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

Plants cultivated for ecosystem restoration can evolve toward a domestication syndrome

The UN Decade on Ecosystem Restoration calls for upscaling restoration efforts, but many terrestrial restoration projects are constrained by seed availability. To overcome these constraints, wild plants are increasingly propagated on farms to produce seeds for restoration projects. During on-farm propagation, the plants face non-natural conditions with different selection pressures, and they might evolve adaptations to cultivation that parallel those of agricultural crops, which could be detrimental to restoration success. To test this, we compared traits of 19 species grown from wild-collected seeds to those from their farm-propagated offspring of up to four cultivation generations, produced by two European seed growers, in a common garden experiment. We found that some plants rapidly evolved across cultivated generations towards increased size and reproduction, lower within-species variability, and more synchronized flowering. In one species, we found evolution towards less seed shattering. These trait changes are typical signs of the crop domestication syndrome, and our study demonstrates that it can also occur during cultivation of wild plants, within only few cultivated generations. However, there was large variability between cultivation lineages, and the observed effect sizes were generally rather moderate, which suggests that the detected evolutionary changes are unlikely to compromise farm-propagated seeds for ecosystem restoration. To mitigate the potential negative effects of unintended selection, we recommend to limit the maximum number of generations the plants can be cultivated without replenishing the seed stock from new wild collections.

Complex migration history is revealed by genetic diversity of tomato samples collected in Italy during the eighteenth and nineteenth centuries

Native to South America, the tomato is now grown almost worldwide. During its domestication and improvement, important selection signatures were fixed in certain agronomic and adaption traits. Such traits include fruit morphology, which became a major target for selection over the centuries. However, little is known about precisely when some mutations arose and how they spread through the germplasm. For instance, elongated fruit variants, originating both via mutations in SUN and OVATE genes, may have arisen prior to domestication or during tomato cultivation in Europe. To gain insights into the tomato admixture and selection pattern, the genome of two tomato herbarium specimens conserved in the Herbarium Porticense (PORUN) was sequenced. Comparison of the DNA of herbarium samples collected in Italy between 1750 and 1890 with that of living tomato accessions yielded insights into the history of tomato loci selection. Interestingly, the genotype of the more recent sample (LEO90), classified in 1890 as the oblungum variety, shows several private variants in loci implicated in fruit shape determination, also present also in wild tomato samples. In addition, LEO90, sampled in the nineteenth century, is genetically more distant from cultivated varieties than the SET17 genotype, collected in the eighteenth century, suggesting that elongated tomato varieties may originate from a cross between a landrace and a wild ancestor. Findings from our study have major implications for the understanding of tomato migration patterns and for the conservation of allelic diversity and loci recovery.

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

Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant^1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture^3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, ¹⁴C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.

The Promise of Paleogenomics Beyond Our Own Species

Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions.

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

How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over deep timescales. A second approach focuses on the direct identification of genomic changes at a shorter timescale by sequencing ancient DNA preserved in subfossil remains. Merged within the nascent field of paleogenomics, these complementary approaches provide insights into the evolutionary forces that shaped the organization and regulation of modern genomes and open novel perspectives in fostering genetic gain in breeding programs and establishing tools to predict future population changes in response to anthropogenic pressure and global warming.

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

Eriophyoid mites (Acari Eriophyoidea) are phytophagous arthropods forming intimate relationships with their host plants. These mites are associated with annual and perennial plants including ferns, and are highly specialized with a dominant monophagy. They can be classified in different ecological classes, i.e., vagrant, gall-making and refuge-seeking species. Many of them are major pests and some of them are vectors of plant pathogens. This paper critically reviews the knowledge on eriophyoids of agricultural importance with emphasis on sources for host plant resistance to these mites. The role of species belonging to the family Eriophyidae as vectors of plant viruses is discussed. Eriophyoid-host plant interactions, the susceptibility within selected crops and main host plant tolerance/resistance mechanisms are discussed. Fundamental concepts, subjects, and problems emerged in this review are pointed out and studies are suggested to clarify some controversial points.