Wheat Evolution Research Articles

Low molecular weight glutenin subunit gene composition at Glu-D3 loci of Aegilops tauschii and common wheat and a further view of wheat evolution.

A comprehensive comparison of LMW-GS genes between Ae. tauschii and its progeny common wheat. Low molecular weight glutenin subunits (LMW-GSs) are determinant of wheat flour processing quality. However, the LMW-GS gene composition in Aegilops tauschii, the wheat D genome progenitor, has not been comprehensively elucidated and the impact of allohexaploidization on the Glu-D3 locus remains elusive. In this work, using the LMW-GS gene molecular marker system and the full-length gene-cloning method, LMW-GS genes at the Glu-D3 loci of 218 Ae. tauschii and 173 common wheat (Triticum aestivum L.) were characterized. Each Ae. tauschii contained 11 LMW-GS genes, and the whole collection was divided into 25 haplotypes (AeH01-AeH25). The Glu-D3 locus in common wheat lacked the LMW-GS genes D3-417, D3-507 and D3-552, but shared eight genes of identical open reading frame (ORF) sequences when compared to that of Ae. tauschii. Therefore, the allohexaploidization induces deletions, but exerts no influence on LMW-GS gene coding sequences at the Glu-D3 locus. 92.17% Ae. tauschii had 7-9 LMW-GSs, more than the six subunits in common wheat. The haplotypes AeH16, AeH20 and AeH23 of Ae. tauschii ssp. strangulate distributed in southeastern Caspian Iran were the main putative D genome donor of common wheat. These results facilitate the utilization of the Ae. tauschii glutenin gene resources and the understanding of wheat evolution.

Impact of transposable elements on genome structure and evolution in bread wheat

BackgroundTransposable elements (TEs) are major components of large plant genomes and main drivers of genome 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.ResultsThe overall TE content is very similar between the A, B, and D subgenomes, although we find no evidence for bursts of TE amplification after the polyploidization events. Despite the near-complete turnover of TEs since the subgenome lineages diverged from a common ancestor, 76% of TE families are still present in similar proportions in each subgenome. Moreover, spacing between syntenic genes is also conserved, even though syntenic TEs have been replaced by new insertions over time, suggesting that distances between genes, but not sequences, are under evolutionary constraints. The TE composition of the immediate gene vicinity differs from the core intergenic regions. We find the same TE families to be enriched or depleted near genes in all three subgenomes. Evaluations at the subfamily level of timed long terminal repeat-retrotransposon insertions highlight the independent evolution of the diploid A, B, and D lineages before polyploidization and cases of concerted proliferation in the AB tetraploid.ConclusionsEven though the intergenic space is changed by the TE turnover, an unexpected preservation is observed between the A, B, and D subgenomes for features like TE family proportions, gene spacing, and TE enrichment near genes.

Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat.

Genome duplications aid in the formation of novel molecular networks through regulatory differentiation of the duplicated genes and facilitate adaptation to environmental change. Hexaploid wheat, Triticum aestivum, contains three homoeologous chromosome sets, the A-, B-, and D-subgenomes, which evolved through interspecific hybridization and subsequent whole-genome duplication. The divergent expression patterns of the homoeologs in hexaploid wheat suggest that they have undergone transcriptional and/or functional differentiation during wheat evolution. However, the distribution of transcriptionally differentiated homoeologs in gene regulatory networks and their related biological functions in hexaploid wheat are still largely unexplored. Therefore, we retrieved 727 publicly available wheat RNA-sequencing (RNA-seq) datasets from various tissues, developmental stages, and conditions, and identified 10,415 expressed homoeologous triplets. Examining the co-expression modules in the wheat transcriptome, we found that 66% of the expressed homoeologous triplets possess all three homoeologs grouped in the same co-expression modules. Among these, 15 triplets contain co-expressed homoeologs with differential expression levels between homoeoalleles across ≥ 95% of the 727 RNA-seq datasets, suggesting a consistent trend of homoeolog expression bias. In addition, we identified 2,831 differentiated homoeologs that showed gene expression patterns that deviated from those of the other two homoeologs. We found that seven co-expression modules contained a high proportion of such differentiated homoeologs, which accounted for ≥ 20% of the genes in each module. We also found that five of the co-expression modules are abundantly composed of genes involved in biological processes such as chloroplast biogenesis, RNA metabolism, putative defense response, putative posttranscriptional modification, and lipid metabolism, thereby suggesting that, the differentiated homoeologs might highly contribute to these biological functions in the gene network of hexaploid wheat.

Insights into a century of breeding of durum wheat in Tunisia: The properties of flours and starches isolated from landraces, old and modern genotypes

The present work had a dual objective: to assess if the evolution of durum wheat from landraces to modern genotypes as function of breeding programs impacted proteins and starch fractions, as well as starch properties. Flours and starches isolated from Tunisian durum wheat landraces, old and modern lines were thoroughly characterized for their compositional, morphological, and gel properties. Statistical results showed significant (p ≤ 0.05) differences among the studied set. Protein and starch fractions assessment revealed that modern genotypes had the highest total starch and albumin contents, old genotypes had the highest amylose and glutenin contents, and landraces had the highest protein and gliadin contents. Starch properties screening allowed several findings: no significant (p > 0.05) differences were found among starch granules morphology, significant (p ≤ 0.05) differences were recorded in terms of technological properties, and old genotypes had the highest starch gel hardness. Overall, these results indicated that the influence of genotype on flour and starch properties was more relevant than breeding history.

Impact of DNA reorganization on recombination suppression of 5b chromosome during wheat evolution

Impact of DNA reorganization on recombination suppression of 5b chromosome during wheat evolution

Three genomes differentially contribute to the seedling lateral root number in allohexaploid wheat: evidence from phenotype evolution and gene expression.

Common wheat is an allohexaploid (BBAADD) that originated from the hybridization and polyploidization of the diploid Aegilops tauschii (DD) with the allotetraploid Triticum turgidum (BBAA). Phenotypic changes often arise with the formation and evolution of allopolyploid wheat, but little is known about the evolution of root traits in different wheat species with varying ploidy levels. Here, we reported that the lateral root number on the primary root (LRNPR) of synthetic and natural allohexaploid wheats (BBAADD) is significantly higher than that of their allotetraploid (BBAA) and diploid (AA and SS) progenitors, but is much lower than that of their diploid (DD) progenitors. The expression of the wheat gene TaLBD16, an ortholog of the Arabidopsis LATERAL ORGAN BOUNDARIES-DOMAIN16/ASYMMETRIC LEAVES2-LIKE18 (LBD16), which is involved in lateral root development in Arabidopsis, was positively correlated with the LRNPR in diploid and allopolyploid wheats. In natural and synthetic allohexaploid wheats, the transcript of the TaLBD16 from the D genome (TaLBD16-D) was relatively more abundant compared with TaLBD16-A and TaLBD16-B. Consistent with the observed variation in LRNPR, the divergence in the expression of TaLBD16 homoeologous genes occurred before the formation of polyploidy wheat. Collectively, our observations indicate that the D genome played a crucial role in the increased lateral root number of allohexaploid wheats compared with their allotetraploid progenitors, and that TaLBD16-D was one of the key genes involved in the formation of lateral root number during wheat evolution.

Red fruit, orange fruit, orange fruit, red fruit: genome editing in tomato.

Red fruit, orange fruit, orange fruit, red fruit: genome editing in tomato.

Mechanisms, origin and heredity of Glu-1Ay silencing in wheat evolution and domestication.

Allotetraploidization drives Glu-1Ay silencing in polyploid wheat. The high-molecular-weight glutenin subunit gene, Glu-1Ay, is always silenced in common wheat via elusive mechanisms. To investigate its silencing and heredity during wheat polyploidization and domestication, the Glu-1Ay gene was characterized in 1246 accessions containing diploid and polyploid wheat worldwide. Eight expressed Glu-1Ay alleles (in 71.81% accessions) and five silenced alleles with a premature termination codon (PTC) were identified in Triticum urartu; 4 expressed alleles (in 41.21% accessions), 13 alleles with PTCs and 1 allele with a WIS 2-1A retrotransposon were present in wild tetraploid wheat; and only silenced alleles with PTC or WIS 2-1A were in cultivated tetra- and hexaploid wheat. Both the PTC number and position in T. urartu Glu-1Ay alleles (one in the N-terminal region) differed from its progeny wild tetraploid wheat (1-5 PTCs mainly in the repetitive domain). The WIS 2-1A insertion occurred ~ 0.13 million years ago in wild tetraploid wheat, much later than the allotetraploidization event. The Glu-1Ay alleles with PTCs or WIS 2-1A that arose in wild tetraploid wheat were fully succeeded to cultivated tetraploid and hexaploid wheat. In addition, the Glu-1Ay gene in wild einkorn inherited to cultivated einkorn. Our data demonstrated that the silencing of Glu-1Ay in tetraploid and hexaploid wheat was attributed to the new PTCs and WIS 2-1A insertion in wild tetraploid wheat, and most silenced alleles were delivered to the cultivated tetraploid and hexaploid wheat, providing a clear evolutionary history of the Glu-1Ay gene in the wheat polyploidization and domestication processes.

Identification and characterisation of RNA editing sites in chloroplast transcripts of einkorn wheat (Triticum monococcum)

AbstractRNA editing is a biological process that the RNA molecule occurred base change or modification to result in the change of genetic information at the post‐transcription level, which played the vital roles in plant growth and development as well as in response to diverse stresses. To understand the composition and characteristic of chloroplast RNA editing patterns in einkorn wheat, the progenitor of wheat A subgenome, we systematically predicted and identified the RNA editing sites in plastome of three einkorn wheat species using bioinformatics analysis combined with RT‐PCR method. A total of 33 sites distributed in 15 genes, 34 in 15 genes and 33 in 14 genes were predicted in Triticum urartu, Triticum boeoticum and Triticum monococcum, respectively, all of which were C to U conversion and most of them could be validated by RNA‐seq data. Furthermore, all of the predicted editing sites were validated experimentally in T. urartu. Totally, 24 sites were found to be consistent with the prediction. The secondary structure and transmembrane domains of these five transcripts with the most abundant editing sites were further investigated. The results showed that the secondary structures of all five genes were changed, together with the transmembrane domains of ndhB were also altered as the result of editing, suggesting that RNA editing could have impact on the biological function of target genes. Finally, comparative analysis of the RNA editing patterns among Triticum species was performed to identify the conserved and species‐specific editing sites. This study reported the chloroplast RNA editing in einkorn wheat, which laid the foundation for further study on the biological function of chloroplast RNA editing in wheat, and also provided the important information to reveal the origin and evolution of wheat from the perspective of RNA editing.

Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat.

Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding.

Genetic mapping of a novel recessive allele for non-glaucousness in wild diploid wheat Aegilops tauschii: implications for the evolution of common wheat.

Cuticular wax on the aerial surface of plants has a protective function against many environmental stresses. The bluish-whitish appearance of wheat leaves and stems is called glaucousness. Most modern cultivars of polyploid wheat species exhibit the glaucous phenotype, while in a wild wheat progenitor, Ae. tauschii, both glaucous and non-glaucous accessions exist. Iw2, a wax inhibitor locus on the short arm of chromosome 2D, is the main contributor to this phenotypic variation in Ae. tauschii, and the glaucous/non-glaucous phenotype of Ae. tauschii is usually inherited by synthetic hexaploid wheat. However, a few synthetic lines show the glaucous phenotype although the parental Ae. tauschii accessions are non-glaucous. Molecular marker genotypes indicate that the exceptional non-glaucous Ae. tauschii accessions share the same genotype in the Iw2 chromosomal region as glaucous accessions, suggesting that these accessions have a different causal locus for their phenotype. This locus was assigned to the long arm of chromosome 3D using an F2 mapping population and designated W4, a novel glaucous locus in Ae. tauschii. The dominant W4 allele confers glaucousness, consistent with phenotypic observation of Ae. tauschii accessions and the derived synthetic lines. These results implied that glaucous accessions of Ae. tauschii with the W2W2iw2iw2W4W4 genotype could have been the D-genome donor of common wheat.

Characterization of the CCT family and analysis of gene expression in Aegilops tauschii.

Flowering is crucial for reproductive success in flowering plant. The CCT domain-containing genes widely participate in the regulation of flowering process in various plant species. So far, the CCT family in common wheat is largely unknown. Here, we characterized the structure, organization, molecular evolution and expression of the CCT genes in Aegilops tauschii, which is the D genome donor of hexaploid wheat. Twenty-six CCT genes (AetCCT) were identified from the full genome of A. tauschii and these genes were distributed on all 7 chromosomes. Phylogenetic analysis classified these AetCCT genes into 10 subgroups. Thirteen AetCCT members in group A, C, H and G achieved rapid evolution based on evolutionary rate analysis. The AetCCT genes respond to different exogenous hormones and abiotic treatments, the expression of AetCCT4, 7, 8, 11, 12, 16, 17, 19, 21 and 22 showed a significant 24 h rhythm. This study may provide a reference for common wheat's evolution, domestication and evolvement rules, and also help us to understand the ecological adaptability of A. tauschii.

Growth plasticity and yield formation in dryland wheat (Triticum aestivum) under artificial selection

Dryland wheat has gone through double selections, including natural and artificial selection, in the evolutionary process. During this process, artificial selection played a key role in variety domestication and improvement. This paper summarized a few relatively independent but interrelated issues including evolutionary characteristics, physiological plasticity, morphological plasticity and population attribute transition in dryland wheat under artificial selection. It provided an overview on physiological and ecological mechanism of dryland wheat adapting to stress conditions, and an outline of wheat evolution route. In the long-term evolutionary history of dryland wheat from diploid to hexaploid, natural selection acted as a key role for wheat adaptation to stress environments. With the intervention of artificial selection, the yield-oriented phenotyping has been continuously strengthened, and morphological characteristics of wheat tended to display a fine adaptation to adverse environments at population level. As a product of artificial selection, water and nutrient use efficiencies were improved constantly, and biomass allocation pattern showed the characteristics of lowering below-ground parts and increasing above-ground parts. In the meantime, the tolerance to density and high temperature stresses tended to be enhanced, while photosynthetic rate per unit area was decreased gradually. Dryland wheat production was a complex population process, rather than a simple individual performance. Artificial selection increased population fitness and individual reproductive allocation in dryland wheat, which in turn strengthened its coordination with environment, but weakened its attributes of natural population. This paper also drew an outline of dryland wheat evolution, and provided a few suggestions for breeding strategies and cultivation management of dryland wheat under climate change.

Identification of QTL for Grain Size and Shape on the D Genome of Natural and Synthetic Allohexaploid Wheats with Near-Identical AABB Genomes.

Grain size and shape associated with yield and milling quality are important traits in wheat domestication and breeding. To reveal the genetic factors on the D genome that control grain size and shape variation, we conducted analysis of quantitative trait loci (QTL) using the F2 and F2:3 populations derived from a common allohexaploid wheat line TAA10 and a synthetic allohexaploid wheat XX329, which have near-identical AABB genomes and different DD genomes. Based on genotyping using wheat 660K single nucleotide polymorphism (SNP) array, TAA10 and XX329 exhibited 96.55, 98.10, and 66.26% genetic similarities of A, B, and D genomes, respectively. Phenotypic evaluation revealed that XX329 had higher thousand grain weight (TGW), grain length, width, area and perimeter than TAA10 across all environments, and the grain yield per plot of XX329 increased by 17.43–30.36% compared with that of TAA10 in two environments. A total of nine environmentally stable QTL associated with grain size and shape were mapped on chromosomes 2D and 7D and verified using near isogenic lines (NILs), with the synthetic allohexaploid wheat XX329 contributing favorable alleles. Notably, a novel QTL QTgw.cau-2D controlling grain weight was first identified from the synthetic allohexaploid wheat, which may be a more desirable target for genetic improvement in wheat breeding. Collectively, these results provide further insights into the genetic factors that shaped the grain morphology during wheat evolution and domestication.

MYC gene family in cereals: Transformations during evolution of hexaploid bread wheat and its relatives

MYC gene family in cereals: Transformations during evolution of hexaploid bread wheat and its relatives

Altered expression of the TaRSL2 gene contributed to variation in root hair length during allopolyploid wheat evolution.

Altered expression of the TaRSL2 gene was positively correlated with variation in root hair length during allopolyploid wheat evolution, and overexpression of TaRSL2 in Arabidopsis increases root hair length. Root hairs aid nutrient and water uptake and anchor the plant in the soil. Allopolyploid wheats display significant growth vigor in terms of root hair length compared to their diploid progenitors, but little is known about the molecular basis of variation in root hair length during wheat allopolyploidization. Here, we isolated three orthologs of the Arabidopsis root hair gene ROOT HAIR DEFECTIVE SIX-LIKE 2 (AtRSL2) in allohexaploid wheat, designated TaRSL2-4A, TaRSL2-4B and TaRSL2-4D. The deduced polypeptides of these three TaRSL2 homoeologous genes shared high similarity, and a conserved basic helix-loop-helix (bHLH) domain was present in their C-terminal regions. Notably, the expression of TaRSL2 was positively correlated with root hair length of wheat accessions with different ploidy levels. Moreover, ectopic overexpression of TaRSL2-4D in Arabidopsis could increase root hair length. We found that the transcript levels of TaRSL2 homoeologous genes dynamically changed during allopolyploid wheat evolution, implicating the complexity of the underlying molecular mechanism. Collectively, we propose that altered expression of the TaRSL2 gene contributed to variation in root hair length in allopolyploid wheats.

Uncovering the dispersion history, adaptive evolution and selection of wheat in China.

SummaryWheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro‐ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome‐wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication.

Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.

Gametocidal genes of Aegilops: segregation distorters in wheat-Aegilops wide hybridization.

Aegilops is a genus belonging to the family Poaceace, which have played an indispensible role in the evolution of bread wheat and continues to do so by transferring genes by wide hybridization. Being the secondary gene pool of wheat, gene transfer from Aegilops poses difficulties and segregation distortion is common. Gametocidal genes are the most well characterized class of segregation distorters reported in interspecific crosses of wheat with Aegilops. These "selfish" genetic elements ensure their preferential transmission to progeny at the cost of gametes lacking them without providing any phenotypic benefits to the plant, thereby causing a proportional reduction in fertility. Gametocidal genes (Gc) have been reported in different species of Aegilops belonging to the sections Aegilops (Ae. geniculata and Ae. triuncialis), Cylindropyrum (Ae. caudata and Ae. cylindrica), and Sitopsis (Ae. longissima, Ae. sharonensis, and Ae. speltoides). Gametocidal activity is mostly confined to 2, 3, and 4 homeologous groups of C, S, S1, Ssh, and Mg genomes. Removal of such genes is necessary for successful alien gene introgression and can be achieved by mutagenesis or allosyndetic pairing. However, there are some instances where Gc genes are constructively utilized for development of deletion stocks in wheat, improving genetic variability and chromosome engineering.

Genetic Characterization of Genetic Resources of <i>Aegilops tauschii</i>, Wheat D Genome Donor, Newly Collected in North Caucasia

For the purpose of broadening the available genetic resources to improve wheat breeding and to elucidate wheat evolution, 16 accessions of Aegilops tauschii newly collected in North Caucasia named NCT accessions were characterized genetically based on morphology, chloroplast SSR variation and AFLP. Ae. tauschii is one of the most important wild wheat genetic resources because it is the progenitor of the D genome of hexaploid wheat. Since Caucasia is considered to be a center of diversity of both cultivated and wild wheat, a lot of studies have been conducted to evaluate the diversity of Caucasian genetic resources including Ae. tauschii. Such kind of analyses, however, focused on Transcaucasia but little attention has been paid to North Caucasia because of the lack of available genetic resources. Based on the molecular analyses in this study, the 16 NCT accessions were generally divided into two groups although morphologically those are classified into the same subspecies. The grouping also represented geographical distribution, that is, the northern part group and Derbent group. This division is consistent with the two major genepools in Ae. tauschii reported in previous studies. The northern part and Derbent groups correspond to Eurasian wide genepool (called Tauschii genepool) and Caucasia and Caspian coast limited genepool (Strangulata genepool), respectively. Regarding to chloroplast, all the 16 accessions were genotyped as HG7, the most major haplogroup of the species. Although all the 16 NCT accessions were categorized into ssp. tauschii morphologically, accessions of Derbent group showed a tendency to have larger spikelets. Among them, especially NCT3 had the quite large size of spikelets and grains that are at almost the largest level in ssp. tauschii. The results of this study filled the missing information of Ae. tauschii and will be helpful for future utilization.