Rescuing the adaptive secrets of ancient quinoa

Project Information

PALEOQUINOA

Grant agreement ID: 101032990

DOI

10.3030/101032990

Project closed

EC signature date 4 March 2021

Start date 1 July 2022

End date 30 June 2024

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 184 707,84

EU contribution

€ 184 707,84

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 1 - PALEOQUINOA (Rescuing the adaptive secrets of ancient quinoa)

Reporting period: 2022-07-01 to 2024-06-30

Summary of the context and overall objectives of the project

Food security is one of the most pressing global challenges today, as the world’s population is expected to reach nearly 10 billion people by 2050. To meet the nutritional needs of this growing population, food production must increase by approximately 70%. However, this goal faces significant obstacles, including limited land availability, water scarcity, and the impacts of climate change. A key issue is the reduced genetic diversity in many crop species cultivated through millennia of domestication, which limits their ability to adapt to changing environmental conditions and threatens future food security. The PALEOQUINOA project focused on studying the domestication history and the ancient diversity of quinoa, a highly nutritious and resilient Andean pseudo-cereal increasingly recognised as a promising crop for sustaining food security. PALEOQUINOA has applied advanced ancient DNA methods and modern genomic techniques (1) to generate the first genome-scale dataset of ancient quinoa DNA variation, and (2) to clarify current models of quinoa domestication. The PALEOQUINOA data sheds new light on the evolutionary history of quinoa and represents the first paleogenomic time series assembled for this important crop species. It announces a new era of ancient DNA research investigations, non-Eurocentric and not centred on animal material, but focused on the process of plant domestication. The approach developed will facilitate future improvements in the genetic make-up of quinoa to increase its suitability as a crop.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

PALEOQUINOA has achieved significant advancements in understanding the genetic history and diversity of quinoa through comprehensive ancient DNA analysis, whole-genome sequencing, and genomic target enrichment techniques. Genomic characterisation of archaeological quinoa samples from Antofagasta de la Sierra, Argentina, spanning over 3,500 years suggests a more complex phylogenetic history than previously understood, potentially involving unknown ancestral populations that have given origin to modern highland varieties. These results provide a new perspective on the domestication and adaptation processes of quinoa, challenging earlier assumptions about its evolutionary history. To further investigate the genetic diversity of quinoa, the project developed a custom target enrichment array, focusing on SNPs informative of ancestry, population structure and genetic diversity of quinoa. This technique allowed for the efficient characterisation of highly degraded ancient quinoa samples, enhancing the understanding of the quinoa genetic variation over time. The findings of PALEOQUINOA have been widely and effectively disseminated through multiple channels. Several manuscripts are being prepared for submission to peer-reviewed journals, detailing the phylogenetic history, genomic adaptations, and genetic diversity of quinoa. These publications are expected to make substantial contributions to archaeobotany, ancient crop genomics, and food security. The results of the project have been presented at international conferences, which has facilitated collaboration with other researchers and increased the visibility of the results in the scientific community. Additionally, the project has engaged in extensive outreach activities to communicate the significance of its findings to broader audiences, including stakeholders in agriculture, policy, and the general public. These efforts have highlighted the importance of quinoa research for understanding crop domestication and addressing future food security challenges. Overall, PALEOQUINOA has provided valuable insights into the domestication and genetic diversity of quinoa, contributing to both scientific knowledge and public awareness of crop diversity and food security.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The PALEOQUINOA project has made notable contributions to enhancing innovation capacity, particularly in the domain of crop improvement and sustainable agriculture. By uncovering ancient allelic variants that have been lost in modern quinoa populations, the project provides critical insights that could be leveraged to improve the genetic diversity and resilience of quinoa. These genetic discoveries offer valuable resources for increasing the adaptability of quinoa to climate change, disease resistance, and overall productivity, which are crucial for addressing global food security as the world population grows. The development of new methodologies, such as the custom SNPs target enrichment array, can be applied to other Chenopodium crops, accelerating the identification of key genetic traits and improving breeding programs. Additionally, PALEOQUINOA provides insights into how ancient societies adapted their agricultural practices in response to environmental changes, informing the development of more sustainable and resilient agricultural systems today. This focus on preserving and utilising genetic diversity in crops addresses both environmental sustainability and food security needs. The impact of PALEOQUINOA extends beyond academia, as outreach activities, including public lectures and scientific meetings, have raised awareness of the importance of genetic diversity in crops. These efforts have engaged the public and policymakers in discussions about the role of ancient crops like quinoa in tackling contemporary challenges related to food security and climate change.