Growing larger with domestication: a matter of physiology, morphology or allocation?

Arabidopsis CDF3 transcription factor increases carbon and nitrogen assimilation and yield in trans-grafted tomato plants

Grafting in tomato (Solanum lycopersicum L.) has mainly been used to prevent damage by soil-borne pathogens and the negative effects of abiotic stresses, although productivity and fruit quality can also be enhanced using high vigor rootstocks. In the context of a low nutrients input agriculture, the grafting of elite cultivars onto rootstocks displaying higher Nitrogen Use Efficiency (NUE) supports a direct strategy for yield maximization. In this study we assessed the use of plants overexpressing the Arabidopsis (AtCDF3) or tomato (SlCDF3) CDF3 genes, previously reported to increase NUE in tomato, as rootstocks to improve yield in the grafted scion under low N inputs. We found that the AtCDF3 gene induced greater production of sugars and amino acids, which allowed for greater biomass and fruit yield under both sufficient and limiting N supplies. Conversely, no positive impact was found with the SlCDF3 gene. Hormone analyses suggest that gibberellins (GA4), auxin and cytokinins (tZ) might be involved in the AtCDF3 responses to N. The differential responses triggered by the two genes could be related, at least in part, to the mobility of the AtCDF3 transcript through the phloem to the shoot. Consistently, a higher expression of the target genes of the transcription factor, such as glutamine synthase 2 (SlGS2) and GA oxidase 3 (SlGA3ox), involved in amino acid and gibberellin biosynthesis, respectively, was observed in the leaves of this graft combination. Altogether, our results provided further insights into the mode of action of CDF3 genes and their biotechnology potential for transgrafting approaches.

Diversification of quantitative morphological traits in wheat

BACKGROUND AND AIMS

The development and morphology of crop plants have been profoundly altered by evolution under cultivation, initially through unconscious selection, without deliberate foresight, and later by directed breeding. Wild wheats remain an important potential source of variation for modern breeders; however, the sequence and timing of morphological changes during domestication are not fully resolved.

METHODS

We grew and measured 142 wheat accessions representing different stages in wheat evolution, including three independent domestication events, and compared their morphological traits to define the morphospace of each group.

KEY RESULTS

The results show that wild and domesticated wheats have overlapping morphospaces, but each also occupies a distinct area of morphospace from one another. Polyploid formation in wheat increased leaf biomass and seed weight but had its largest effects on tiller loss. Domestication continued to increase the sizes of wheat leaves and seeds and made wheat grow taller, with more erect architecture. Associated changes to the biomass of domesticated wheats generated more grains and achieved higher yields. Landrace improvement subsequently decreased the numbers of tillers and spikes, to focus resource allocation to the main stem, accompanied by a thicker main stem and larger flag leaves. During the Green Revolution, wheat height was reduced to increase the harvest index and therefore yield. Modern wheats also have more erect leaves and larger flower biomass proportions than landraces.

CONCLUSIONS

Quantitative trait history in wheat differs by trait. Some trait values show progressive changes in the same direction (e.g. leaf size, grain weight), whereas others change in a punctuated way at particular stages (e.g. canopy architecture), and other trait values switch directions during wheat evolution (e.g. plant height, flower biomass proportion). Agronomically valued domestication traits arose during different stages of wheat history, such that modern wheats are the product of >10 000 years of morphological evolution.

Early human selection of crops' wild progenitors explains the acquisitive physiology of modern cultivars

Crops have resource-acquisitive leaf traits, which are usually attributed to the process of domestication. However, early choices of wild plants amenable for domestication may also have played a key role in the evolution of crops' physiological traits. Here we compiled data on 1,034 annual herbs to place the ecophysiological traits of 69 crops' wild progenitors in the context of global botanical variation, and we conducted a common-garden experiment to measure the effects of domestication on crop ecophysiology. Our study found that crops' wild progenitors already had high leaf nitrogen, photosynthesis, conductance and transpiration and soft leaves. After domestication, ecophysiological traits varied little and in idiosyncratic ways. Crops did not surpass the trait boundaries of wild species. Overall, the resource-acquisitive strategy of crops is largely due to the inheritance from their wild progenitors rather than to further breeding improvements. Our study concurs with recent literature highlighting constraints of crop breeding for faster ecophysiological traits.

The ORGAN SIZE (ORG) locus modulates both vegetative and reproductive gigantism in domesticated tomato

BACKGROUND AND AIMS

Gigantism is a key component of the domestication syndrome, a suite of traits that differentiates crops from their wild relatives. Allometric gigantism is strongly marked in horticultural crops, causing disproportionate increases in the size of edible parts such as stems, leaves or fruits. Tomato (Solanum lycopersicum) has attracted attention as a model for fruit gigantism, and many genes have been described controlling this trait. However, the genetic basis of a corresponding increase in size of vegetative organs contributing to isometric gigantism has remained relatively unexplored.

METHODS

Here, we identified a 0.4-Mb region on chromosome 7 in introgression lines (ILs) from the wild species Solanum pennellii in two different tomato genetic backgrounds (cv. 'M82' and cv. 'Micro-Tom') that controls vegetative and reproductive organ size in tomato. The locus, named ORGAN SIZE (ORG), was fine-mapped using genotype-by-sequencing. A survey of the literature revealed that ORG overlaps with previously mapped quantitative trait loci controlling tomato fruit weight during domestication.

KEY RESULTS

Alleles from the wild species led to lower cell number in different organs, which was partially compensated by greater cell expansion in leaves, but not in fruits. The result was a proportional reduction in leaf, flower and fruit size in the ILs harbouring the alleles from the wild species.

CONCLUSIONS

Our findings suggest that selection for large fruit during domestication also tends to select for increases in leaf size by influencing cell division. Since leaf size is relevant for both source-sink balance and crop adaptation to different environments, the discovery of ORG could allow fine-tuning of these parameters.

Increased stomatal conductance and leaf biochemical capacity, not mesophyll conductance, contributing to the enhanced photosynthesis in Oryza plants during domestication

MAIN CONCLUSION

Leaf biochemical capacity and the ratio of leaf biochemical capacity to stomatal conductance are promising to enhance leaf photosynthetic rate and water use efficiency in rice plants, respectively. Domestication may have great impact on crop photosynthetic rate, which has not been fully understood, especially from the perspective of stomatal conductance, mesophyll conductance, and leaf biochemical capacity simultaneously. In this study, we constructed a database consisting of 141 and 92 sets of data from wild and cultivated rice, respectively, including leaf gas exchange parameters, hydraulic conductance, structural traits, and nitrogen content. We found that, compared to wild rice, enhanced leaf photosynthetic rate in cultivated rice was mainly resulted by the increased stomatal conductance and leaf biochemical capacity, rather than mesophyll conductance. The unchanged mesophyll conductance observed during domestication suggested that it might have been optimized during plant evolution in wild rice. Additionally, the positive relationship between stomatal density and stomatal conductance disappeared in Oryza plants during domestication, suggesting that stomatal conductance in cultivated rice is less restricted by stomatal density, compared to wild rice. Moreover, in both wild and cultivated rice, leaf photosynthetic rate was mainly determined by leaf biochemical capacity, rather than stomatal conductance and mesophyll conductance. This study highlighted the important role of stomatal conductance and leaf biochemical capacity in improvement of leaf photosynthetic rate in rice during domestication. Leaf biochemical capacity and the ratio of leaf biochemical capacity to stomatal conductance should be further investigated to enhance leaf photosynthetic rate and water use efficiency in rice plants, respectively.

Plant trait relationships are maintained within a major crop species: lack of artificial selection signal and potential for improved agronomic performance

The exploration of phenotypic spaces of large sets of plant species has considerably increased our understanding of diversification processes in the plant kingdom. Nevertheless, such advances have predominantly relied on interspecific comparisons that hold several limitations. Here, we grew in the field a unique set of 179 inbred lines of durum wheat, Triticum turgidum spp. durum, characterized by variable degrees of artificial selection. We measured aboveground and belowground traits as well as agronomic traits to explore the functional and agronomic trait spaces and to investigate trait-to-agronomic performance relationships. We showed that the wheat functional trait space shared commonalities with global cross-species spaces previously described, with two main axes of variation: a root foraging axis and a slow-fast trade-off axis. Moreover, we detected a clear signature of artificial selection on the variation of agronomic traits, unlike functional traits. Interestingly, we identified alternative phenotypic combinations that can optimize crop performance. Our work brings insightful knowledge about the structure of phenotypic spaces of domesticated plants and the maintenance of phenotypic trade-offs in response to artificial selection, with implications for trade-off-free and multi-criteria selection in plant breeding.

Morphometric approaches to Cannabis evolution and differentiation from archaeological sites: interpreting the archaeobotanical evidence from bronze age Haimenkou, Yunnan

Cannabis grains are frequently reported from archaeological sites in Asia, and hypothesized centers of origins are China and Central Asia. Chinese early cannabis remains are often interpreted as evidence of hemp fabric production, in line with early textual evidence describing ritualistic hemp cloth use and hemp cultivation as a grain crop. Modern measurements on cannabis varieties show distinct sizes between fibre or oil/fibre and psychoactive varieties, the former having larger seeds on average than the latter. This paper reviews the current macro-botanical evidence for cannabis across East, Central and South Asia and builds a comparative framework based on modern cannabis seed measurements to help identify cannabis use in the past, through the metric analysis of archaeologically preserved seeds. Over 800 grains of cannabis were retrieved from the 2008 excavation of Haimenkou, Yunnan, Southwest China, dating to between 1650 and 400 bc. These are compared with other known archaeological cannabis and interpreted through the metric framework. This offers a basis for exploration of the seed morphometrics potential to infer cannabis cultivation and diversification in uses. At Haimenkou, cannabis seeds size mostly plot in the range of overlapping psychoactive/fibre types; we therefore suggest that the cannabis assemblage from Haimenkou is indicative of a crop beginning to undergo evolution from its early domesticated form towards a diversified crop specialized for alternative uses, including larger oilseed/fibre adapted varieties.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00334-023-00966-6.

Changes in crop trait plasticity with domestication history: Management practices matter

Crop domestication has led to the development of distinct trait syndromes, a series of constrained plant trait trade-offs to maximize yield in high-input agricultural environments, and potentially constrained trait plasticity. Yet, with the ongoing transition to organic and diversified agroecosystems, which create more heterogeneous nutrient availability, this constrained plasticity, especially in root functional traits, may be undesirable for nutrient acquisition. Such agricultural systems require a nuanced understanding of the soil-crop continuum under organic amendments and with intercropping, and the role crop genetic resources play in governing nutrient management and design. In this study, we use a functional traits lens to determine if crops with a range of domestication histories express different functional trait plasticity and how this expression changes with soil amendments and intercropping. We utilize a common garden experiment including five wheat (Triticum aestivum) varietals with a range of domestication histories planted in a factorial combination with amendment type (organic and inorganic) and cropping design (monoculture or intercropped with soybean). We use bivariate, multivariate and trait space analyses to quantify trait variation and plasticity in five leaf and five root functional traits. Almost all leaf and root traits varied among varieties. Yet, amendment type was nearly inconsequential for explaining trait expression across varieties. However, intercropping was linked to significant differences in root acquisitive strategies, regardless of the varietals' distinct history. Our findings show substantial leaf and root trait plasticity, with roots expressing greater trait space occupation with domestication, but also the strong role of management in crop trait expression. We underscore the utility of a functional trait-based approach to understand plant-soil dynamics with organic amendments, as well as the role of crop genetic histories in the successful transition to low-input and diversified agroecosystems.

Unpredicted, rapid and unintended structural and functional changes occurred during early domestication of Silphium integrifolium, a perennial oilseed

MAIN CONCLUSION

Selection for increased yield changed structure, physiology and overall resource-use strategy from conservative towards acquisitive leaves. Alternative criteria can be considered, to increase yield with less potentially negative traits. We compared the morphology, anatomy and physiology of wild and semi-domesticated (SD) accessions of Silphium integrifolium (Asteraceae), in multi-year experiments. We hypothesized that several cycles of selection for seed-yield would result in acquisitive leaves, including changes predicted by the leaf economic spectrum. Early-selection indirectly resulted in leaf structural and functional changes. Leaf anatomy changed, increasing mesophyll conductance and the size of xylem vessels and mesophyll cells increased. Leaves of SD plants were larger, heavier, with lower stomatal conductance, lower internal CO₂ concentration, and lower resin concentration than those of wild types. Despite increased water use efficiency, SD plants transpired 25% more because their increase in leaf area. Unintended and undesired changes in functional plant traits could quickly become fixed during domestication, shortening the lifespan and increasing resource consumption of the crop as well as having consequences in the provision and regulation of ecosystem services.

Does Domestication Affect Structural and Functional Leaf Epidermal Traits? A Comparison between Wild and Cultivated Mexican Chili Peppers (Capsicum annuum)

During domestication, lineages diverge phenotypically and genetically from wild relatives, particularly in preferred traits. In addition to evolutionary divergence in selected traits, other fitness-related traits that are unselected may change in concert. For instance, the selection of chili pepper fruits was not intended to change the structure and function of the leaf epidermis. Leaf stomata and trichome densities play a prominent role in regulating stomatal conductance and resistance to herbivores. Here, we assessed whether domestication affected leaf epidermis structure and function in Capsicum annuum. To do this, we compared leaf stomata and trichome densities in six cultivated varieties of Mexican Capsicum annuum and their wild relative. We measured stomatal conductance and resistance to herbivores. Resistance to (defense against) herbivores was measured as variation in the herbivory rate and larvae mortality of Spodoptera frugiperda fed with leaves of wild and cultivated plants. As expected, the different varieties displayed low divergence in stomatal density and conductance. Leaf trichome density was higher in the wild relative, but variation was not correlated with the herbivory rate. In contrast, a higher mortality rate of S. frugiperda larvae was recorded when fed with the wild relative and two varieties than larvae fed with four other varieties. Overall, although domestication did not aim at resistance to herbivores, this evolutionary process produced concerted changes in defensive traits.

Leaf trait covariation and controls on leaf mass per area (LMA) following cotton domestication

BACKGROUND AND AIMS

The process of domestication has driven dramatic shifts in plant functional traits, including leaf mass per area (LMA). It remains unclear whether domestication has produced concerted shifts in the lower-level anatomical traits that underpin LMA and how these traits in turn affect photosynthesis.

METHODS

In this study we investigated controls of LMA and leaf gas exchange by leaf anatomical properties at the cellular, tissue and whole-leaf levels, comparing 26 wild and 31 domesticated genotypes of cotton (Gossypium).

KEY RESULTS

As expected, domesticated plants expressed lower LMA, higher photosynthesis and higher stomatal conductance, suggesting a shift towards the 'faster' end of the leaf economics spectrum. At whole-leaf level, variation in LMA was predominantly determined by leaf density (LD) both in wild and domesticated genotypes. At tissue level, higher leaf volume per area (Vleaf) in domesticated genotypes was driven by a simultaneous increase in the volume of epidermal, mesophyll and vascular bundle tissue and airspace, while lower LD resulted from a lower volume of palisade tissue and vascular bundles (which are of high density), paired with a greater volume of epidermis and airspace, which are of low density. The volume of spongy mesophyll exerted direct control on photosynthesis in domesticated genotypes but only indirect control in wild genotypes. At cellular level, a shift to larger but less numerous cells with thinner cell walls underpinned a lower proportion of cell wall mass, and thus a reduction in LD.

CONCLUSIONS

Taken together, cotton domestication has triggered synergistic shifts in the underlying determinants of LMA but also photosynthesis, at cell, tissue and whole-leaf levels, resulting in a marked shift in plant ecological strategy.

Environment of origin and domestication affect morphological, physiological, and agronomic response to water deficit in chile pepper (Capsicum sp.)

Global climate change is having a significant effect on agriculture by causing greater precipitation variability and an increased risk of drought. To mitigate these effects, it is important to identify specific traits, adaptations, and germplasm that improve tolerance to soil water deficit. Local varieties, known as landraces, have undergone generations of farmer-mediated selection and can serve as sources of variation, specifically for tolerance to abiotic stress. Landraces can possess local adaptations, where accessions adapted to a particular environment will outperform others grown under the same conditions. We explore adaptations to water deficit in chile pepper landraces from across an environmental gradient in Mexico, a center of crop domestication and diversity, as well in improved varieties bred for the US. In the present study, we evaluated 25 US and Mexico accessions in a greenhouse experiment under well-watered and water deficit conditions and measured morphological, physiological, and agronomic traits. Accession and irrigation regime influenced plant biomass and height, while branching, CO2 assimilation, and fruit weight were all influenced by an interaction between accession and irrigation. A priori group contrasts revealed possible adaptations to water deficit for branching, CO2 assimilation, and plant height associated with geographic origin, domestication level, and pepper species. Additionally, within the Mexican landraces, the number of primary branches had a strong relationship with precipitation from the environment of origin. This work provides insight into chile pepper response to water deficit and adaptation to drought and identifies possibly tolerant germplasm.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F_2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F_2:3 population in a Kenyan field trial. The F_2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.

Disparities among crop species in the evolution of growth rates: the role of distinct origins and domestication histories

Growth rates vary widely among plants with different strategies. For crops, evolution under predictable and high-resource environments might favour rapid resource acquisition and growth, but whether this strategy has consistently evolved during domestication and improvement remains unclear. Here we report a comprehensive study of the evolution of growth rates based on comparisons among wild, landrace, and improved accessions of 19 herbaceous crops grown under common conditions. We also examined the underlying growth components and the influence of crop origin and history on growth evolution. Domestication and improvement did not affect growth consistently, that is growth rates increased or decreased or remained unchanged in different crops. Crops selected for fruits increased the physiological component of growth (net assimilation rate), whereas leaf and seed crops showed larger domestication effects on morphology (leaf mass ratio and specific leaf area). Moreover, climate and phylogeny contributed to explaining the effects of domestication and changes in growth. Crop-specific responses to domestication and improvement suggest that selection for high yield has not consistently changed growth rates. The trade-offs between morpho-physiological traits and the distinct origins and histories of crops accounted for the variability in growth changes. These findings have far-reaching implications for our understanding of crop performance and adaptation.

Crop Domestication, Root Trait Syndromes, and Soil Nutrient Acquisition in Organic Agroecosystems: A Systematic Review

Selecting crops that express certain reproductive, leaf, and root traits has formed detectable, albeit diverse, crop domestication syndromes. However, scientific and informal on-farm research has primarily focused on understanding and managing linkages between only certain domestication traits and yield. There is strong evidence suggesting that functional traits can be used to hypothesize and detect trade-offs, constraints, and synergies among crop yield and other aspects of crop biology and agroecosystem function. Comparisons in the functional traits of crops vs. wild plants has emerged as a critical avenue that has helped inform a better understanding of how plant domestication has reshaped relationships among yield and traits. For instance, recent research has shown domestication has led important economic crops to express extreme functional trait values among plants globally, with potentially major implications for yield stability, nutrient acquisition strategies, and the success of ecological nutrient management. Here, we present an evidence synthesis of domestication effects on crop root functional traits, and their hypothesized impact on nutrient acquisition strategies in organic and low input agroecosystems. Drawing on global trait databases and published datasets, we show detectable shifts in root trait strategies with domestication. Relationships between domestication syndromes in root traits and nutrient acquisition strategies in low input systems underscores the need for a shift in breeding paradigms for organic agriculture. This is increasingly important given efforts to achieve Sustainable Development Goal (SDG) targets of Zero Hunger via resilient agriculture practices such as ecological nutrient management and maintenance of genetic diversity.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

Comparative Analysis of Early Life Stage Traits in Annual and Perennial Phaseolus Crops and Their Wild Relatives

Herbaceous perennial species are receiving increased attention for their potential to provide both edible products and ecosystem services in agricultural systems. Many legumes (Fabaceae Lindl.) are of special interest due to nitrogen fixation carried out by bacteria in their roots and their production of protein-rich, edible seeds. However, herbaceous perennial legumes have yet to enter widespread use as pulse crops, and the response of wild, herbaceous perennial species to artificial selection for increased seed yield remains under investigation. Here we compare cultivated and wild accessions of congeneric annual and herbaceous perennial legume species to investigate associations of lifespan and cultivation with early life stage traits including seed size, germination, and first year vegetative growth patterns, and to assess variation and covariation in these traits. We use "cultivated" to describe accessions with a history of human planting and use, which encompasses a continuum of domestication. Analyses focused on three annual and four perennial species of the economically important genus Phaseolus. We found a significant association of both lifespan and cultivation status with seed size (weight, two-dimensional lateral area, length), node number, and most biomass traits (with cultivation alone showing additional significant associations). Wild annual and perennial accessions primarily showed only slight differences in trait values. Relative to wild forms, both cultivated annual and cultivated perennial accessions exhibited greater seed size and larger overall vegetative size, with cultivated perennials showing greater mean trait differences relative to wild accessions than cultivated annuals. Germination proportion was significantly lower in cultivated relative to wild annual accessions, while no significant difference was observed between cultivated and wild perennial germination. Regardless of lifespan and cultivation status, seed size traits were positively correlated with most vegetative traits, and all biomass traits examined here were positively correlated. This study highlights some fundamental similarities and differences between annual and herbaceous perennial legumes and provides insights into how perennial legumes might respond to artificial selection compared to annual species.

Plant domestication disrupts biodiversity effects across major crop types

Plant diversity fosters productivity in natural ecosystems. Biodiversity effects might increase agricultural yields at no cost in additional inputs. However, the effects of diversity on crop assemblages are inconsistent, probably because crops and wild plants differ in a range of traits relevant to plant-plant interactions. We tested whether domestication has changed the potential of crop mixtures to over-yield by comparing the performance and traits of major crop species and those of their wild progenitors under varying levels of diversity. We found stronger biodiversity effects in mixtures of wild progenitors, due to larger selection effects. Variation in selection effects was partly explained by within-mixture differences in leaf size. Our results indicate that domestication might disrupt the ability of crops to benefit from diverse neighbourhoods via reduced trait variance. These results highlight potential limitations of current crop mixtures to over-yield and the potential of breeding to re-establish variance and increase mixture performance.

Diversity of a wall-associated kinase gene in wild and cultivated barley

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.

Phylogenetic patterns and phenotypic profiles of the species of plants and mammals farmed for food

The origins of agriculture were key events in human history, during which people came to depend for their food on small numbers of animal and plant species. However, the biological traits determining which species were domesticated for food provision, and which were not, are unclear. Here, we investigate the phylogenetic distribution of livestock and crops, and compare their phenotypic traits with those of wild species. Our results indicate that phylogenetic clustering is modest for crop species but more intense for livestock. Domesticated species explore a reduced portion of the phenotypic space occupied by their wild counterparts and have particular traits in common. For example, herbaceous crops are globally characterized by traits including high leaf nitrogen concentration and tall canopies, which make them fast-growing species and proficient competitors. Livestock species are relatively large mammals with low basal metabolic rates, which indicate moderate to slow life histories. Our study therefore reveals ecological differences in domestication potential between plants and mammals. Domesticated plants belong to clades with traits that are advantageous in intensively managed high-resource habitats, whereas domesticated mammals are from clades adapted to moderately productive environments. Combining comparative phylogenetic methods with ecologically relevant traits has proven useful to unravel the causes and consequences of domestication.

Impacts of domestication on the arbuscular mycorrhizal symbiosis of 27 crop species

The arbuscular mycorrhizal (AM) symbiosis is key to plant nutrition, and hence is potentially key in sustainable agriculture. Fertilization and other agricultural practices reduce soil AM fungi and root colonization. Such conditions might promote the evolution of low mycorrhizal responsive crops. Therefore, we ask if and how evolution under domestication has altered AM symbioses of crops. We measured the effect of domestication on mycorrhizal responsiveness across 27 crop species and their wild progenitors. Additionally, in a subset of 14 crops, we tested if domestication effects differed under contrasting phosphorus (P) availabilities. The response of AM symbiosis to domestication varied with P availability. On average, wild progenitors benefited from the AM symbiosis irrespective of P availability, while domesticated crops only profited under P-limited conditions. Magnitudes and directions of response were diverse among the 27 crops, and were unrelated to phylogenetic affinities or to the coordinated evolution with fine root traits. Our results indicate disruptions in the efficiency of the AM symbiosis linked to domestication. Under high fertilization, domestication could have altered the regulation of resource trafficking between AM fungi and associated plant hosts. Provided that crops are commonly raised under high fertilization, this result has important implications for sustainable agriculture.

The Domestication of the Amazon Tree Grape (Pourouma cecropiifolia) Under an Ecological Lens

Domestication studies traditionally focus on the differences in morphological characteristics between wild and domesticated populations that are under direct selection, the components of the domestication syndrome. Here, we consider that other aspects can be modified, because of the interdependence between plant characteristics and the forces of natural selection. We investigated the ongoing domestication of Pourouma cecropiifolia populations cultivated by the Ticuna people in Western Amazonia, using traditional and ecological approaches. We compared fruit characteristics between wild and domesticated populations to quantify the direct effects of domestication. To examine the characteristics that are not under direct selection and the correlated effects of human selection and natural selection, we investigated the differences in vegetative characteristics, changes in seed:fruit allometric relations and the relations of these characteristics with variation in environmental conditions summarized in a principal component analysis. Domestication generated great changes in fruit characteristics, as expected in fruit crops. The fruits of domesticated plants had 20× greater mass and twice as much edible pulp as wild fruits. The plant height:DBH ratio and wood density were, respectively, 42% and 22% smaller in domesticated populations, probably in response to greater luminosity and higher sand content of the cultivated landscapes. Seed:fruit allometry was modified by domestication: although domesticated plants have heavier seeds, the domesticated fruits have proportionally (46%) smaller seed mass compared to wild fruits. The high light availability and poor soils of cultivated landscapes may have contributed to seed mass reduction, while human selection promoted seed mass increase in correlation with fruit mass increase. These contrasting effects generated a proportionately smaller increase in seed mass in domesticated plants. In this study, it was not possible to clearly dissociate the environmental effects from the domestication effects in changes in morphological characteristics, because the environmental conditions were intensively modified by human management, showing that plant domestication is intrinsically related to landscape domestication. Our results suggest that evaluation of environmental conditions together with human selection on domesticated phenotypes provide a better understanding of the changes generated by domestication in plants.

Unconscious selection drove seed enlargement in vegetable crops

Domesticated grain crops evolved from wild plants under human cultivation, losing natural dispersal mechanisms to become dependent upon humans, and showing changes in a suite of other traits, including increasing seed size. There is tendency for seed enlargement during domestication to be viewed as the result of deliberate selection for large seeds by early farmers. However, like some other domestication traits, large seeds may have evolved through natural selection from the activities of people as they gathered plants from the wild, or brought them into cultivation in anthropogenic settings. Alternatively, larger seeds could have arisen via pleiotropic effects or genetic linkage, without foresight from early farmers, and driven by selection that acted on other organs or favored larger plants. We have separated these unconscious selection effects on seed enlargement from those of deliberate selection, by comparing the wild and domesticated forms of vegetable crops. Vegetables are propagated by planting seeds, cuttings, or tubers, but harvested for their edible leaves, stems, or roots, so that seed size is not a direct determinant of yield. We find that landrace varieties of seven vegetable crops have seeds that are 20% to 2.5‐times larger than those of their closest wild relatives. These domestication effect sizes fall completely within the equivalent range of 14% to 15.2‐times for grain crops, although domestication had a significantly larger overall effect in grain than vegetable crops. Seed enlargement in vegetable crops that are propagated vegetatively must arise from natural selection for larger seeds on the occasions when plants recruit from seed and are integrated into the crop gene pool, or via a genetic link to selection for larger plants or organs. If similar mechanisms operate across all species, then unconscious selection during domestication could have exerted stronger effects on the seed size of our staple crops than previously realized.