Threshing efficiency as an incentive for rapid domestication of emmer wheat

The Domestication of the Seasons: The Exploitation of Variations in Crop Seasonality Responses by Later Prehistoric Farmers

Discussions of domestication and its associated genetic traits has focused upon dispersal mechanisms, for example in the rachis structure of cereals. Here we consider another trait of importance to domesticated crops – their seasonality response. We particularly consider flowering response to changing daylength, and how that relates to domesticated species that are carried by farmers considerable distances from their regions of origin. We consider the implications of cultivating crops in regions whose seasonality patterns contrast with those of the crop’s region of origin, and consider the consequent genetic changes. Reference is made to the particular case of barley, and a discussion of archaeogenetic research into its photoperiod response mechanism is provided.

QTL for seed shattering and threshability in intermediate wheatgrass align closely with well-studied orthologs from wheat, barley, and rice

Perennial grain crops have the potential to improve agricultural sustainability but few existing species produce sufficient grain yield to be economically viable. The outcrossing, allohexaploid, and perennial forage species intermediate wheatgrass (IWG) [Thinopyrum intermedium (Host) Barkworth & D. R. Dewey] has shown promise in undergoing direct domestication as a perennial grain crop using phenotypic and genomic selection. However, decades of selection will be required to achieve yields on par with annual small-grain crops. Marker-aided selection could accelerate progress if important genomic regions associated with domestication were identified. Here we use the IWG nested association mapping (NAM) population, with 1,168 F₁ progeny across 10 families to dissect the genetic control of brittle rachis, floret shattering, and threshability. We used a genome-wide association study (GWAS) with 8,003 single nucleotide polymorphism (SNP) markers and linkage mapping-both within-family and combined across families-with a robust phenotypic dataset collected from four unique year-by-location combinations. A total of 29 quantitative trait loci (QTL) using GWAS and 20 using the combined linkage analysis were detected, and most large-effect QTL were in common across the two analysis methods. We reveal that the genetic control of these traits in IWG is complex, with significant QTL across multiple chromosomes, sometimes within and across homoeologous groups and effects that vary depending on the family. In some cases, these QTL align within 216 bp to 31 Mbp of BLAST hits for known domestication genes in related species and may serve as precise targets of selection and directions for further study to advance the domestication of IWG.

Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat

Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

Despite the large morphological and physiological changes that plants have undergone through domestication, little is known about their impact on their microbiome. Here we characterized rhizospheric bacterial and fungal communities as well as the abundance of N-cycling microbial guilds across thirty-nine accessions of tetraploid wheat, Triticum turgidum, from four domestication groups ranging from the wild subspecies to the semi dwarf elite cultivars. We identified several microbial phylotypes displaying significant variation in their relative abundance depending on the wheat domestication group with a stronger impact of domestication on fungi. The relative abundance of potential fungal plant pathogens belonging to the Sordariomycetes class decreased in domesticated compared to wild emmer while the opposite was found for members of the Glomeromycetes, which are obligate plant symbionts. The depletion of nitrifiers and of arbuscular mycorrhizal fungi in elite wheat cultivars compared to primitive domesticated forms suggests that the Green Revolution has decreased the coupling between plant and rhizosphere microbes that are potentially important for plant nutrient availability. Both plant diameter and fine root percentage exhibited the highest number of associations with microbial taxa, highlighting their putative role in shaping the rhizosphere microbiota during domestication. Aside from domestication, significant variation of bacterial and fungal community composition was found among accessions within each domestication group. In particular, the relative abundances of Ophiostomataceae and of Rhizobiales were strongly dependent on the host accession, with heritability estimates of ~ 27% and ~ 25%, indicating that there might be room for genetic improvement via introgression of ancestral plant rhizosphere-beneficial microbe associations.

Drought and heat stress tolerance screening in wheat using computed tomography

BACKGROUND

Improving abiotic stress tolerance in wheat requires large scale screening of yield components such as seed weight, seed number and single seed weight, all of which is very laborious, and a detailed analysis of seed morphology is time-consuming and visually often impossible. Computed tomography offers the opportunity for much faster and more accurate assessment of yield components.

RESULTS

An X-ray computed tomographic analysis was carried out on 203 very diverse wheat accessions which have been exposed to either drought or combined drought and heat stress. Results demonstrated that our computed tomography pipeline was capable of evaluating grain set with an accuracy of 95-99%. Most accessions exposed to combined drought and heat stress developed smaller, shrivelled seeds with an increased seed surface. As expected, seed weight and seed number per ear as well as single seed size were significantly reduced under combined drought and heat compared to drought alone. Seed weight along the ear was significantly reduced at the top and bottom of the wheat spike.

CONCLUSIONS

We were able to establish a pipeline with a higher throughput with scanning times of 7 min per ear and accuracy than previous pipelines predicting a set of agronomical important seed traits and to visualize even more complex traits such as seed deformations. The pipeline presented here could be scaled up to use for high throughput, high resolution phenotyping of tens of thousands of heads, greatly accelerating breeding efforts to improve abiotic stress tolerance.

Btr1-A Induces Grain Shattering and Affects Spike Morphology and Yield-Related Traits in Wheat

Spike brittleness represents an important domestication trait in crops. Although the brittle rachis of wild wheat was cloned, however, the molecular mechanism underlying spike brittleness is yet to be elucidated. Here, we identified a single dominant brittle rachis gene Br-Ab on chromosome arm 3AbS using an F2 population of diploid wheat and designated Btr1-Ab. Sequence analysis of the Btr1-A gene in 40 diploid wheat accessions, 80 tetraploid wheat accessions and 38 hexaploid wheat accessions showed that two independent mutations (Ala119Thr for diploid and Gly97* for polyploids) in the Btr1-A coding region resulting in the nonbrittle rachis allele. Overexpression of Btr1-Ab in nonbrittle hexaploid wheat led to brittle rachis in transgenic plants. RNA-Seq analysis revealed that Btr1-A represses the expression of cell wall biosynthesis genes during wheat rachis development. In addition, we found that Btr1-A can modify spike morphology and reduce threshability, grain size and thousand grain weight in transgenic wheat. These results demonstrated that Btr1-A reduces cell wall synthesis in rachis nodes, resulting in natural spikelet shattering, and that the transition from Btr1-A to btr1-A during wheat domestication had profound effects on evolution of spike morphology and yield-related traits.

Genetic analysis of threshability and other spike traits in the evolution of cultivated emmer to fully domesticated durum wheat

Genetic mutations in genes governing wheat threshability were critical for domestication. Knowing when these genes mutated during wheat evolution will provide more insight into the domestication process and lead to further exploitation of primitive alleles for wheat improvement. We evaluated a population of recombinant inbred lines derived from a cross between the durum variety Rusty and the cultivated emmer accession PI 193883 for threshability, rachis fragility, and other spike-related traits. Quantitative trait loci (QTL) associated with spike length, spikelets per spike, and spike compactness were primarily associated with known genes such as the pleiotropic domestication gene Q. Interestingly, rachis fragility was not associated with the Q locus, suggesting that this trait, usually a pleiotropic effect of the q allele, can be influenced by the genetic background. Threshability QTL were identified on chromosome arms 2AS, 2BS, and 5AL corresponding to the tenacious glume genes Tg^2A and Tg^2B as well as the Q gene, respectively, further demonstrating that cultivated emmer harbors the primitive non-free-threshing alleles at all three loci. Genetic analysis indicated that the effects of the three genes are mostly additive, with Q having the most profound effects on threshability, and that free-threshing alleles are necessary at all three loci to attain a completely free-threshing phenotype. These findings provide further insight into the timeline and possible pathways of wheat domestication and evolution that led to the formation of modern day domesticated wheats.

Near Eastern Plant Domestication: A History of Thought

The Agricultural Revolution and plant domestication in the Near East (among its components) have fascinated generations of scholars. Here, we narrate the history of ideas underlying plant domestication research since the late 19th century. Biological and cultural perspectives are presented through two prevailing models: one views plant domestication as a protracted, unconscious evolutionary mutualistic (noncentric) process. The second advocates a punctuated, knowledge-based human initiative (centric). We scrutinize the research landscape while assessing the underlying evolutionary and cultural mechanisms. A parsimony measure indicates that the punctuated-centric view better accords with archaeological records, and the geobotany and biology of the species, and requires fewer assumptions. The protracted alternative requires many assumptions, does not account for legume biology, fails to distinguish domestication from postdomestication changes, and, therefore, is less parsimonious.

Transcriptome profiling of wheat glumes in wild emmer, hulled landraces and modern cultivars

Background

Wheat domestication is considered as one of the most important events in the development of human civilization. Wheat spikelets have undergone significant changes during evolution under domestication, resulting in soft glumes and larger kernels that are released easily upon threshing. Our main goal was to explore changes in transcriptome expression in glumes that accompanied wheat evolution under domestication.

Methods

A total of six tetraploid wheat accessions were selected for transcriptome profiling based on their rachis brittleness and glumes toughness. RNA pools from glumes of the central spikelet at heading time were used to construct cDNA libraries for sequencing. The trimmed reads from each library were separately aligned to the reference sub-genomes A and B, which were extracted from wheat survey sequence. Differentially expression analysis and functional annotation were performed between wild and domesticated wheat, to identity candidate genes associated with evolution under domestication. Selected candidate genes were validated using real time PCR.

Results

Transcriptome profiles of wild emmer wheat, wheat landraces, and wheat cultivars were compared using next generation sequencing (RNA-seq). We have found a total of 194,893 transcripts, of which 73,150 were shared between wild, landraces, and cultivars. From 781 differentially expressed genes (DEGs), 336 were down-regulated and 445 were up-regulated in the domesticated compared to wild wheat genotypes. Gene Ontology (GO) annotation assigned 293 DEGs (37.5 %) to GO term groups, of which 134 (17.1 %) were down-regulated and 159 (20.4 %) up-regulated in the domesticated wheat. Some of the down-regulated DEGs in domesticated wheat are related to the biosynthetic pathways that eventually define the mechanical strength of the glumes, such as cell wall, lignin, pectin and wax biosynthesis. The reduction in gene expression of such genes, may explain the softness of the glumes in the domesticated forms. In addition, we have identified genes involved in nutrient remobilization that may affect grain size and other agronomic traits evolved under domestication.

Conclusions

The comparison of RNA-seq profiles between glumes of wheat groups differing in glumes toughness and rachis brittleness revealed a few DEGs that may be involved in glumes toughness and nutrient remobilization. These genes may be involved in processes of wheat improvement under domestication.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1996-0) contains supplementary material, which is available to authorized users.

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor-domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events.

Were Fertile Crescent crop progenitors higher yielding than other wild species that were never domesticated?

During the origin of agriculture in the Fertile Crescent, the broad spectrum of wild plant species exploited by hunter-gatherers narrowed dramatically. The mechanisms responsible for this specialization and the associated domestication of plants are intensely debated. We investigated why some species were domesticated rather than others, and which traits they shared. We tested whether the progenitors of cereal and pulse crops, grown individually, produced a higher yield and less chaff than other wild grasses and legumes, thereby maximizing the return per seed planted and minimizing processing time. We compared harvest traits of species originating from the Fertile Crescent, including those for which there is archaeological evidence of deliberate collection. Unexpectedly, wild crop progenitors in both families had neither higher grain yield nor, in grasses, less chaff, although they did have larger seeds. Moreover, small-seeded grasses actually returned a higher yield relative to the mass of seeds sown. However, cereal progenitors had threefold fewer seeds per plant, representing a major difference in how seeds are packaged on plants. These data suggest that there was no intrinsic yield advantage to adopting large-seeded progenitor species as crops. Explaining why Neolithic agriculture was founded on these species, therefore, remains an important unresolved challenge.

Towards a comprehensive characterization of durum wheat landraces in Moroccan traditional agrosystems: analysing genetic diversity in the light of geography, farmers' taxonomy and tetraploid wheat domestication history

BACKGROUND

Crop diversity managed by smallholder farmers in traditional agrosystems is the outcome of historical and current processes interacting at various spatial scales, and influenced by factors such as farming practices and environmental pressures. Only recently have studies started to consider the complexity of these processes instead of simply describing diversity for breeding purposes. A first step in that aim is to add multiple references to the collection of genetic data, including the farmers' varietal taxonomy and practices and the historical background of the crop.

RESULTS

On the basis of interview data collected in a previous study, we sampled 166 populations of durum wheat varieties in two traditional Moroccan agrosystems, in the Pre-Rif and Atlas Mountains regions. Using a common garden experiment, we detected a high phenotypic variability on traits indicative of taxonomical position and breeding status, namely spike shape and plant height. Populations often combined modern (short) with traditional-like (tall) statures, and classical durum squared spike shape (5 flowers/spikelet) with flat spike shape (3 flowers/ spikelet) representative of primitive domesticated tetraploid wheat (ssp. dicoccum). By contrast, the genetic diversity assessed using 14 microsatellite markers was relatively limited. When compared to the genetic diversity found in a large collection of tetraploid wheat, it corresponded to free-threshing tetraploid wheat. Within Morocco, the two studied regions differed for both genetic diversity and variety names. Within regions, neither geography nor variety names nor even breeding status constituted strong barriers to gene exchange despite a few significant patterns.

CONCLUSIONS

This first assessment of morphological and genetic diversity allowed pointing out some important factors that may have influenced the structure and evolutionary dynamics of durum wheat in Morocco: the significance of variety names, the occurrence of mixtures within populations, the relative strength of seed exchange between farmers and local adaptation, as well as the fate of modern varieties once they have been introduced. Further, multidisciplinary studies at different spatial scales are needed to better understand these complex agrosystems of invaluable importance for food security.

Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today's fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

Plant domestication versus crop evolution: a conceptual framework for cereals and grain legumes

'Domestication syndrome' (DS) denotes differences between domesticated plants and their wild progenitors. Crop plants are dynamic entities; hence, not all parameters distinguishing wild progenitors from cultigens resulted from domestication. In this opinion article, we refine the DS concept using agronomic, genetic, and archaeobotanical considerations by distinguishing crucial domestication traits from traits that probably evolved post-domestication in Near Eastern grain crops. We propose that only traits showing a clear domesticated-wild dimorphism represent the pristine domestication episode, whereas traits showing a phenotypic continuum between wild and domesticated gene pools mostly reflect post-domestication diversification. We propose that our approach may apply to other crop types and examine its implications for discussing the timeframe of plant domestication and for modern plant science and breeding.

The 'Human Mind' as a common denominator in plant domestication

The role of conscious versus unconscious selection is a central issue in plant domestication. While some authors hold that domesticated plants arose due to unconscious dynamics driven by selection pressures exerted by the ancient 'cultivation regime', others attribute an indispensable role to conscious and knowledge-based selection as an imperative component of Neolithic Near Eastern plant domestication. Recent experimental work demonstrated that, contrary to commonly held views, deep seed burial as part of the ancient cultivation regime cannot be considered as a general selection pressure underlying the increased seed size of domesticated legumes compared with their wild ancestors. This is a robust conclusion since, in three out of the eight legume species studied from different world regions, there was no association between larger seed size and better seedling emergence from depth. We concur with the authors that these legume crops were most likely under various and multiple (often interacting) selection pressures under domestication, thereby causing the observed parallel/convergent evolution of their larger grain size. However, it is puzzling that these authors did not mention the ever-present common denominator in plant domestication, i.e. conscious human decision-making. In our view, the human 'Mind' and the 'Science of the Concrete' à la Lévi-Strauss deserved to be discussed as an integral component of plant domestication.