishment of crops to novel environments, using whole genome sequencing of about 200 accessions from India and more than 100 from the crop's native distribution. The comparison of genetic diversity yielded comparable or even higher diversity in India than in the Americas, despite the likely population bottleneck during the introduction to India. Surprisingly, the three grain amaranth species that were introduced do not show signs of gene flow, while the strong signals of gene flow were detected in the native range. Correspondingly, the genetic differentiation between grain species was higher within India than within the native range, indicating a strong isolation between otherwise interbreeding populations. The reconstruction of the population history through demographic modelling of different scenarios suggested rapid expansion in the Indian population but a strong bottleneck in the native population, explaining the increase in diversity with isolation. We also identified a few putative genomic loci under selection in India as compared to native range, probably allowing preferential adaptation to the local environment. Considerable amount of loci were also associated with climate suggesting for local adaptive genetic variation. Negligible genomic offset was evident on introducing Indian accessions to native range, suggesting they could act as restorer of the native site. Our results suggest that introduced crops can act as reservoirs of acquired diversity, providing additional adaptive potential and resilience to future environmental change