Precise investigation of the TSD, proof of TE insertion event and then unambiguously rejecting TE excision, established that 16, 43 and 36 insertions are associated with TSDs and shared between, respectively, the A/B, A/D and B/D subgenomes. These results clearly suggest an average of 19%, 43.5% and 37.5% relatedness between the A/B, A/D and B/D wheat subgenomes, respectively. Over 2000 NBS-encoding genes have been identified in bread wheat, which is the largest … Artificial selection in breeding extensively enriched a functional allelic variation in TaPHS1 for pre-harvest sprouting resistance in wheat. In fact, at the time when the Milling wheat for flour only became common in the 12 th century, but by the turn of the 19 th century, wheat was the UK’s most significant crop grown for human consumption. However, little is known about the physio- logical basis of this trait or about the relative contributions of allohexaploidization and subsequent evolutionary genetic changes on the trait development. either mono‐ or polyphyletic). Domestication of wheat led to changes in grain size, shape, and range of phenotypic variation. In comparison, 61% of homoeoSNPs observed in the A subgenome in the hexaploid (6x), but not inherited from T. urartu (2x), were identified in the A subgenome of the tetraploid (4x), thus making 39% of such homoeoSNPs specific from the A subgenome in the hexaploid. Overall, based on the chromosome‐to‐chromosome synteny relationships established between the 21 bread wheat chromosomes and the rice, sorghum and Brachypodium genomes, it was then possible to produce the wheat syntenome consisting finally of 72 900 (73.4% of the 99 386 gene models) ordered genes on the 21 chromosomes (Fig. B; red circle; derived from the hybridization of, I have read and accept the Wiley Online Library Terms and Conditions of Use, Genomics as the key to unlocking the polyploid potential of wheat, Deciphering the diploid ancestral genome of the Mesohexaploid, Biased gene fractionation and dominant gene expression among the subgenomes of, Genome triplication drove the diversification of, Structural evolution of wheat chromosomes 4A, 5A and 7B and its impact on recombination, Tempos of gene locus deletions and duplications and their relationship to recombination rate during diploid and polyploid evolution in the Aegilops‐Triticum alliance, Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat, Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes, Organization and evolution of the 5S ribosomal RNA gene family in wheat and related species, Gene and genome duplications: the impact of dosage‐sensitivity on the fate of nuclear genes, The impact of genome triplication on tandem gene evolution in, Identification of unpaired chromosomes in F, Role of cytoplasm specific introgression in the evolution of the polyploid wheats, Genes encoding plastid acetyl‐CoA carboxylase and 3‐phosphoglycerate kinase of the, International Brachypodium Initiative (IBI), Genome sequencing and analysis of the model grass, International Rice Genome Sequencing Project (IRGSP), The map‐based sequence of the rice genome, International Wheat Genome Sequencing Consortium (IWGSC), A chromosome‐based draft sequence of the hexaploid bread wheat (, Different species‐specific chromosome translocations in, Independent wheat B and G genome origins in outcrossing, A re‐evaluation of the homoploid hybrid origin of, Multiple rounds of ancient and recent hybridizations have occurred within the, Draft genome of the wheat A‐genome progenitor, A 4‐gigabase physical map unlocks the structure and evolution of the complex genome of, Structural chromosome differentiation between, International Wheat Genome Sequencing Consortium, Ancient hybridizations among the ancestral genomes of bread wheat, Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes, Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops, Arm homoeology of wheat and rye chromosomes, DRIMM‐synteny: decomposing genomes into evolutionary conserved segments, RNA‐seq in grain unveils fate of neo‐ and paleopolyploidization events in bread wheat (, Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo‐ and neoduplicated subgenomes, Paleogenomics as a guide for traits improvement: volume 1. Recently available wheat genomic resources offered the opportunity to gain novel insights into the origin of wheat with the release of the genome shotgun sequences of hexaploid and tetraploid wheat (IWGSC, 2014) as well as diploid progenitors (Jia et al., 2013; Ling et al., 2013; Luo et al., 2013). 1b). For the 188 triplets considered, we found that 15%, 44% and 41% of homoeoSNPs were shared between, respectively, the A/B, A/D and B/D subgenomes, a similar rate to that observed for the insertional TE (MITE) fingerprints. durum (AABB genome) and Aegilops tauschii (DD genome) 10 000 yr ago, forming the modern hexaploid bread wheat … Evolution of bread-making quality in wheat: implications about cancer prevention Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. A total of 13 168 protogenes matched to genetic markers from the most accurate wheat genetic map (Wang et al., 2014) involving 40 267 markers that allowed us to intercalate 59 732 wheat syntenic genes between 13 168 conserved markers (Fig. The overall TE content is very similar between the A, … Genome-wide impacts of alien chromatin introgression on wheat gene transcriptions. 26 013 A, B and D gene copies; Fig. Fig. Hybridization preceded radiation in diploid wheats. The authors argued that, in Marcussen et al. Wheat paleohistory created asymmetrical genomic evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. prone to the observed mutation accumulation). This spontaneous hybridisation created the tetraploid species Triticum turgidum (durum wheat) 580,000–820,000 years ago. It is suggested that Ae. 2830 homoeoSNPs in 523 genes with an average size of 3.98 kbp per gene) from the transition between 4x and 6x. The authors also conducted quantitative trait locus (QTL) analysis on six doubled haploid elite winter wheat populations. 1a, center circle), 5157 pairs (involving 10 314 genes), 15 761 singletons and 10 143 groups of genes (involving 47 298 genes) corresponding to two homologous copies or more but not defining strict homoeologous relationships (i.e. 14 519 homoeoSNPs in 1258 genes with an average size of 3.66 kbp per gene) originated from the transition from 2x to 4x and 5.4 homoeoSNPs/genes (i.e. 1a, circle 3), which probably represents the most accurate wheat reference genome available until complete pseudomolecules are publicly released for the 21 chromosomes. Common or bread wheat Triticum aestivum accounts for some 95 percent of all the consumed wheat in the world today; the other five percent is made up of durum or hard wheat T. turgidum ssp. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office. The second neohexaploidization event (< 0.3 Ma) led potentially to a supra‐dominance where the tetraploid became sensitive (subgenomes A and B) and the D subgenome dominant (i.e. However, no research on the dynamic evolution of these genes in domesticated species and their progenitors has been reported. This gene‐based phylogenetic approach then revealed that the A and B subgenomes are more closely related individually to the D subgenome than to each other. Dynamic evolution of NBS-LRR genes in bread wheat and its progenitors. Defining such clusters of eight orthologous genes (three from the hexaploid, two from the tetraploid and one from each of the three diploids) allows us to assess the transmission of mutations during evolution from the diploid to the tetraploid and finally to the hexaploid, ultimately defining homoeoSNPs between the A, B and D subgenomes. The former has been associated with successful germination and growth of seedlings in cultivated fields, whereas the latter trait (a hallmark of domestication) prevents natural seed dispersal and allows humans to harvest and collect the seed with optimal timing (reviewed in Fuller, 2007; Purugganan and Fuller, 2009). aestivum) is one of the most successful crops on 45 earth since the Neolithic Age. ssp. In addition to the previous insertional dynamics of TEs, accumulation of mutations at the gene level should provide additional insights into the origin of the A, B and D wheat subgenomes. In order to test the accuracy of using homoeoSNP dynamics as a proxy to investigate the origin of the wheat genome, we initially considered the previous 188 homoeologous gene triplets with shared TE insertions for which 19%, 43.5% and 37.5% relatedness between, respectively, the A/B, A/D and B/D subgenomes have been identified (cf. (2015a), confirmed in Li et al. Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.). The Never-Ending Story of the Phylogeny and Taxonomy of Genus Triticum L.. Science 345, doi: 10.1126/science.1251788 Google Scholar Jampates R, Dvorak J (1986) Location of the Ph1 locus in the metaphase chromosome map and the linkage map of the 5Bq arm of wheat. By contrast, we propose an alternative scenario where the increased divergence of the B subgenome in the hexaploid wheat compared to A. speltoides at the sequence (homoeoSNPs) level is the consequence of a differential evolutionary plasticity of the B subgenome compared with the A and D subgenomes in response to polyploidization events. Eighty‐four per cent of homoeoSNPs observed in the B subgenome in the hexaploid (6x), but not inherited (absent) from A. speltoides (2x), were identified in the B subgenome of the tetraploid (4x), thus making the remaining homoeoSNPs (16%) specific from the B subgenome in the hexaploid. The modern cultivated wheat has passed a long evolution involving origin of wild emmer (WEM), development of cultivated emmer, formation of spelt wheat and finally establishment of modern bread wheat and durum wheat. In the same manner, for the B subgenome, that is, homoeoSNPs observed in the B subgenome in the hexaploid and absent from A. speltoides, 11.5 homoeoSNPs/genes (i.e. Wheat Varieties . The contrasting plasticity between the MF and LF compartments in B. rapa has been associated with bias in (1) gene retention and with genes retained in pairs or triplets enriched in functional categories such as transcriptional regulation, ribosomes, response to abiotic or biotic stimuli, response to hormonal stimuli, cell organization and transporter functions; (2) gene expression, with genes located in the LF subgenome proposed to be dominantly expressed over those located in the two proposed fractionated subgenomes (MF1 and MF2); and (3) single nucleotide polymorphism (SNP) at the population level, with genes located in LF showing fewer nonsynonymous or frameshift mutations than genes in MF fractions (Edger & Pires, 2009; Cheng et al., 2012, 2013, 2014; Fang et al., 2012). Ripe for the Picking: Finding the Gene Behind Variation in Strawberry Fruit Color, by The American Society of Plant Biologists, © 2010 American Society of Plant Biologists. Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. Copyright © 2021 by The American Society of Plant Biologists. Polyploidization has been shown to be followed by a subgenome dominance phenomenon with contrasting plasticity of the post‐duplication blocks leading, at the whole‐chromosome or genome level, to dominant (D; retention of duplicated genes; also termed least fractionated (LF)) and sensitive (S; loss of duplicated genes; also termed most fractionated (MF)) compartments (Salse, 2013). Phenotype Them Fast, Accurately, and Easily with ARADEEPOPSIS! managed the research project; J.S. ‘ It is like having tens of billions of Scrabble letters; you know which letters are present, and their quantities, but they need to be assembled on the board in the right sequence before you can spell out their order into genes’ Professor Neil Hall. In this scenario (from top to bottom), from the three ancestral progenitors (termed AncA, AncS and AncD), whereas the evolution of the A subgenome from hexaploid bread wheat appears quite simple, the evolution of the other two subgenomes is more complex than initially reported. The domestication of wheat around 10,000 years ago marked a dramatic turn in the development and evolution of human civilization, as it enabled the transition from a hunter-gatherer and nomadic pastoral society to a more sedentary agrarian one. Grains are representative of modern elite varieties (top) and ancestral wheat species (bottom). Subgenome integrity in bread wheat (Triticum aestivum; BBAADD) makes possible the extraction of its BBAA component to restitute a novel plant type. In these geologically new environments, a group of plants that have symbiotic association with humans evolved from wild plants through domestication in both the Old and New Worlds. Taking into account that the exact founder diploid individual(s) will never be known and that the progenitors and their resultant polyploids (4x and 6x) may have evolved differentially through differences in mutation rates, genetic drift, genetic admixture or may even have experienced distinct rounds of domestication, perfect homoeoSNP inheritance between 2x, 4x and 6x wheats is not expected. This work has been supported by grants from INRA (‘Génétique et Amélioration des Plantes, ref: ‘Appel d'Offre Front de Science’ projet TransWHEAT), the Agence Nationale de la Recherche (program ANR Blanc‐PAGE, ref: ANR‐2011‐BSV6‐00801), the Agreenskills program (‘TransGRAIN’, session 2014, ID: 459) and the ‘Région Auvergne, Allocation de recherche Territoire, Agriculture, Alimentation, Nutrition et Santé Humaine’ (contract no. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat Homoeologous (A, B and D) genes and their parental orthologs (diploid A, B and D and tetraploid A and B) were aligned (eight genes in total) using Mafft with default parameters and homoeoSNPs were automatically detected using a custom PERL script. tauschii. The diploid species diverged from a common ancestor, about 2–4 million years ago, presumably in the marginal Mediterranean region of Southwest Asia. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, and D subgenomes. The hexaploid bread wheat (Triticum aestivum L., AABBDD) is believed to have originated through one or more rare hybridization events between Aegilops tauschii (DD) … (2015b), re‐evaluated the origin of hexaploid bread wheat based on the phylogenomic investigation of 20 chloroplast genomes, which are maternally inherited in this species complex. (genome DD) (3), … Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. . Following the proposed hybrid origin of the D subgenome (Marcussen et al., 2014; Sandve et al., 2015), TEs shared (located at orthologous positions) between A and B homoeologs (i.e. ancestral) or lineage‐specific (i.e. The genetic mechanisms of this … A large number of QTL with dispersed effects between the parents were identified and were consistent with independent inheritance of grain size and shape parameters. The comprehensive analysis provides solid evidence that size and shape of grain are independently inherited traits and that wheat domestication resulted in a switch from production of a relatively small grain with a long, thin shape to a more uniform larger grain with a short, wide shape (see figure). The availability of such a ploidy-reversed wheat (extracted tetraploid wheat [ETW]) provides a unique opportunity to address whether and to what extent the BBAA component of bread wheat has been modified in phenotype, karyotype, and gene expression … Both a and b types have two subunits, named x and y types. It is suggested that Ae. Li et al. durum, used in pasta and semolina products. Wheat and other cereals are significant sources of both of these minerals, contributing 44% of the daily intake of iron (15% in bread) and 25% of the daily intake of zinc (11% in bread) in the UK (Henderson et al., 2007). They concluded that grain shape and size are independent traits in both modern varieties and primitive wheat species that are under the control of distinct genetic components. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. Learn more. The A (43.5%) and B (37.5%) genomes are more closely related individually to the D genome than to each other (19%). It evolved in the northern ecogeographical region of the upper Jordan River in the eastern Upper Galilee Mountains and Golan Heights. This suggests a more ancient origin of the B progenitor (84% of B homoeoSNPs acquired between 2x and 4x) compared with the A progenitor (61% of A homoeoSNPs acquired between 2x and 4x), or, more precisely, a more ancient speciation between A. speltoides (2x)/B subgenome (6x and 4x) compared with T. urartu (2x)/A subgenome (6x and 4x). From the latest version of the hexaploid wheat genome survey sequence (IWGSC, 2014), consisting of 99 386 gene models (10.2 Mb with 10.8 million scaffolds; Borrill et al., 2015), we produced the most accurate wheat syntenic (also termed ‘computed’; Pont et al., 2011, 2013) gene order. The five genes on each of the three chromosome arms consisted of two x-type genes, two y-type genes, and one c-type gene. Taking into account not only the A, B and D progenitor genomes but also the M, N, T, U and C (referred to as S) diploid relatives within this species complex, the authors reported that the chloroplast genome of A. taushii (D) is more closely related to other D and S genomes than to the genomes of A. speltoides (S) and T. urartu (A). Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Bread wheat (Triticum aestivum) evolved through two polyploidization events between Triticum urartu (AA genome) and an Aegilops speltoides‐related species (BB genome) 0.5 million yr ago (hereafter Ma), forming Triticum turgidum ssp. Learn about our remote access options, INRA/UBP UMR 1095 GDEC (Genetics, Diversity and Ecophysiology of Cereals), 5 chemin de Beaulieu, Clermont Ferrand, 63100 France, INRA UR1164 URGI (Research Unit in Genomics‐Info), Université Paris‐Saclay, Versailles, 78026 France. We established that 40, 79 and 69 insertions are shared between, respectively, the A/B, A/D and B/D subgenomes. Heat stress effects on source–sink relationships and metabolome dynamics in wheat. Here, we show that extensive and, to an extent, functionally distinct changes in gene expression to the BBAA component of bread wheat have indeed occurred during its evolutionary … Aegilops tauschii The strategy consists of aligning the ancestral genome (made up of conserved gene adjencies retained in modern species), reconstructed from the lineage of interest (grasses in the current study), to the genetic map of the species of interest (wheat in the current study). . Bread wheat expanded its habitat from a core area of the Fertile Crescent to global environments within ~10,000 years. Transgenerationally Precipitated Meiotic Chromosome Instability Fuels Rapid Karyotypic Evolution and Phenotypic Diversity in an Artificially Constructed Allotetraploid Wheat (AADD). Two of the most important traits in the evolution of bread wheat and other cultivated grasses were an increase in grain size and the development of nonshattering seed. T.aestivum is an excellent modern species for studying concerted evolution of sub-genomes in polyploid species, because of its large chromosome size and three well-known genome donors. Bread wheats retain three subgenomes, each of which represents about 35,000 genes from the three original grass species, and about 80 percent to 90 percent of bread wheat… (2014) and AGK genes yielded orthologs between these two resources. Instead, the authors reported a nested topology of the A. taushii chloroplast genome. Wheat Quality For Improving Processing And Human Health. (a) (left) Illustration of the identified TEs shared between A and B (upper), A and D (middle) and B and D (lower) homoeologs (exons in blue with numbers) defining sequence conservation (gray blocks) breaks (illuminated by the sequence alignment) defining target site duplication (TSD) and terminal inverted repeat (TIR) elements. mutations from T. urartu not transmitted to the tetraploid), the number of A. speltoides mutations that were either transmitted to the tetraploid/hexaploid wheat (i.e. (Adapted from Figures 1 and 4 of Gegas et al. Recently published genome sequences of bread wheat and its two ancestors provide a good opportunity for comparing NBS-encoding genes between ancestors and their progeny. tauschii (Tg-D1/Tg-D1)(Dvorak et al. Of the six sets of chromosomes, two come from Triticum urartu (einkorn wheat) and two from Aegilops speltoides. During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. and J.S. The availability of such a ploidy-reversed wheat (extracted tetraploid wheat [ETW]) provides a unique opportunity to address whether and to what extent the BBAA component of bread wheat has been modified in phenotype, karyotype, and gene expression during its evolutionary history at the allohexaploid level. Taken together, the findings of these studies suggest two hypotheses, the first being that the progenitor of the B genome is a unique and ancient Aegilops species that remains unknown (i.e. Common wheat (Triticum aestivum L.) is one of the most important crops because it provides about 20% of the total calories for humans. Here, our findings also support a recent evolutionary scenario introducing the concept of subgenome dominance between the A, B and D subgenomes of wheat following polyploidizations (Pont et al., 2013), where the modern bread wheat genome has been shaped by a first neotetraploidization event (< 0.5 Ma) leading to subgenome dominance where the A subgenome was dominant and the B subgenome sensitive (i.e. Mesophyll porosity is modulated by the presence of functional stomata. Briefly, for each position of the alignment, bases are scored to classify shared homoeoSNPs into three different classes: A/B, A/D and B/D. Author information: (1)State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat … In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat cv. The breakthrough of sequencing the bread wheat genome and progenitor genomes lays the foundation to decipher the complexity of wheat origin and evolutionary process as well as the genetic consequences of polyploidization. ‘département’. Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum. (right) Illustration of the observed percentage (and associated mean value, Wheat evolutionary model. (2015), estimated the phylogenetic history of the A, B and D subgenomes from 2269 gene trees involving A, B and D homoeologs conserved between the hexaploid wheat subgenomes, among which 275 trees include orthologous sequences from five diploid relatives (T. urartu, A. speltoides, A. tauschii, Triticum monococcum and Aegilops sharonensis). Use the link below to share a full-text version of this article with your friends and colleagues. Wheat has been cultivated for more than 10,000 years, beginning in the Fertile Crescent and arriving in the UK around 5,000 years ago. We do not capture any email address. The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientiﬁc community over the last few decades. Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat. Recent research suggest that T. macha origin… Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. . The earliest evidence for both domesticated einkorn and emmer wheat found to date was at the Syrian site of Abu Hureyra, in occupation layers dated to the Late Epi-paleolithic period, the beginning of the Younger Dryas, ca 13,000–12,000 cal BP; some scholars have argued, however, that the evidence does not show deliberate cultivation at this time, although it does indicate a broadening of the diet … Taking into account the ‘polyploid‐specific homoeoSNPs’ (Fig. Bread wheat is an allohexaploid (an allopolyploid with six sets of chromosomes: two sets from each of three different species). relatedness) of the considered triplets. Preferential Subgenome Elimination and Chromosomal Structural Changes Occurring in Newly Formed Tetraploid Wheat—Aegilops ventricosa Amphiploid (AABBDvDvNvNv). An investigation of the evolutionary dynamics of TEs and mutations in wheat allowed us to propose a scenario in which the A subgenome derived from an ancestral genome closely related to the modern T. urartu, with 71% of mutations detected in the ancestor (AncA) transmitted to the modern subgenome; the B genome derived from an ancient mono‐ or polyphyletic progenitor and experienced accelerated plasticity following polyploidization, which together explained why only 42% of mutations identified in the modern subgenome were inherited from the ancestral genome (AncB) closely related to the modern A. speltoides; and the D subgenome derived from a complex hybridization pattern of the three A, B and D progenitors accounting, respectively, for on average 38%, 43% and 19% of the modern D subgenome in hexaploid bread wheat, based on TE (from 188 triplets) and mutation (from 8671 triplets) insertional dynamics. 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