The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties

Loginova, D. B.; Silkova, O. G.

doi:10.1134/s1022795418040105

Cited by 5 publications

(4 citation statements)

References 109 publications

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“…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 – 7 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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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+/Ca2+ 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.

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Section: Introductionmentioning

confidence: 99%

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

et al. 2020

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“…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 and Silkova 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.…”

Section: Discussionmentioning

confidence: 99%

Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu & R.-C. Wang

Kroupin¹,

Kuznetsova²,

Nikitina³

et al. 2019

CCG

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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.

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Section: Introductionmentioning

confidence: 99%

“…The studies of complex traits in this species are challenging because of its intricate genome structure. This allohexapolyploid (2 n =6 x =42, AABBDD) contains three subgenomes of 16 Gb with 85% of repetitive sequences (Loginova and Silkova 2018; IWGSC 2018). Efforts from the International Wheat Genome Sequencing Consortium (IWGSC) have allowed the release of fully annotated and highly contiguous chromosome-level assemblies of diverse bread wheat lines (Montenegro et al 2017; Shi and Ling 2018; IWGSC 2018; Borrill et al 2019; Walkowiak et al 2020; Zhu et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Expression interplay of calcium-binding genes and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Duarte-Delgado,

Vogt,

Dadshani

et al. 2024

Preprint

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Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3'-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding genes was found to be specific for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of EF-hand genes, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding genes, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3'-UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability.

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The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties

Cited by 5 publications

References 109 publications

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu & R.-C. Wang

Expression interplay of calcium-binding genes and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

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The Genome of Bread Wheat Triticum aestivum L.: Unique Structural and Functional Properties

Cited by 5 publications

References 109 publications

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes

Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu &amp; R.-C. Wang

Expression interplay of calcium-binding genes and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

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Development of new cytogenetic markers for Thinopyrum ponticum (Podp.) Z.-W. Liu & R.-C. Wang