Ancient plant DNA to the rescue: unlocking crop genetic diversity from the past

Abstract

The domestication of animals and plants around 12,000 years ago triggered one of the most transcendental revolutions in human society; from a hunter-gatherer lifestyle to a sedentary, agricultural-based society. Since that time, it is estimated that almost 2,500 species of plants have been subject to domestication. However, the domestication history of most of these species remains unclear, with fundamental questions about the identity of wild ancestors, selected phenotypes (domestication traits), and timing and origin of domestication still to be answered. The impact of the extensive selective pressures exerted by humans on the genomes of staple crops can potentially be understood by reconstructing the genomes of ancient plant specimens. This doctorate thesis aims to develop and apply new methods to access the genetic information of historical and ancient plant specimens of staple crops such as wheat and quinoa. Using modern genomic techniques such as hybridisation capture, high-throughput sequencing (HTS) and bioinformatic data mining and analysis, I reconstructed the phylogeny and examined the genetic diversity of modern and historical specimens of wheat (Triticum aestivum, T. timopheevii, and T. turgidum) and ancient specimens of quinoa (Chenopodium quinoa). Two newly designed hybridisation capture arrays unearthed a large amount of genetic variability occurring 100 years ago in historical wheat species from Georgia, a region with a significant number of native varieties. Additionally, deep sequencing of ancient quinoa specimens (~1,400 years-old) from the highlands of north Argentina led to the reconstruction of the first known ancient genomes reported from a crop domesticated in South America and identified a bottleneck in the recent history of quinoa. The new knowledge gained provides a potential resource for further research on plant ancient DNA and plant domestication, as well as the investigation of genetic changes that occurred in loci of breeding value.