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Special Issue "Molecular Advances in Wheat and Barley"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 March 2019).

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Special Issue Editor

Prof. Dr. Manuel Martinez
Website
Guest Editor
Universidad Politecnica de Madrid, Madrid, Spain
Interests: molecular plant–pest interactions; plant proteolysis; comparative genomics; signalling pathways; Arabidopsis; barley
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Special Issue Information

Dear Colleagues,

Allohexaploid bread wheat and diploid barley are the most cultivated crops in the world, after maize and rice. Their economic importance and close relationship supports a parallel study of both cereals. Nowadays, analyses based on high-throughput sequencing have become a key approach in genome-wide biology for crop improvement. Advances in genomics have resulted in the development of new technologies and strategies that give support to the experimental research. Release of the genomic sequences of wheat and barley has permitted the application of genome-scale approaches, such as those related to metabolomics, proteomics, transcriptomics, and phenomics analyses. In addition, new tools for gene identification, such are Genome-Editing and Genome-Wide Association Studies, are being developed. Modern research based in this new technological scenario is focused into understand regulatory systems critical to improving crop productivity. The final goal should be the functional genomic analysis of genes and regulatory networks that control important agronomic traits and biological processes; such as yield, grain quality, pathogen and pest resistance, nutrient-use efficiency, and abiotic stress resistance. This Special Issue aims to report novel research and reviews concerning the use of modern technologies to understand the molecular bases for wheat and barley improvement.

Prof. Manuel Martinez
Guest Editor

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Keywords

  • wheat
  • barley
  • functional genomics
  • systems biology
  • molecular pathways
  • agronomic traits
  • yield improvement
  • biotic resistance
  • abiotic resistance
  • grain quality

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Published Papers (19 papers)

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Editorial

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Open AccessEditorial
Editorial for Special Issue “Molecular Advances in Wheat and Barley”
Int. J. Mol. Sci. 2019, 20(14), 3501; https://doi.org/10.3390/ijms20143501 - 16 Jul 2019
Abstract
Along with maize and rice, allohexaploid bread wheat and diploid barley are the most cultivated crops in the world (FAOSTAT database, http://www [...] Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available

Research

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Open AccessArticle
The Dark Matter of Large Cereal Genomes: Long Tandem Repeats
Int. J. Mol. Sci. 2019, 20(10), 2483; https://doi.org/10.3390/ijms20102483 - 20 May 2019
Cited by 4
Abstract
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at [...] Read more.
Reference genomes of important cereals, including barley, emmer wheat and bread wheat, were released recently. Their comparison with genome size estimates obtained by flow cytometry indicated that the assemblies represent not more than 88–98% of the complete genome. This work is aimed at identifying the missing parts in two cereal genomes and proposing techniques to make the assemblies more complete. We focused on tandemly organised repetitive sequences, known to be underrepresented in genome assemblies generated from short-read sequence data. Our study found arrays of three tandem repeats with unit sizes of 1242 to 2726 bp present in the bread wheat reference genome generated from short reads. However, this and another wheat genome assembly employing long PacBio reads failed in integrating correctly the 2726-bp repeat in the pseudomolecule context. This suggests that tandem repeats of this size, frequently incorporated in unassigned scaffolds, may contribute to shrinking of pseudomolecules without reducing size of the entire assembly. We demonstrate how this missing information may be added to the pseudomolecules with the aid of nanopore sequencing of individual BAC clones and optical mapping. Using the latter technique, we identified and localised a 470-kb long array of 45S ribosomal DNA absent from the reference genome of barley. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Fine Mapping of the Wheat Leaf Rust Resistance Gene Lr42
Int. J. Mol. Sci. 2019, 20(10), 2445; https://doi.org/10.3390/ijms20102445 - 17 May 2019
Cited by 5
Abstract
Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both [...] Read more.
Leaf rust caused by Puccinia triticina Eriks is one of the most problematic diseases of wheat throughout the world. The gene Lr42 confers effective resistance against leaf rust at both seedling and adult plant stages. Previous studies had reported Lr42 to be both recessive and dominant in hexaploid wheat; however, in diploid Aegilops tauschii (TA2450), we found Lr42 to be dominant by studying segregation in two independent F2 and their F2:3 populations. We further fine-mapped Lr42 in hexaploid wheat using a KS93U50/Morocco F5 recombinant inbred line (RIL) population to a 3.7 cM genetic interval flanked by markers TC387992 and WMC432. The 3.7 cM Lr42 region physically corresponds to a 3.16 Mb genomic region on chromosome 1DS based on the Chinese Spring reference genome (RefSeq v.1.1) and a 3.5 Mb genomic interval on chromosome 1 in the Ae. tauschii reference genome. This region includes nine nucleotide-binding domain leucine-rich repeat (NLR) genes in wheat and seven in Ae. tauschii, respectively, and these are the likely candidates for Lr42. Furthermore, we developed two kompetitive allele-specific polymorphism (KASP) markers (SNP113325 and TC387992) flanking Lr42 to facilitate marker-assisted selection for rust resistance in wheat breeding programs. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Overexpression of a Wheat Aquaporin Gene, TdPIP2;1, Enhances Salt and Drought Tolerance in Transgenic Durum Wheat cv. Maali
Int. J. Mol. Sci. 2019, 20(10), 2389; https://doi.org/10.3390/ijms20102389 - 14 May 2019
Cited by 6
Abstract
In this study, we generated transgenic durum wheat cv. Maali overexpressing the wheat plasma membrane aquaporin TdPIP2;1 gene under the control of PrTdPIP2;1 promoter or under the constitutive PrCaMV35S promoter. Histochemical analysis of the fusion PrTdPIP2;1::TdPIP2;1::GusA [...] Read more.
In this study, we generated transgenic durum wheat cv. Maali overexpressing the wheat plasma membrane aquaporin TdPIP2;1 gene under the control of PrTdPIP2;1 promoter or under the constitutive PrCaMV35S promoter. Histochemical analysis of the fusion PrTdPIP2;1::TdPIP2;1::GusA in wheat plants showed that the β-glucuronidase (GUS) activity was detected in the leaves, stems and roots of stably transformed wheat T3 plants. Our results showed that transgenic wheat lines overexpressing the TdPIP2;1 gene exhibited improved germination rates and biomass production and retained low Na+ and high K+ concentrations in their shoots under high salt and osmotic stress conditions. In a long-term study under greenhouse conditions on salt or drought stress, transgenic TdPIP2;1 lines produced filled grains, whereas wild-type (WT) plants either died at the vegetative stage under salt stress or showed drastically reduced grain filling under drought stress. Performing real time RT-PCR experiments on wheat plants transformed with the fusion PrTdPIP2;1::GusA, we showed an increase in the accumulation of GusA transcripts in the roots of plants challenged with salt and drought stress. Study of the antioxidant defence system in transgenic wheat TdPIP2;1 lines showed that these lines induced the antioxidative enzymes Catalase (CAT) and Superoxide dismutase (SOD) activities more efficiently than the WT plants, which is associated with lower malondialdehyde and hydrogen peroxide contents. Taken together, these results indicate the high potential of the TdPIP2;1 gene for reducing water evaporation from leaves (water loss) in response to water deficit through the lowering of transpiration per unit leaf area (stomatal conductance) and engineering effective drought and salt tolerance in transgenic TdPIP2;1 lines. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Instability of Alien Chromosome Introgressions in Wheat Associated with Improper Positioning in the Nucleus
Int. J. Mol. Sci. 2019, 20(6), 1448; https://doi.org/10.3390/ijms20061448 - 22 Mar 2019
Cited by 7
Abstract
Alien introgressions introduce beneficial alleles into existing crops and hence, are widely used in plant breeding. Generally, introgressed alien chromosomes show reduced meiotic pairing relative to the host genome, and may be eliminated over generations. Reduced pairing appears to result from a failure [...] Read more.
Alien introgressions introduce beneficial alleles into existing crops and hence, are widely used in plant breeding. Generally, introgressed alien chromosomes show reduced meiotic pairing relative to the host genome, and may be eliminated over generations. Reduced pairing appears to result from a failure of some telomeres of alien chromosomes to incorporate into the leptotene bouquet at the onset of meiosis, thereby preventing chiasmate pairing. In this study, we analysed somatic nuclei of rye introgressions in wheat using 3D-FISH and found that while introgressed rye chromosomes or chromosome arms occupied discrete positions in the Rabl’s orientation similar to chromosomes of the wheat host, their telomeres frequently occupied positions away from the nuclear periphery. The frequencies of such abnormal telomere positioning were similar to the frequencies of out-of-bouquet telomere positioning at leptotene, and of pairing failure at metaphase I. This study indicates that improper positioning of alien chromosomes that leads to reduced pairing is not a strictly meiotic event but rather a consequence of a more systemic problem. Improper positioning in the nuclei probably impacts the ability of introgressed chromosomes to migrate into the telomere bouquet at the onset of meiosis, preventing synapsis and chiasma establishment, and leading to their gradual elimination over generations. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Genome-Wide Genetic Diversity and Population Structure of Tunisian Durum Wheat Landraces Based on DArTseq Technology
Int. J. Mol. Sci. 2019, 20(6), 1352; https://doi.org/10.3390/ijms20061352 - 18 Mar 2019
Cited by 8
Abstract
Tunisia, being part of the secondary center of diversity for durum wheat, has rich unexploited landraces that are being continuously lost and replaced by high yielding modern cultivars. This study aimed to investigate the genetic diversity and population structure of 196 durum wheat [...] Read more.
Tunisia, being part of the secondary center of diversity for durum wheat, has rich unexploited landraces that are being continuously lost and replaced by high yielding modern cultivars. This study aimed to investigate the genetic diversity and population structure of 196 durum wheat lines issued from landraces collected from Tunisia using Diversity Array Technology sequencing (DArTseq) and to understand possible ways of introduction in comparing them to landraces from surrounding countries. A total of 16,148 polymorphic DArTseq markers covering equally the A and B genomes were effective to assess the genetic diversity and to classify the accessions. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish five distinct groups that matched well with the farmer’s variety nomenclature. Interestingly, Mahmoudi and Biskri landraces constitute the same gene pool while Jenah Zarzoura constitutes a completely different group. Analysis of molecular variance (AMOVA) showed that the genetic variation was among rather than within the landraces. DAPC analysis of the Tunisian, Mediterranean and West Asian landraces confirmed our previous population structure and showed a genetic similarity between the Tunisian and the North African landraces with the exception of Jenah Zarzoura being the most distant. The genomic characterization of the Tunisian collection will enhance their conservation and sustainable use. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)
Int. J. Mol. Sci. 2019, 20(4), 962; https://doi.org/10.3390/ijms20040962 - 22 Feb 2019
Cited by 8
Abstract
Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of [...] Read more.
Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts’ activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in “essential” genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a ‘regulator’ to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Comparative Proteomic Analysis of Wheat Carrying Pm40 Response to Blumeria graminis f. sp. tritici Using Two-Dimensional Electrophoresis
Int. J. Mol. Sci. 2019, 20(4), 933; https://doi.org/10.3390/ijms20040933 - 21 Feb 2019
Cited by 3
Abstract
Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is considered a major wheat leaf disease in the main wheat producing regions of the world. Although many resistant wheat cultivars to this disease have been developed, little is known [...] Read more.
Wheat powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt) is considered a major wheat leaf disease in the main wheat producing regions of the world. Although many resistant wheat cultivars to this disease have been developed, little is known about their resistance mechanisms. Pm40 is a broad, effective resistance gene against powdery mildew in wheat line L699. The aim of this study was to investigate the resistance proteins after Bgt inoculation in wheat lines L699, Neimai836, and Chuannong26. Neimai836 with Pm21 was used as the resistant control, and Chuannong26 without any effective Pm genes was the susceptible control. Proteins were extracted from wheat leaves sampled 2, 4, 8, 12, and 24 h after Bgt inoculation, separated by two-dimensional electrophoresis, and stained with Coomassie brilliant blue G-250. The results showed that different proteins were upregulated and downregulated in three wheat cultivars at different time points. For the wheat cultivar L699, a total of 62 proteins were upregulated and 71 proteins were downregulated after Bgt inoculation. Among these, 46 upregulated proteins were identified by mass spectrometry analysis using the NCBI nr database of Triticum. The identified proteins were predicted to be associated with the defense response, photosynthesis, signal transduction, carbohydrate metabolism, energy pathway, protein turnover, and cell structure functions. It is inferred that the proteins are not only involved in defense response, but also other physiological and cellular processes to confer wheat resistance against Bgt. Therefore, the resistance products potentially mediate the immune response and coordinate other physiological and cellular processes during the resistance response to Bgt. The lipoxygenase, glucan exohydrolase, glucose adenylyltransferasesmall, phosphoribulokinase, and phosphoglucomutase are first reported to be involved in the interactions of wheat-Bgt at early stage. The further study of these proteins will deepen our understanding of their detailed functions and potentially develop more efficient disease control strategies. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Development of SNP, KASP, and SSR Markers by BSR-Seq Technology for Saturation of Genetic Linkage Map and Efficient Detection of Wheat Powdery Mildew Resistance Gene Pm61
Int. J. Mol. Sci. 2019, 20(3), 750; https://doi.org/10.3390/ijms20030750 - 11 Feb 2019
Cited by 5
Abstract
The gene Pm61 that confers powdery mildew resistance has been previously identified on chromosome arm 4AL in Chinese wheat landrace Xuxusanyuehuang (XXSYH). To facilitate the use of Pm61 in breeding practices, the bulked segregant analysis-RNA-Seq (BSR-Seq) analysis, in combination with the information on [...] Read more.
The gene Pm61 that confers powdery mildew resistance has been previously identified on chromosome arm 4AL in Chinese wheat landrace Xuxusanyuehuang (XXSYH). To facilitate the use of Pm61 in breeding practices, the bulked segregant analysis-RNA-Seq (BSR-Seq) analysis, in combination with the information on the Chinese Spring reference genome sequence, was performed in the F2:3 mapping population of XXSYH × Zhongzuo 9504. Two single nucleotide polymorphism (SNP), two Kompetitive Allele Specific PCR (KASP), and six simple sequence repeat (SSR) markers, together with previously identified polymorphic markers, saturated the genetic linkage map for Pm61, especially in the proximal side of the target gene that was short of gene-linked markers. In the newly established genetic linkage map, Pm61 was located in a 0.71 cM genetic interval and can be detected in a high throughput scale by the KASP markers Xicsk8 and Xicsk13 or by the standard PCR-based markers Xicscx497 and Xicsx538. The newly saturated genetic linkage map will be useful in molecular marker assisted-selection of Pm61 in breeding for disease resistant cultivar and in its map-based cloning. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Overexpression of Arabidopsis OPR3 in Hexaploid Wheat (Triticum aestivum L.) Alters Plant Development and Freezing Tolerance
Int. J. Mol. Sci. 2018, 19(12), 3989; https://doi.org/10.3390/ijms19123989 - 11 Dec 2018
Cited by 6
Abstract
Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid [...] Read more.
Jasmonates are plant hormones that are involved in the regulation of different aspects of plant life, wherein their functions and molecular mechanisms of action in wheat are still poorly studied. With the aim of gaining more insights into the role of jasmonic acid (JA) in wheat growth, development, and responses to environmental stresses, we have generated transgenic bread wheat plants overexpressing Arabidopsis 12-OXOPHYTODIENOATE REDUCTASE 3 (AtOPR3), one of the key genes of the JA biosynthesis pathway. Analysis of transgenic plants showed that AtOPR3 overexpression affects wheat development, including germination, growth, flowering time, senescence, and alters tolerance to environmental stresses. Transgenic wheat plants with high AtOPR3 expression levels have increased basal levels of JA, and up-regulated expression of ALLENE OXIDE SYNTHASE, a jasmonate biosynthesis pathway gene that is known to be regulated by a positive feedback loop that maintains and boosts JA levels. Transgenic wheat plants with high AtOPR3 expression levels are characterized by delayed germination, slower growth, late flowering and senescence, and improved tolerance to short-term freezing. The work demonstrates that genetic modification of the jasmonate pathway is a suitable tool for the modulation of developmental traits and stress responses in wheat. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Using the 6RLKu Minichromosome of Rye (Secale cereale L.) to Create Wheat-Rye 6D/6RLKu Small Segment Translocation Lines with Powdery Mildew Resistance
Int. J. Mol. Sci. 2018, 19(12), 3933; https://doi.org/10.3390/ijms19123933 - 07 Dec 2018
Cited by 9
Abstract
Long arms of rye (Secale cereale L.) chromosome 6 (6RL) carry powdery mildew resistance genes. However, these sources of resistance have not yet been successfully used in commercial wheat cultivars. The development of small segment translocation chromosomes carrying resistance may result in [...] Read more.
Long arms of rye (Secale cereale L.) chromosome 6 (6RL) carry powdery mildew resistance genes. However, these sources of resistance have not yet been successfully used in commercial wheat cultivars. The development of small segment translocation chromosomes carrying resistance may result in lines carrying the 6R chromosome becoming more commercially acceptable. However, no wheat-rye 6RL small segment translocation line with powdery mildew resistance has been reported. In this study, a wheat-rye 6RLKu minichromosome addition line with powdery mildew resistance was identified, and this minichromosome was derived from the segment between L2.5 and L2.8 of the 6RLKu chromosome arm. Following irradiation, the 6RLKu minichromosome divided into two smaller segments, named 6RLKumi200 and 6RLKumi119, and these fragments participated in the formation of wheat-rye small segment translocation chromosomes 6DS/6RLKumi200 and 6DL/6RLKumi119, respectively. The powdery mildew resistance gene was found to be located on the 6RLKumi119 segment. Sixteen 6RLKumi119-specific markers were developed, and their products were cloned and sequenced. Nucleotide BLAST searches indicated that 14 of the 16 sequences had 91–100% similarity with nine scaffolds derived from 6R chromosome of S. cereale L. Lo7. The small segment translocation chromosome 6DL/6RLKumi119 makes the practical utilization in agriculture of powdery mildew resistance gene on 6RLKu more likely. The nine scaffolds are useful for further studying the structure and function of this small segment. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat
Int. J. Mol. Sci. 2018, 19(12), 3749; https://doi.org/10.3390/ijms19123749 - 26 Nov 2018
Cited by 3
Abstract
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) [...] Read more.
Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessArticle
Genome-Wide Association Study Reveals Novel Genomic Regions Associated with 10 Grain Minerals in Synthetic Hexaploid Wheat
Int. J. Mol. Sci. 2018, 19(10), 3237; https://doi.org/10.3390/ijms19103237 - 19 Oct 2018
Cited by 19
Abstract
Synthetic hexaploid wheat (SHW; Triticum durum L. × Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, [...] Read more.
Synthetic hexaploid wheat (SHW; Triticum durum L. × Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting a potential role in grain mineral concentration. Twenty-four MTAs on the D-genome were novel and showed the potential of Ae. tauschii for improving grain mineral concentrations such as Ca, Co, Cu, Li, Mg, Mn, and Ni. Interestingly, the large number of novel MTAs (36) identified on the AB genome of these SHWs indicated that there is a lot of variation yet to be explored and to be used in the A and B genome along with the D-genome. Regression analysis identified a positive correlation between a cumulative number of favorable alleles at MTA loci in a genotype and grain mineral concentration. Additionally, we identified multi-traits and stable MTAs and recommended 13 top 10% SHWs with a higher concentration of beneficial grain minerals (Cu, Fe, Mg, Mn, Ni, and Zn), a large number of favorable alleles compared to low ranking genotypes and checks that could be utilized in the breeding program for the genetic biofortification. This study will further enhance our understanding of the genetic architecture of grain minerals in wheat and related cereals. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Review

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Open AccessReview
Cas Endonuclease Technology—A Quantum Leap in the Advancement of Barley and Wheat Genetic Engineering
Int. J. Mol. Sci. 2019, 20(11), 2647; https://doi.org/10.3390/ijms20112647 - 29 May 2019
Cited by 5
Abstract
Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or [...] Read more.
Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or mutagenic chemicals facilitated dramatically increased mutation rates, which remarkably extended the genetic diversity of crop plants. However, a major drawback of conventionally induced mutagenesis is that genetic alterations occur simultaneously across the whole genome and at very high numbers per individual plant. By contrast, the newly emerging Cas endonuclease technology allows for the induction of mutations at user-defined positions in the plant genome. In fundamental and breeding-oriented research, this opens up unprecedented opportunities for the elucidation of gene functions and the targeted improvement of plant performance. This review covers historical aspects of the development of customizable endonucleases, information on the mechanisms of targeted genome modification, as well as hitherto reported applications of Cas endonuclease technology in barley and wheat that are the agronomically most important members of the temperate cereals. Finally, current trends in the further development of this technology and some ensuing future opportunities for research and biotechnological application are presented. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessReview
Molecular Advances on Phytases in Barley and Wheat
Int. J. Mol. Sci. 2019, 20(10), 2459; https://doi.org/10.3390/ijms20102459 - 18 May 2019
Cited by 8
Abstract
Phytases are pro-nutritional enzymes that hydrolyze phytate and make associated nutrients, such as phosphorous, iron, and zinc, bioavailable. Single-stomached animals and humans depend on phytase supplied through the diet or the action of phytase on the food before ingestion. As a result, phytases—or [...] Read more.
Phytases are pro-nutritional enzymes that hydrolyze phytate and make associated nutrients, such as phosphorous, iron, and zinc, bioavailable. Single-stomached animals and humans depend on phytase supplied through the diet or the action of phytase on the food before ingestion. As a result, phytases—or lack thereof—have a profound impact on agricultural ecosystems, resource management, animal health, and public health. Wheat, barley and their Triticeae relatives make exceptionally good natural sources of phytase. This review highlights advances in the understanding of the molecular basis of the phytase activity in wheat and barley, which has taken place over the past decade. It is shown how the phytase activity in the mature grains of wheat and barley can be ascribed to the PAPhy_a gene, which exists as a single gene in barley and in two or three homeologous copies in tetra- and hexaploid wheat, respectively. It is discussed how understanding the function and regulation of PAPhy_a may support the development of improved wheat and barley with even higher phytase activity. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessReview
Insights on the Proteases Involved in Barley and Wheat Grain Germination
Int. J. Mol. Sci. 2019, 20(9), 2087; https://doi.org/10.3390/ijms20092087 - 28 Apr 2019
Cited by 7
Abstract
Seed storage proteins must be hydrolyzed by proteases to deliver the amino acids essential for embryo growth and development. Several groups of proteases involved in this process have been identified in both the monocot and the dicot species. This review focuses on the [...] Read more.
Seed storage proteins must be hydrolyzed by proteases to deliver the amino acids essential for embryo growth and development. Several groups of proteases involved in this process have been identified in both the monocot and the dicot species. This review focuses on the implication of proteases during germination in two cereal species, barley and wheat, where proteolytic control during the germination process has considerable economic importance. Formerly, the participation of proteases during grain germination was inferred from reports of proteolytic activities, the expression of individual genes, or the presence of individual proteins and showed a prominent role for papain-like and legumain-like cysteine proteases and for serine carboxypeptidases. Nowadays, the development of new technologies and the release of the genomic sequences of wheat and barley have permitted the application of genome-scale approaches, such as those used in functional genomics and proteomics. Using these approaches, the repertoire of proteases known to be involved in germination has increased and includes members of distinct protease families. The development of novel techniques based on shotgun proteomics, activity-based protein profiling, and comparative and structural genomics will help to achieve a general view of the proteolytic process during germination. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessReview
Resistance to Cereal Cyst Nematodes in Wheat and Barley: An Emphasis on Classical and Modern Approaches
Int. J. Mol. Sci. 2019, 20(2), 432; https://doi.org/10.3390/ijms20020432 - 19 Jan 2019
Cited by 14
Abstract
Cereal cyst nematodes (CCNs) are among the most important nematode pests that limit production of small grain cereals like wheat and barley. These nematodes alone are estimated to reduce production of crops by 10% globally. This necessitates a huge enhancement of nematode resistance [...] Read more.
Cereal cyst nematodes (CCNs) are among the most important nematode pests that limit production of small grain cereals like wheat and barley. These nematodes alone are estimated to reduce production of crops by 10% globally. This necessitates a huge enhancement of nematode resistance in cereal crops against CCNs. Nematode resistance in wheat and barley in combination with higher grain yields has been a preferential research area for cereal nematologists. This usually involved the targeted genetic exploitations through natural means of classical selection breeding of resistant genotypes and finding quantitative trait luci (QTLs) associated with resistance genes. These improvements were based on available genetic diversity among the crop plants. Recently, genome-wide association studies have widely been exploited to associate nematode resistance or susceptibility with particular regions of the genome. Use of biotechnological tools through the application of various transgenic strategies for enhancement of nematode resistance in various crop plants including wheat and barley had also been an important area of research. These modern approaches primarily include the use of gene silencing, exploitation of nematode effector genes, proteinase inhibitors, chemodisruptive peptides and a combination of one or more of these approaches. Furthermore, the perspective genome editing technologies including CRISPR-Cas9 could also be helpful for improving CCN resistance in wheat and barley. The information provided in this review will be helpful to enhance resistance against CCNs and will attract the attention of the scientific community towards this neglected area. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessReview
Host-Induced Gene Silencing: A Powerful Strategy to Control Diseases of Wheat and Barley
Int. J. Mol. Sci. 2019, 20(1), 206; https://doi.org/10.3390/ijms20010206 - 08 Jan 2019
Cited by 24
Abstract
Wheat and barley are the most highly produced and consumed grains in the world. Various pathogens—viruses, bacteria, fungi, insect pests, and nematode parasites—are major threats to yield and economic losses. Strategies for the management of disease control mainly depend on resistance or tolerance [...] Read more.
Wheat and barley are the most highly produced and consumed grains in the world. Various pathogens—viruses, bacteria, fungi, insect pests, and nematode parasites—are major threats to yield and economic losses. Strategies for the management of disease control mainly depend on resistance or tolerance breeding, chemical control, and biological control. The discoveries of RNA silencing mechanisms provide a transgenic approach for disease management. Host-induced gene silencing (HIGS) employing RNA silencing mechanisms and, specifically, silencing the targets of invading pathogens, has been successfully applied in crop disease prevention. Here, we cover recent studies that indicate that HIGS is a valuable tool to protect wheat and barley from diseases in an environmentally friendly way. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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Open AccessBrief Report
New ND-FISH-Positive Oligo Probes for Identifying Thinopyrum Chromosomes in Wheat Backgrounds
Int. J. Mol. Sci. 2019, 20(8), 2031; https://doi.org/10.3390/ijms20082031 - 25 Apr 2019
Cited by 4
Abstract
Thinopyrum has been widely used to improve wheat (Triticum aestivum L.) cultivars. Non-denaturing fluorescence in situ hybridization (ND-FISH) technology using oligonucleotides (oligo) as probes provides a convenient and efficient way to identify alien chromosomes in wheat backgrounds. However, suitable ND-FISH-positive oligo probes [...] Read more.
Thinopyrum has been widely used to improve wheat (Triticum aestivum L.) cultivars. Non-denaturing fluorescence in situ hybridization (ND-FISH) technology using oligonucleotides (oligo) as probes provides a convenient and efficient way to identify alien chromosomes in wheat backgrounds. However, suitable ND-FISH-positive oligo probes for distinguishing Thinopyrum chromosomes from wheat are lacking. Two oligo probes, Oligo-B11 and Oligo-pThp3.93, were designed according to the published Thinopyrum ponticum (Th. ponticum)-specific repetitive sequences. Both Oligo-B11 and Oligo-pThp3.93 can be used for ND-FISH analysis and can replace conventional GISH and FISH to discriminate some chromosomes of Th. elongatum, Th. intermedium, and Th. ponticum in wheat backgrounds. The two oligo probes provide a convenient way for the utilization of Thinopyrum germplasms in future wheat breeding programs. Full article
(This article belongs to the Special Issue Molecular Advances in Wheat and Barley) Printed Edition available
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