Functional Traits Differ between Cereal Crop Progenitors and Other Wild Grasses Gathered in the Neolithic Fertile Crescent

The reasons why some plant species were selected as crops and others were abandoned during the Neolithic emergence of agriculture are poorly understood. We tested the hypothesis that the traits of Fertile Crescent crop progenitors were advantageous in the fertile, disturbed habitats surrounding early settlements and in cultivated fields. We screened functional traits related to competition and disturbance in a group of grass species that were increasingly exploited by early plant gatherers, and that were later domesticated (crop progenitors); and in a set of grass species for which there is archaeological evidence of gathering, but which were never domesticated (wild species). We hypothesised that crop progenitors would have greater seed mass, growth rate, height and yield than wild species, as these traits are indicative of greater competitive ability, and that crop progenitors would be more resilient to defoliation. Our results show that crop progenitors have larger seed mass than wild species, germinate faster and have greater seedling size. Increased seed size is weakly but positively correlated with a higher growth rate, which is primarily driven by greater biomass assimilation per unit leaf area. Crop progenitors also tend to have a taller stature, greater grain yield and higher resilience to defoliation. Collectively, the data are consistent with the hypothesis that adaptations to competition and disturbance gave crop progenitors a selective advantage in the areas surrounding early human settlements and in cultivated environments, leading to their adoption as crops through processes of unconscious selection.     

Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication

Archaeological remains indicate that the origin of western agriculture occurred in a brief period about 10,500 years ago in a region of the Middle East known as the Fertile Crescent, where the wild progenitors of several key agricultural cereal species are endemic. Domestication entailed the appearance of agronomic traits such as seed size and threshability. For a representative sample of 20 domesticated barley (Hordeum vulgare) lines, including 13 two-rowed and 7 six-rowed varieties, we determined the haplotypes at seven loci-Adh2, Adh3, Amy1, Dhn9, GAPDH, PEPC and WAXY encompassing 5,616 bases per line-and compared them to the haplotypes at the same loci for 25 wild forms (Hordeum spontaneum) collected within and outside the Fertile Crescent. In comparisons of wild versus domesticated barley, the number of haplotypes (70 vs. 17), average nucleotide diversity, pi, (0.0077 vs. 0.0028), and Watterson's theta at silent sites (0.0104 vs. 0.0028) was reduced in domesticated lines. Two loci, Amy1 and PEPC, were monomorphic in domesticated lines; Amy1 and GAPDH produced significant values of Tajima's D. At GAPDH, pi was slightly higher in domesticated than wild forms, due to divergent high-frequency haplotypes; for the remaining six loci, 87% of nucleotide diversity has been lost in the domesticated forms. Bottlenecks acting on neutrally evolving loci either during the domestication process, during subsequent breeding, or both, are sufficient to account for reduced diversity and the results of Tajima's test, without the need to evoke selection at these loci. Phylogenetic networks data uncover distinct wild and domesticated barley genotypes and suggest that barley may have been domesticated in the Jordan valley. Because, based on AFLP data, the domesticated Turkish cultivars had a genetic basis as large as that present in large germplasm collections, all comparisons provided in this paper are of general value more than being restricted to the Turkish barley germplasm.     

DNA sequence diversity and the origin of cultivated safflower (<Emphasis Type="Italic">Carthamus tinctorius</Emphasis>L.; Asteraceae)

Background  

Safflower (Carthamus tinctorius L.) is a diploid oilseed crop whose origin is largely unknown. Safflower is widely believed to have been domesticated over 4,000 years ago somewhere in the Fertile Crescent. Previous hypotheses regarding the origin of safflower have focused primarily on two other species from sect. Carthamus – C. oxyacanthus and C. palaestinus – as the most likely progenitors, although some attention has been paid to a third species (C. persicus) as a possible candidate. Here, we describe the results of a phylogenetic analysis of the entire section using data from seven nuclear genes.     

Origin and domestication of the fungal wheat pathogen Mycosphaerella graminicola via sympatric speciation

The Fertile Crescent represents the center of origin and earliest known place of domestication for many cereal crops. During the transition from wild grasses to domesticated cereals, many host-specialized pathogen species are thought to have emerged. A sister population of the wheat-adapted pathogen Mycosphaerella graminicola was identified on wild grasses collected in northwest Iran. Isolates of this wild grass pathogen from 5 locations in Iran were compared with 123 M. graminicola isolates from the Middle East, Europe, and North America. DNA sequencing revealed a close phylogenetic relationship between the pathogen populations. To reconstruct the evolutionary history of M. graminicola, we sequenced 6 nuclear loci encompassing 464 polymorphic sites. Coalescence analyses indicated a relatively recent origin of M. graminicola, coinciding with the known domestication of wheat in the Fertile Crescent around 8,000-9,000 BC. The sympatric divergence of populations was accompanied by strong genetic differentiation. At the present time, no genetic exchange occurs between pathogen populations on wheat and wild grasses although we found evidence that gene flow may have occurred since genetic differentiation of the populations.     

Molecular diversity at 18 loci in 321 wild and 92 domesticate lines reveal no reduction of nucleotide diversity during Triticum monococcum (Einkorn) domestication: implications for the origin of agriculture

The diploid wheat Triticum monococcum L. (einkorn) was among the first crops domesticated by humans in the Fertile Crescent 10,000 years ago. During the last 5,000 years, it was replaced by tetraploid and hexaploid wheats and largely forgotten by modern breeders. Einkorn germplasm is thus devoid of breeding bottlenecks and has therefore preserved in unfiltered form the full spectrum of genetic variation that was present during its domestication. We investigated haplotype variation among >12 million nucleotides sequenced at 18 loci across 321 wild and 92 domesticate T. monococcum lines. In contrast to previous studies of cereal domestication, we sampled hundreds of wild lines, rather than a few dozen. Unexpectedly, our broad sample of wild lines reveals that wild einkorn underwent a process of natural genetic differentiation, most likely an incipient speciation, prior to domestication. That natural differentiation was previously overlooked within wild einkorn, but it bears heavily upon inferences concerning the domestication process because it brought forth 3 genetically, and to some extent morphologically, distinct wild einkorn races that we designate here as alpha, beta, and gamma. Only one of those natural races, beta, was exploited by humans for domestication. Nucleotide diversity and haplotype diversity in domesticate einkorn is higher than in its wild sister group, the einkorn beta race, indicating that einkorn underwent no reduction of diversity during domestication. This is in contrast to findings from previous studies of domestication history among more intensely bred crop species. Taken together with archaeological findings from the Fertile Crescent, the data indicate that a specific wild einkorn race that arose without human intervention was subjected to multiple independent domestication events.     

Comment on "AFLP data and the origins of domesticated crops".

We review some concepts and methods of handling and using DNA fingerprinting in phylogenetic analyses related to crop domestication. Particular reference is made to AFLP markers and mode and place of einkorn, barley, and tetraploid wheat domestication in the Neolithic by human communities in the Fertile Crescent. The reconsideration of AFLP databases of domesticated and wild lines demonstrates that phylogenetic tree topologies, originally described for the three species, match closely the new results obtained by principle coordinate analyse.     

Reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in sympatry

• Reproductive isolation is a necessary condition for plant domestication in their domestication centre where crops co‐occur with their wild progenitors. However, the identification of reproductive barriers and their relative contribution to reproductive isolation have been overlooked in plants under domestication.
• We assessed pre‐ and post‐pollination reproductive barriers and their relative contribution to reproductive isolation between wild and domesticated chaya (Cnidoscolus aconitifolius) in its domestication centre.
• We found that wild and domesticated chaya both exhibit a high degree of reproductive isolation. However, the reproductive isolation barriers exhibited some asymmetry: while pre‐pollination barriers (differential pollen production and pollinator specificity) were only detected in wild plants, post‐pollination barriers (pollen–pistil incompatibility and/or failure to set fruit) were observed in both wild and domesticated plants.
• We conclude that complete reproductive isolation has evolved in sympatry in co‐occurring domesticated and wild chaya.

     

Limited evolutionary divergence of seedlings after the domestication of plant species

The most vulnerable stage in the life of plants is the seedling. The transition from wild to agricultural land that plants experienced during and after domestication implied a noticeable change in the seedlings′ environment. Building on current knowledge of seedling ecology, and on previous studies of cassava, we hypothesise that cultivation should have promoted epigeal germination of seedlings, and more exposed and photosynthetic cotyledons. To test this hypothesis, we phenotyped seedling morpho‐functional traits in a set of domesticated and wild progenitor accessions of 20 Eudicot herbaceous crop species. Qualitative traits like epi‐ versus hypogeal germination, leafy versus storage type of cotyledons, or crypto‐ versus phanerocotyledonar germination, remained conserved during the domestication of all 20 species. Lengths of hypocotyls and epicotyls, of cotyledon petioles, and indices of cotyledon exposure to the aboveground environment changed during evolution under cultivation. However, those changes occurred in diverse directions, depending on the crop species. No common seedling phenotypic convergence in response to domestication was thus detected among the group of species studied here. Also, none of the 20 crops evolved in accordance with our initial hypothesis. Our results reject the idea that strong selective filters exerted unconsciously by artificial selection should have resulted in generalised channelling of seedling morphology towards more productive and more herbivore risky phenotypes. This result opens up unexplored opportunities for directional breeding of seedling traits.     

Fast and furious: Early differences in growth rate drive short‐term plant dominance and exclusion under eutrophication

1. The reduction of plant diversity following eutrophication threatens many ecosystems worldwide. Yet, the mechanisms by which species are lost following nutrient enrichment are still not completely understood, nor are the details of when such mechanisms act during the growing season, which hampers understanding and the development of mitigation strategies.
2. Using a common garden competition experiment, we found that early‐season differences in growth rates among five perennial grass species measured in monoculture predicted short‐term competitive dominance in pairwise combinations and that the proportion of variance explained was particularly greater under a fertilization treatment.
3. We also examined the role of early‐season growth rate in determining the outcome of competition along an experimental nutrient gradient in an alpine meadow. Early differences in growth rate between species predicted short‐term competitive dominance under both ambient and fertilized conditions and competitive exclusion under fertilized conditions.
4. The results of these two studies suggest that plant species growing faster during the early stage of the growing season gain a competitive advantage over species that initially grow more slowly, and that this advantage is magnified under fertilization. This finding is consistent with the theory of asymmetric competition for light in which fast‐growing species can intercept incident light and hence outcompete and exclude slower‐growing (and hence shorter) species. We predict that the current chronic nutrient inputs into many terrestrial ecosystems worldwide will reduce plant diversity and maintain a low biodiversity state by continuously favoring fast‐growing species. Biodiversity management strategies should focus on controlling nutrient inputs and reducing the growth of fast‐growing species early in the season.

     

Global patterns in seed germination after ingestion by mammals

1. Mammals play an important role in seed germination through the ingestion of fruits and seeds. Since seed germination is a basic step in seedling recruitment, understanding how mammals affect germination improves our understanding of the effect of loss of mammal populations on the dynamics of plant communities.
2. We used meta-analytical methods to describe global patterns in the effect of seed ingestion by mammals on seed germination success and rate. We collected data from 154 studies that included 115 mammal species and 448 plant species.
3. Our results showed a positive cumulative effect of mammals on seed germination. However, this effect differed between mammalian orders; thus, some groups such as elephants, primates, and new world marsupials emerged as important enhancers of seed germination. Also, the effect varied depending on the plant family and the bioregion. Increased seed germination after ingestion was positively related to fast germination.
4. This meta-analysis, the first to synthesise and compare most of the information presently available on how mammals affect seed germination after ingestion, shows a global positive effect of mammals as enhancers of seed germination. However, behind that positive effect lies a diversity of neutral, negative, and positive effects of different magnitudes, which may have multifactorial explanations. We hope that the patterns presented here open up new questions and help guide future research efforts.

     

Plant use in three Pre-Pottery Neolithic sites of the northern and eastern Fertile Crescent: a preliminary report

The beginnings of agriculture throughout the Fertile Crescent are still not completely understood, particularly at the eastern end of the Fertile Crescent in the area of modern Iran. Archaeobotanical samples from Epipalaeolithic/PPNA Körtik Tepe in southeastern Turkey and from the Pre-Pottery Neolithic sites of Chogha Golan and East Chia Sabz in south western Iran were studied in order to define the status of cultivation at these sites. Preliminary results show the presence of abundant wild progenitor species of crops at the Iranian sites before 10600 cal. b.p., and very few wild progenitor species at Körtik Tepe dated to 11700–11250 cal. b.p. The Iranian sites also indicate size increase of wild barley grain across a sequence of 400 years through either cultivation or changing moisture conditions.     

Consequences of Seed Origin and Biological Invasion for Early Establishment in Restoration of a North American Grass Species

Local, wild-collected seeds of native plants are recommended for use in ecological restoration to maintain patterns of adaptive variation. However, some environments are so drastically altered by exotic, invasive weeds that original environmental conditions may no longer exist. Under these circumstances, cultivated varieties selected for improved germination and vigor may have a competitive advantage at highly disturbed sites. This study investigated differences in early establishment and seedling performance between wild and cultivated seed sources of the native grass, Poa secunda, both with and without competition from the invasive exotic grass, Bromus tectorum. We measured seedling survival and above-ground biomass at two experimental sites in western Montana, and found that the source of seeds selected for restoration can influence establishment at the restoration site. Cultivars had an overall advantage when compared with local genotypes, supporting evidence of greater vigor among cultivated varieties of native species. This advantage, however, declined rapidly in the presence of B. tectorum and most accessions were not significantly different for growth and survival in competition plots. Only one cultivar had a consistent advantage despite a strong decline in its performance when competing with invasive plants. As a result, cultivated varieties did not meet expectations for greater establishment and persistence relative to local genotypes in the presence of invasive, exotic species. We recommend the use of representative local or regional wild seed sources in restoration to minimize commercial selection, and a mix of individual accessions (wild, or cultivated when necessary) in highly invaded settings to capture vigorous genotypes and increase the odds native plants will establish at restoration sites.     

Effect of the grass Leersia hexandra on the dispersal,seed germination,and establishment of Pachira aquatica seedlings

1. In wetlands, hydrochory is one of the main mechanisms of seed dispersal and there is often synchrony between propagule production and the flood season. Different sources of disturbance can prevent seed dispersal to suitable sites, and if environmental conditions are not adequate for germination and seedling establishment, recruitment will be limited, affecting succession.
2. We worked in a disturbed tropical freshwater swamp where the native grass Leersia hexandra has dominated open areas, creating a grass matrix that surrounds patches of swamp forest. Leersia grows vigorously, forming cushions of dry matter that cover the soil, forming a potential obstacle to seed dispersal. We asked whether the vegetative growth of this grass prevents the entry and dispersal of seeds of the tropical swamp tree Pachira aquatica, thwarting seed germination and seedling establishment, and arresting succession. We set up transects in the grass matrix in two zones: close to the river (R) and bordering the tree patches or fragments (F). We quantified tree seed and seedling presence, survival and growth in situ and experimentally introduced seeds and seedlings in the field and monitored seed germination and the survival and growth of their seedlings, as well as that of transplanted seedlings.
3. There was a negative relationship between the number of seeds and established seedlings, and the distance to river or fragment (r = −0.86, p < 0.001 for zone R; and r = −0.77, p < 0.001 for zone F) and with the grass cushion (r = −0.68, p = 0.005 for zone R; and r = −0.66, p = 0.007 for zone F); the grass creating a barrier to dispersal. When seeds were sown after clearing the grass cushion, germination success was high, so this stage is not limited. The transplanted seedlings had better survival and a greater final height than the seedlings of the sown seeds. Grass cover had a negative effect on both types of seedlings. Seedling survival rates were inversely related to grass cover, showing that seedlings overgrown by grass had low survival rates. Flooding is a stress factor for seedlings and produced mortality, in addition to the effects of the grass.
4. Together, the field survey and the experiment show that succession is being arrested in two ways: (1) by limiting seed dispersal because the grass cushion slows the dispersal and penetration of seeds into the vegetation; and (2) by limiting seedling establishment because the grass competes for space and light. Our results show that even where the grass is native, slower growing, seed-dependent species may struggle to compete and establish. If grass cover is increasing, these swamps are very vulnerable to a decrease in area because it is very difficult for them to regenerate naturally.

     

Heteromorphic seeds of wheat wild relatives show germination niche differentiation

• Crop wild relatives are fundamental genetic resources for crop improvement. Wheat wild relatives often produce heteromorphic seeds that differ in morphological and physiological traits. Several Aegilops and Triticum species possess, within the same spikelet, a dimorphic seed pair, with one seed being larger than the other. A comprehensive analysis is needed to understand which traits are involved in seed dimorphism and if these aspects of variation in dimorphic pairs are functionally related.
• To this end, dispersal units of Triticum urartu and five Aegilops species were X‐rayed and the different seed morphs weighed. Germination tests were carried out on seeds, both dehulled and left in their dispersal units. Controlled ageing tests were performed to detect differences in seed longevity among seed morphs, and the antioxidant profile was assessed in terms of antioxidant compounds equipment and expression of selected antioxidant genes. We used PCA to group seed morphs sharing similar patterns of germination traits, longevity estimates and antioxidant profile.
• Different seed morphs differed significantly in terms of mass, final germination, germination timing, longevity estimates and antioxidant profile in most of the tested species. Small seeds germinated slower, had lower germination when left in their dispersal units, a higher antioxidant potential and were longer‐lived than large seeds. The antioxidant gene expression varied between morphs, with different patterns across species but not clearly reflecting the phenotypic observations.
• The results highlight different trait trade‐offs in dimorphic seeds of Aegilops and T. urartu, affecting their germination phenology and longevity, thereby resulting in recruitment niche differentiation.

     

Polyploidy affects the seed,dormancy and seedling characteristics of a perennial grass,conferring an advantage in stressful climates

• Polyploidy (the state of having more than two genome copies) is widely distributed in flowering plants and can vary within species, with polyploid races often associated with broad ecological tolerances. Polyploidy may influence within‐species variation in seed development, germination and establishment. We hypothesized that interactions between polyploidy and the seed developmental environment would affect subsequent dormancy, germination and early growth traits, particularly in stressful environments.
• Using seeds developed in a common garden under ambient and warmed conditions, we conducted germination trials under drought and temperature stress, and monitored the subsequent growth of seedlings. The study species, Themeda triandra, is a widespread, keystone, Australian native grass and a known polyploid complex.
• Tetraploid plants produced heavier, more viable seeds than diploids. Tetraploids were significantly more dormant than diploids, regardless of seed developmental environment. Non‐dormant tetraploids were more sensitive to germination stress compared to non‐dormant diploids. Finally, tetraploid seedlings were larger and grew faster than diploids, usually when maternal plants were exposed to developmental temperatures atypical to the source environment.
• Seed and seedling traits suggest tetraploids are generally better adapted to stressful environments than diploids. Because tetraploid seeds of T. triandra are more dormant they are less likely to germinate under stress, and when they do germinate, seedling growth is rapid and independent of seed developmental environment. These novel results demonstrate that polyploidy, sometimes in interaction with developmental environment and possibly also asexuality, can have within‐species variation in seed and seedling traits that increase fitness in stressful environments.

     

Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica×Setaria viridis

Drought tolerance is an important breeding target for enhancing the yields of grain crop species in arid and semi-arid regions of the world. Two species of Setaria, domesticated foxtail millet (S. italica) and its wild ancestor green foxtail (S. viridis) are becoming widely adopted as models for functional genomics studies in the Panicoid grasses. In this study, the genomic regions controlling germination and early seedling drought tolerance in Setaria were identified using 190 F₇ lines derived from a cross between Yugu1, a S. italica cultivar developed in China, and a wild S. viridis genotype collected from Uzbekistan. Quantitative trait loci were identified which contribute to a number of traits including promptness index, radical root length, coleoptile length and lateral root number at germinating stage and seedling survival rate was characterized by the ability of desiccated seedlings to revive after rehydration. A genetic map with 128 SSR markers which spans 1293.9 cM with an average of 14 markers per linkage group of the 9 linkage groups was constructed. A total of eighteen QTLs were detected which included nine that explained over 10% of the phenotypic variance for a given trait. Both the wild green foxtail genotype and the foxtail millet cultivar contributed the favorite alleles for traits detected in this trial, indicating that wild Setaria viridis populations may serve as a reservoir for novel stress tolerance alleles which could be employed in foxtail millet breeding.     

Effects of NaCl stress on seed germination and seedling development of Brassica insularis Moris (Brassicaceae)

• Brassica insularis is a protected plant that grows on both coastal and inland cliffs in the western Mediterranean Basin. The objective of this study was to test if any variability exists in the salt stress response during seed germination and seedling development in this species relative to its provenance habitat.
• Variability among three populations in the salt stress effects on seed germination and recovery under different temperatures was evaluated. The effect of nebulisation of a salt solution on seedling development was evaluated between populations growing at different distances from the sea.
• Seeds of B. insularis could germinate at NaCl concentrations up to 200 mm . Seed viability was negatively affected by salt, and recovery ability decreased with increasing temperature or salinity. Inter‐population variability was detected in salt response during the seed germination phase, as well as in seedling salt spray tolerance. The inland population seedlings had drastically decreased survival and life span and failed to survive to the end of the experiment. In contrast, at least 90% of the coastal seedlings survived, even when sprayed at the highest frequency with salt solution.
• This study allowed investigation of two natural factors, soil salinity and marine aerosols, widely present in the B. insularis habitat, and provided the first insights into ecology of this protected species and its distribution in the Mediterranean. These results might be useful in understanding the actual distributions of other species with the same ecology that experience these same abiotic parameters.

     

Responses of Primula vulgaris to light quality in the maternal and germination environments

• In the model species Arabidopsis thaliana phytochromes mediate dormancy and germination responses to seasonal cues experienced during seed maturation on the maternal plants. However, the effect of the maternal light environment on seed germination in native wild species has not been well studied. This is particularly important given its practical application in the context of environmental restoration, when there can be marked changes in the canopy.
• Plants of Primula vulgaris were grown in the field over two vegetative seasons under four shading treatments from low to high ratio of red to far‐red light (R:FR). Leaf and seed traits were assessed in response to the light treatments. The germination of seeds from these four maternal environments (pre‐dispersal) was investigated at seven light and five temperature treatments (post‐dispersal).
• Thinner leaves, larger leaf area and greater chlorophyll content were found in plants growing in reduced R:FR. Shading in the maternal environment led to increased seed size and yield, although the conditions experienced by the maternal plants had no effect on seed germination. Seeds responded strongly to the cues experienced in their immediate germination environment. Germination was always enhanced under higher R:FR conditions.
• The observed phenotypic trait variation plays a major role in the ability of P. vulgaris to grow in a wide range of light conditions. However, the increased germination capacity in response to a higher R:FR for all maternal environments suggests potential for seedling establishment under vegetative shade only in the presence of canopy gaps.

     

Germination profiling of lentil genotypes subjected to salinity stress

• Salinity is one of the most severe environmental stresses, negatively affecting productivity of salt‐sensitive crop species. Given that germination is the most critical phase in the plant life cycle, the present study aimed to determine seed germination potential and associated traits under salt stress conditions as a simple approach to identify salt‐tolerant lentil genotypes.
• The genetic material consisted of six lentil genotypes whose adaptation to various agroclimatic conditions is not well elucidated. Salinity stress was applied by addition of NaCl at three different levels of stress, while non‐stressed plants were included as controls. Evaluation of tolerance was performed on the basis of germination percentage, seed water absorbance, root and shoot length, seedling water content, seedling vigour index and number of seedlings with an abnormal phenotype.
• Overall, our findings revealed that salinity stress substantially affects all traits associated with germination and early seedling growth, with the effect of salinity being dependent on the level of stress applied. It is noteworthy, however, that genotypes responded differently to the varying salinity levels. In this context, Samos proved the most salt‐tolerant genotype, indicating its possible use for cultivation under stress conditions.
• In conclusion, the determination of seed germination and early growth potential may be exploited as an efficient strategy to reveal genetic variation in lentil germplasm of unknown tolerance to salinity stress. This approach allows selection of desirable genotypes at early growth stages, thus enabling more efficient application of various breeding methods to achieve stress‐tolerant lentil genotypes.