The diploid species diverged from a common ancestor, about 2–4 million years ago, presumably in the marginal Mediterranean region of Southwest Asia. 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. participated in the data analysis as well as in preparation of the manuscript; R.F., L.B., M.A. A particular pattern of mutation accumulation has thus been observed in the B subgenome, presented previously as proof of a more ancient origin of the B progenitor, or more precisely an ancient speciation between the B subgenome in the tetraploid/hexaploid and A. speltoides (considered as a modern representative of AncB). Genome-wide impacts of alien chromatin introgression on wheat gene transcriptions. The remaining mutations (7%) consist of homoeoSNPs shared between A. speltoides and the tetraploid subgenome B but not transmitted to the hexaploid subgenome B as a result probably of random (and few) substitutions, deletions or alternatively gene conversions between homoeologs. 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. Wild Triticeae use by humans Intense use of wild Triticeae can be seen in the Levant as early as 23,000 years ago. Number of times cited according to CrossRef: Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat. The n = 12 ancestral genome (AGK) consists of 58 933 protogenes (including 17 340 genes conserved between grasses and 41 593 lineage‐specific genes), inferred from the comparison of rice, sorghum and Brachypodium genomes (Murat et al., 2014; cf. Empty TE sites in homoeologs can be a hallmark of either absence of the insertion (demonstrated by the absence of target site duplication (TSD)) or the excision of the considered element (demonstrated by the presence of at least remnants of TSD), as the investigated class II elements transpose via a ‘cut and paste’ mechanism. Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat ‘Chinese spring’, T. turgidum, and Aegilops tauschii. Molecular Marker Development and Application for Improving Qualities in Bread Wheat. 1832 homoeoSNPs in 789 genes with an average size of 3.75 kbp per gene) from the transition between the tetraploid and the hexaploid (termed 4x to 6x). International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat genome. Comparing now the accumulation rate of homoeoSNPs per genes (with genes of similar size as a clear proof of homoeoSNPs density/rate consistency) for the two considered transitions (2x to 4x and 4x to 6x), we observed an accelerated rate of homoeoSNP accumulation for the B subgenome compared with the A subgenome between 2x and 4x (rate of 1.5x = 11.5/7.3) and between 4x and 6x (rate of 2.3x = 5.4/2.3). (a) Circle 1, illustration of the synteny between the, Transposable element (TE) and homoeoSNP evolutionary dynamics. diccocoides, and between Triticum turgidum ssp. Molecular comparisons at the whole‐genome level using germplasm collections have shown that the B subgenome from hexaploid wheat could be related to several A. speltoides lines but not to other species of the Sitopsis section (Salina et al., 2006; Kilian et al., 2007). Regarding the controversial B subgenome paleohistory, it becomes clear that the proposal of an ancestral (more ancient than the A and D progenitors) mono‐ or polyphyletic B subgenome origin cannot explain entirely the observed accumulation of mutations during evolution in shaping the modern bread wheat B subgenome. 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. 2838 homoeoSNPs in 390 genes with an average size of 4.04 kbp per gene) originated from the transition between the diploid and the tetraploid (termed 2x to 4x) and 2.3 homoeoSNPs/genes (i.e. Application of Genomics Tools in Wheat Breeding to Attain Durable Rust Resistance. ‘département’. The authors also conducted quantitative trait locus (QTL) analysis on six doubled haploid elite winter wheat populations. 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. It is suggested that Ae. It evolved in the northern ecogeographical region of the upper Jordan River in the eastern Upper Galilee Mountains and Golan Heights. During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. Wheat Quality For Improving Processing And Human Health. However, another explanation has been proposed introducing a possible polyphyletic origin of AncB resulting from an introgression of several parental Aegilops species from the Sitopsis section (termed S and including Aegilops bicornis, Cb; Aegilops searsi, Ss; Aegilops longissimi, Sl; Aegilops sharonensis, Sh; Aegilops speltoides, S) that need to be identified, if they are not extinct. However, no research on the dynamic evolution of these genes in domesticated species and their progenitors has been reported. The ancestral grass genome (ancestral grass karyotype (AGK)) as reported in Murat et al. ssp. Wheat paleohistory created asymmetrical genomic evolution. Reading Time: 2 minutes. pivotal). 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. Most of the 25,000 different forms of modern wheat are varieties of two broad groups, called common wheat and durum wheat. (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. Given the short evolutionary time span of bread wheat since allohexaploidization and the stable karyotype of ETW, it is conceivable that transcriptome alterations likely contribute to phenotypic abnormality. of bread wheat with each containing five genes. In this study, we sequenced 3286 BACs from chromosome 7DL of bread wheat … To bridge this gap, we analyzed spatial varietal and genetic diversity of bread wheat in France – an important production area – over the 1980–2006 period at a yearly time step and a district scale, i.e. Serpins: Genome-Wide Characterisation and Expression Analysis of the Serine Protease Inhibitor Family in This spontaneous hybridisation created the tetraploid species Triticum turgidum (durum wheat) 580,000–820,000 years ago. In this scenario, early hexaploid would have been hulled due to the tenacious glumes (Tg-D1/Tg-D1) contributed by Ae. durum, used in pasta and semolina products. The illustration shows the distribution routes of wheat based on its genetic similarity patterns. 2830 homoeoSNPs in 523 genes with an average size of 3.98 kbp per gene) from the transition between 4x and 6x. 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. 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). 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. either mono‐ or polyphyletic). wrote the manuscript. The aim of this work is to briefly review wheat breeding, with emphasis on the current advances. In fact, at the time when the The time (T) of divergence was finally estimated using the formula T = Ks/2r. 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. 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. The results show evidence of divergent selection for grain yield … Among the 8671 homoeologous gene triplets, 188 exhibit shared TE (class II miniature inverted repeat transposable elements (MITEs) associated with terminal inverted repeats (TIRs)) insertions (Fig. The 8671 homoeologous gene triplets were automatically scanned using Mummer (http://mummer.sourceforge.net/manual/) in order to detect sequence homology breakpoints between homoeologs that are potentially caused by TE insertions. Zhang H(1), Zhu B(1), Qi B(2), Gou X(1), Dong Y(1), Xu C(3), Zhang B(1), Huang W(4), Liu C(1), Wang X(1), Yang C(1), Zhou H(1), Kashkush K(5), Feldman M(6), Wendel JF(7), Liu B(8). 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. Such a syntenome, which allows navigation between grass genomes, can be considered an applied tool for refining structural and functional annotation of wheat orthologous genes, further improving wheat genome sequence assembly, and accelerating identification of candidate genes or markers driving key agronomic traits in wheat (Salse, 2013; Valluru et al., 2014). 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. Its pictogram is the shape of a round bowl that was used to knead it. (2015a), confirmed in Li et al. For each triplet, the total number of homoeoSNPs belonging to each class was calculated and a statistical pairwise binomial test was performed in order to define the homoeology or subgenome proximity (i.e. Pervasive hybridizations in the history of wheat relatives. durum (AABB genome) and Aegilops tauschii (DD genome) 10 000 yr ago, forming the modern hexaploid bread wheat (AABBDD) genome (Feldman et al., 1995; Huang et al., 2002). 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. 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. not located on A, B or D subgenomes of the same chromosomal group). During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. 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. These data illustrate the complex history of domesticated wheat evolution, suggesting that various traits (even some that are closely related) arose independently at different stages. Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes. 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. Bread, in all its various forms, is the most widely consumed food in the world. From these resources, Marcussen et al. Only triplets with P‐values < 0.05 were considered for further analysis (see Table S2) and associated to a unique subgenome proximity or relatedness class (A/B or A/D or B/D). Several phylogenetic studies have tried to identify the progenitor of the B genome of polyploid wheat based on cytology (Zohary & Feldman, 1962), nuclear and mitochondrial DNA sequences (Dvorak et al., 1989; Dvorak & Zhang, 1990; Terachi et al., 1990) and chromosome rearrangement studies (Feldman, 1966a,b; Hutchinson et al., 1982; Gill & Chen, 1987; Naranjo et al., 1987; Naranjo, 1990; Jiang & Gill, 1994; Devos et al., 1995; Maestra & Naranjo, 1999). Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. 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. 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. [2010].). The current model first reconciles data from previous studies addressing the origin of subgenome D, as our results support the conclusions of two recent studies suggesting that the D subgenome has a homoploid origin (Marcussen et al., 2014; Sandve et al., 2015). Hybridization preceded radiation in diploid wheats. ecosystems impacted by the practice of agriculture) have expanded around the globe and now cover ∼38% of the earth's landmass, excluding Antarctica (FAO 2009). Hexaploid bread wheat (Triticum aestivum L., genome BBAADD) is generally more salt tolerant than its tetraploid wheat progenitor (Triticum turgidum L.). Genes sharing a cumulative identity percentage (CIP) of > 90% and a cumulative alignment length percentage (CALP) of at least 30% (Salse et al., 2009) were grouped in the same cluster using the Markov cluster (mcl) algorithm (http://micans.org/mcl/). aestivum) is one of the most successful crops on 45 earth since the Neolithic Age. Gu L(1), Si W, Zhao L, Yang S, Zhang X. (2014) was used, with 58 933 ordered ancestral genes on 12 ancestral chromosomes based on synteny relationships between the Oryza sativa (rice, IRGSP, 2005), Brachypodium distachyon (Brachypodium, IBI, 2010) and Sorghum bicolor (sorghum, Paterson et al., 2009) genomes. Tracing the ancestry of modern bread wheats. Revisiting Pivotal-Differential Genome Evolution in Wheat. ‘département’. For more than one century, wheat breeding has been based on science, and has been constantly evolving due to on farm agronomy and breeding program improvements. (2014) and AGK genes yielded orthologs between these two resources. The genetic map is then enriched in syntenic (ancestral) genes intercalated between molecular markers, that is, the syntenome (Salse, 2013). Origin of wheat B-genome chromosomes inferred from RNA sequencing analysis of leaf transcripts from section Sitopsis species of In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events. Subsequently, hexaploid bread wheat (T. aestivum L., genome BBAADD) arose from the hybridization of domesticated emmer with the diploid Aegilops tauschii Coss. Here, we studied 21 WEW populations from across their natural range in … Several genes associated with leaf development including the ortholog of maize ZmRAVL1, a B3-domain transcription factor involved in regulation of leaf angle, were predicted in physical intervals harboring these major QTL on reference genomes of bread wheat ‘Chinese spring’, T. turgidum, and Aegilops tauschii. In comparison to 84% T. urartu lineage‐specific mutations identified (i.e. dominance or partitioning) of the subgenomes following polyploidization in wheat (Pont et al., 2013) and more generally in plants (Murat et al., 2014, 2015a,b). . The origin and evolution of the wheat group (the genera Aegilops, Amblyopyrum, and Triticum) in the wild and under cultivation is reviewed. Figs 2b, 1a, circle 4; Table S2). 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. (Thell.) This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Dynamic Evolution of α-Gliadin Prolamin Gene Family in Homeologous Genomes of Hexaploid Wheat. 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. 1a, circle 2). 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. 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. Wild Triticeae use by humans. Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. 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. Using the maximum likelihood method in the reference Paml package (Yang, 2007) Ks (synonymous substitution rate) calculation for orthologs/homoeologs between T. urartu and T. aestivum A subgenome, between A. speltoides and T. aestivum B subgenome, and between A. tauschii and T. aestivum D subgenome was performed. Fig. Instead, the authors reported a nested topology of the A. taushii chloroplast genome. Study, we sequenced 3286 BACs from chromosome 7DL of bread wheat ( Triticumaestivum ) is one of the subgenome... A/D and B/D subgenomes and colleagues copy number variations in the genus,. 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