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![Schematic representation of the hexaploid wheat Triticum aestivum L. karyotype arranged into seven homeologous groups [31]. Geometric figures denote homeologous sequences (n), chromosome-specific sequences (CSSs) (q), genome-specific sequences (GSSs) (s), and dispersed repeats (transposable elements) (e).](profile/Olga-Silkova/publication/324650550/figure/fig1/AS:741681414561793@1553842037218/Schematic-representation-of-the-hexaploid-wheat-Triticum-aestivum-L-karyotype-arranged.png)
Schematic representation of the hexaploid wheat Triticum aestivum L. karyotype arranged into seven homeologous groups [31]. Geometric figures denote homeologous sequences (n), chromosome-specific sequences (CSSs) (q), genome-specific sequences (GSSs) (s), and dispersed repeats (transposable elements) (e).
Source publication
![Fig. 2. Evolution of the wheat genome [17]. Red color indicates...](profile/Olga-Silkova/publication/324650550/figure/fig2/AS:741681414545410@1553842037242/Evolution-of-the-wheat-genome-17-Red-color-indicates-chromosomes-or-their-fragments_Q320.jpg)
Polyploidy is the major mechanism of speciation in flowering plants. All genomes of ancient species that are the progenitors of extant plant species experienced polyploidization. Three consecutive stages of polyploidization, i.e., ancient polyploidization, tetra-, and hexaploidization, resulted in the emergence of modern allohexaploid bread wheat T...
Contexts in source publication
Context 1
... the basis of genetic similarity, 21 pairs of wheat homologous chromosomes are divided into seven homeologous groups, each containing one pair of chromosomes from the A, B, and D subgenomes ( Fig. 1) [30]. The homeologous chromosome groups have similar sets of genes (syntenic genes) and homologous DNA sequences, but differ in noncoding sequences, highly repeated sequences, and functional gene complexes [31,32]. Wheat genome sequences are divided into four groups ( Fig. 1): (1) nonspecific (dispersed repeats), (2) group-specific ...
Context 2
... containing one pair of chromosomes from the A, B, and D subgenomes ( Fig. 1) [30]. The homeologous chromosome groups have similar sets of genes (syntenic genes) and homologous DNA sequences, but differ in noncoding sequences, highly repeated sequences, and functional gene complexes [31,32]. Wheat genome sequences are divided into four groups ( Fig. 1): (1) nonspecific (dispersed repeats), (2) group-specific (homeologous) sequences, (3) genome-specific sequences (GSSs), and (4) chromosome-specific sequences (CSSs) [21,33]. Nonspecific sequences are present in most chromosomes and are represented mainly by transposable elements (TE). Group-specific sequences are, in general, the ...
Citations
... Therefore, breeding programs should emphasize the genetic improvement of complex traits to increase yield potential under growth-limiting conditions [3]. The genetic studies of complex traits in wheat are challenging because it is an allohexapolyploid species containing three subgenomes (AABBDD) with highly repetitive DNA sequences (85%) and a total genome size of 16 Gb [4,5]. Efforts from the International Wheat Genome Sequencing Consortium (IWGSC) have resulted in the release of a fully annotated and highly contiguous chromosome-level assembly sequence draft of the Chinese Spring cultivar that represents 94% of the whole genome [5][6][7]. ...
Background
Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3′-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified.
Results
Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na ⁺ /Ca ²⁺ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat.
Conclusion
The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
... dicoccum (2n=4x=28, AABB) with the diploid Aegilops tauschii (2n=2x=14, DD) occurred about 10000 years ago in the Fertile Crescent of the Middle East (Faris, 2014;Gornicki and Faris, 2014;El Baidouri et al., 2017). The genetic studies of complex agronomic traits in this cereal are challenging because it contains three subgenomes with 85% of repetitive sequences and consequently a large size of 16 Gb (Loginova and Silkova, 2018;IWGSC, 2018). Even though bread wheat is a polyploid species, the pairing of homoeologous chromosomes is prevented by cytological diploidization. ...
Bread wheat is one of the most important crops for the human diet but the increasing soil salinization is causing yield reductions worldwide. The development of appropriate cultivars requires the elucidation of mechanisms of tolerance to salt stress. To study them, physiological, genetic, transcriptomics and bioinformatics analyses were integrated. The dynamic transcriptomic response to salt stress was evaluated using the Massive Analysis of cDNA 3’-Ends (MACE) sequencing protocol in contrasting wheat genotypes from two mapping populations. The leaf transcriptome from Syn86 (salt-susceptible) and Zentos (salt-tolerant) was studied at the photosynthesis turning points identified at the osmotic phase. At the ionic phase, Bobur (salt-susceptible) and Altay2000 (salt-tolerant) were analyzed at 11 days and 24 days after stress exposure. Results revealed that genes involved in calcium-binding and cell wall synthesis were highly expressed in the tolerant genotype at the osmotic phase. On the other hand, the transcriptional suppression of photosynthesis-related and calcium-binding genes in the susceptible genotype was linked with the observed photosynthesis inhibition. At the ionic stage, more ABC transporters and Na+/Ca2+ exchangers were up-regulated in the tolerant genotype, indicating that mechanisms related to Na+ exclusion and transport may be vital for tissue tolerance at this phase. Moreover, genes involved in mechanisms related to protein synthesis and breakdown were identified at both osmotic and ionic phases. Based on the linkage disequilibrium blocks, the possible salt-responsive genes operating in pathways leading to salt stress tolerance were identified in the QTL intervals. These analyses provided systematic insights into the adaptation mechanisms of salt-tolerant and salt-sensitive wheat genotypes at both salt stress phases.
The over-represented calcium-binding category was analyzed with more detail at the expression and sequence level as the Ca2+ signaling events at the early stages of the osmotic phase are crucial for the acclimation response of the plants. Zentos showed primarily the up-regulation of genes at 15 minutes after stress whereas Syn86 displayed the down-regulation at 30 minutes. These results indicated that the distinct timing and the opposite transcriptional regulation of calcium-binding genes during the osmotic phase might represent key factors in the differential salt stress response. The RT-qPCR analysis of two of these genes has confirmed the differential expression in the contrasting genotypes. The comparative phylogenetic analysis revealed that genes that can be involved in the pathway for systemic Reactive Oxygen Species (ROS) production are different and are expressed in different time points in the genotypes studied. The identification of polymorphisms in promoter sequences and 3’-ends of genes provided insights on potential molecular mechanisms controlling the differential expression of these transcripts through differential transcription factor binding affinity or altered mRNA stability. The transcriptional divergences observed in the contrasting genotypes suggest a particular calcium signature in each genotype that can result in the activation or suppression of specific gene networks dependent on Ca2+ signaling. Therefore, these transcriptional events might be crucial in triggering either tolerance or susceptibility responses to salt stress in wheat.
... P720 produced a brighter signal on the D subgenome chromosomes on the chromosomes of bread wheat (Kroupin et al. 2019). The different signal intensity of P720 and P427 in the terminal regions might also be related to the polyploid nature of Th. ponticum and may be important for chromosome differentiation during meiosis because telomeres play a significant role in the formation of bivalents (Garrido-Ramos 2015, Loginova andSilkova 2018). The localization of the P720 and P427 signals in both the pericentromeric and terminal sites may also be explained by the fixation of an occasional chromosomal rearrangement, since it provided differentiation of these chromosomes during meiosis. ...
Thinopyrum ponticum (Podpěra, 1902) Z.-W. Liu & R.-C.Wang, 1993 is an important polyploid wild perennial Triticeae species that is widely used as a source of valuable genes for wheat but its genomic constitution has long been debated. For its chromosome identification, only a limited set of FISH probes has been used. The development of new cytogenetic markers for Th. ponticum chromosomes is of great importance both for cytogenetic characterization of wheat-wheatgrass hybrids and for fundamental comparative studies of phylogenetic relationships between species. Here, we report on the development of five cytogenetic markers for Th. ponticum based on repetitive satellite DNA of which sequences were selected from the whole genome sequence of Aegilops tauschii Cosson, 1849. Using real-time quantitative PCR we estimated the abundance of the found repeats: P720 and P427 had the highest abundance and P132, P332 and P170 had lower quantity in Th. ponticum genome. Using fluorescence in situ hybridization (FISH) we localized five repeats to different regions of the chromosomes of Th. ponticum . Using reprobing multicolor FISH we colocalized the probes between each other. The distribution of these found repeats in the Triticeae genomes and its usability as cytogenetic markers for chromosomes of Th. ponticum are discussed.
