Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops

Abstract

The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.

Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

“…Similarly, the primary material used for DNA extraction includes a whole variety of tissues, such as fruits, seeds, leaves, and woods, preserved in a wide range of conditions, including charred, waterlogged, desiccated, or mineralized remains. Ancient DNA from organelles, which have sequences that are highly conserved among plant species and which is generally better preserved than the nuclear genome, have been widely used in paleogenomics studies on plants over the past decade [137]. Such organellar DNAs include ribosomal (rDNA) and chloroplast (cpDNA) markers such as the rbcL gene (which encodes the large subunit of ribulose-1,5-bisphosphate carboxylase, an important enzyme in photosynthesis), trn introns and spacers (which offer more variable non-coding information), and matK (the maturase K) gene.…”

An Intimate Relationship Between Eriophyoid Mites and Their Host Plants – A Review

“…Mite-plant interactions can be influenced by the environment through its effect on the plant status, i.e., drought stress (Ximenez-Embun et al, 2017; Santamaria et al, 2018), and this aspect appear of particular importance for eriophyoids. Potentially, the results could be used to exploit genomic information and new technologies to accelerate breeding program for resistance and tolerance in crops infested by eriophyoids (Salinas et al, 2013; Martel et al, 2015; Díaz-Riquelme et al, 2016; Gascuel et al, 2017; Karkute et al, 2017; di Donato et al, 2018; Haque et al, 2018). One of the main limitation for the implementation of these types of studies on eriophyoids is the absence of efficient mass rearing methods on artificial substrates (Cazaux et al, 2014; Jonckheere et al, 2016) for which cooperation between plant and mite scientists is needed for its development.…”

A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history

“…This may represent incomplete sampling (particularly from Africa and Arabia) or extinct ancient variation. As has been recently suggested 49 , ancient alleles lost in modern domesticates might be targeted for re-introduction from the wild to boost crop improvement.…”