Gene network simulations provide testable predictions for the molecular domestication syndrome

The domestication of plant species lead to repeatable morphological evolution, often referred to as the phenotypic domestication syndrome. Domestication is also associated with important genomic changes, such as the loss of genetic diversity compared to adequately large wild populations, and modifications of gene expression patterns. Here, we explored theoretically the effect of a domestication-like scenario on the evolution of gene regulatory networks. We ran population genetics simulations in which individuals were featured by their genotype (an interaction matrix encoding a gene regulatory network) and their gene expressions, representing the phenotypic level. Our domestication scenario included a population bottleneck and a selection switch mimicking human-mediated directional and canalizing selection, i.e., change in the optimal gene expression level and selection towards more stable expression across environments. We showed that domestication profoundly alters genetic architectures. Based on four examples of plant domestication scenarios, our simulations predict (i) a drop in neutral allelic diversity, (ii) a change in gene expression variance that depends upon the domestication scenario, (iii) transient maladaptive plasticity, (iv) a deep rewiring of the gene regulatory networks, with a trend towards gain of regulatory interactions, and (v) a global increase in the genetic correlations among gene expressions, with a loss of modularity in the resulting coexpression patterns and in the underlying networks. We provide empirically testable predictions on the differences of genetic architectures between wild and domesticated forms. The characterization of such systematic evolutionary changes in the genetic architecture of traits contributes to define a molecular domestication syndrome.

Enhancing green open spaces while conserving local genetic resources: Evaluating growth performance of five native tree species

Enhancing green open spaces in cities and their buffer areas has gained increasing recognition. While creating a more sustainable, liveable, and comfortable environment, green spaces could also provide an effort for plant domestication and conservation. We consider the potential urban greening and conservation action by planting five tree species consisting of one highly valuable and slow-growing species Eusideroxylon zwageri trees from four different origins and four fast-growing species of Duabanga moluccana, Anthocephalus macrophyllus, Duabanga grandifolia, and kayu papaya at the water reserve in suburban Ciherang-Bogor. Growth performance on mortality rate and the average height of the 4.5-year-old planted seedlings were observed to evaluate the adaptability and suitability of the species in the area. The results of mortality rate revealed that E. zwageri seedlings were ranged from 35% (from South Kalimantan) to 50% (from Jambi), while the four fast-growing species were ranged from 14% (Kayu papaya) to 83% (Duabanga moluccana) indicated that the mortality rate for the five species of seedlings planted varied. Whereas, the results of average height showed that E. zwageri seedlings were ranged from 196.15 cm (South Kalimantan) to 332.50 cm (Natuna), and four fast-growing species was ranged from 582.35 cm (Duabanga grandiflora) to 1411.10 cm (Anthocephalus macrophyllus) indicated that planting fast-growing trees in the suburban area is suitable to increase land coverage in a relatively short time, while slow-growing species are more suitable for species preservation purposes.

Medicinal plant domestication of kayu ules (Helicteres isora Linn.) through stem cuttings: An additional prospective livelihood for the farmer at Bosen Village, East Nusa Tenggara, Indonesia

Kayu ules (Helicteres isora) or screw tree has bioactive compounds benefiting for anti-diabetes, antioxidant and antibacterial. In Indonesia, the fruits have been commercially harnessed for traditional medicine. The benefit of kayu ules has attracted some farmers to evolve this species in their garden, however, the domestication technique has not mastered well yet. Therefore, this study aimed to domesticate kayu ules under a home garden (HG) and analyze the feasibility of cultivating kayu ules through stem cuttings. Kayu ules development underwent two split HG’s: tree shade (HG1) and open area (HG2). Other nursery performances at each home garden were made with no shade (N1), with shading net (N2) and a coco-leaf shade (N3). The result showed that within 60 days on HG1, the best survival was on N2 with 76% of survival and declined on N1 at 30%. Conversely, under HG2, N1 gave the best survival compared to N2, 81% and 46% each. Meanwhile, N3 was in between N1 and N2 on HG1 (56%) and HG2 (58%). The shading treatments, which allowed 20 to 40 % sunlight to pass through, effectively increased the survival of stem cuttings. According to an online market platform at the highest price, nursery N1 delivered the highest IRR at 106% and the second was on N3, followed by N2, which were 104% and 85%, respectively.

Changes in "natural antibiotic" metabolite composition during tetraploid wheat domestication

Gramineous plants protect their seeds from a variety of biotic stresses by producing toxic and deterrent secondary metabolites such as benzoxazinoids. It is unclear how the composition and abundance of these natural toxins has changed over the course of crop-plant domestication. To address this uncertainty, we characterized differences in metabolic levels of benzoxazinoids and their derivatives, between four lines of tetraploid wheat: wild emmer wheat (WEW), the direct progenitor of modern wheat; non-fragile domesticated emmer wheat (DEW), which was first domesticated about 11,000 years ago; the subsequently developed non-fragile and free-threshing durum landraces (LD); and modern durum (MD) varieties. Three-dimensional principal component analysis of mass spectrometry data of wheat metabolites showed with high resolution clear differences between metabolic profiles of WEW, DEW, and durum (LD + MD) and similarity in the metabolic profiles of the two durum lines (LD and MD) that is coherent with the phylogenetic relationship between the corresponding wheat lines. Moreover, our results indicated that some secondary metabolites involved in plant defense mechanisms became significantly more abundant during wheat domestication, while other defensive metabolites decreased or were lost. These metabolic changes reflect the beneficial or detrimental roles the corresponding metabolites might play during the domestication of three taxonomic subspecies of tetraploid wheat (Triticum turgidum).

Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of fruit trees in the Mediterranean

Intense research efforts on phylogeography over the last two decades uncovered major biogeographical trends and renewed our understandings of plant domestication in the Mediterranean. We aim to investigate the evolutionary history and the origin of domestication of the carob tree that has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to identify carob evolutionary units (CEUs) based on genetic diversity structure and geography. We investigated genome-wide diversity and evolutionary patterns of the CEUs with 3557 SNPs generated by restriction-site associated DNA sequencing (RADseq). The 56 populations sampled across the Mediterranean basin, classified as natural, semi-natural or cultivated, were examined. Although, RADseq data are consistent with previous studies identifying a strong West-to-East genetic structure and considerable admixture in some geographic parts, we reconstructed a new phylogeographic scenario with two migration routes occurring from a single refugium likely located in South-Western Morocco. Our results do not favour the regionally bound or single origin of domestication. Indeed, our findings support a cultivation model of locally selected wild genotypes, albeit punctuated by long-distance westward dispersals of domesticated varieties by humans, concomitant with major cultural waves by Romans and Arabs in the regions of dispersal. Ex-situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in South-Western Morocco, South Spain and Eastern Mediterranean. Our study underscores the relevance of natural and seminatural habitats of Mediterranean forests and their refugia in the conservation efforts of tree crops.

Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria

While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.