Genetics and Breeding of Triticeae: Improving Small Grain Crop Plants

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 November 2021) | Viewed by 12018

Special Issue Editors


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Guest Editor
College of Agriculture and Natural Resources, University of Maryland, College Park, MD 20742, USA

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Co-Guest Editor
School of Plant and Environmental Sciences, Virginia Tech University, Blacksburg, VA, USA
Interests: small grain crop plant genetics; plant quantitative genetics; plant genetic improvement

Special Issue Information

Dear Colleagues,

For the global food security, the tribe Triticeae is arguably the most important group of crop species. Triticeae houses approximately 500 annual and perennial species and plays a vital role in nurturing human civilization, livelihood, and food security. Triticeae is the home of a number of the world’s most important cereal crop species including wheat, barley, rye, and triticale, and together, these constitute over 50% of total crop production worldwide (http://www.fao.org/). Additionally, the cereal grains are considered one of the most important renewable resources for food, feed, and industrial raw materials.

The world human population is expected to surpass 9 billion in 2050. Global crop productions will be required to be increased at the rate of ~2% per year up to 2050 to produce enough food to feed this rapidly growing human population. Rapidly increasing human population, changing climatic conditions, and various biotic and abiotic stresses pose big challenges for the production of cereal crop plants and hence affecting world food security. These challenges have led scientists working on Triticeae breeding, genetic, and genomics to generate a breadth of information to develop tools and germplasm, genetic, and genomic resources that enables development of elite cultivars.

Next-generation sequencing and technical advances in sequencing technologies and genome assembly programs have led to the establishment of the reference genomes of several plant species. The complexities of the major small grain crop plants, including wheat, barley, and rye genomes have hampered the development of genomics resources and their application to produce improved Triticeae cultivars. Recently, reference genome, exome, and transcriptome resources were established for the important crop plants (wheat barley and rye) from the tribe Triticeae. These advances in Triticeae genomics will deliver new knowledge and tools to scientists for a better understanding of Triticeae genomes organization, evolution, and function. These new developments will allow crop breeders to incorporate new gene alleles against biotic and abiotic stresses and to improve quality traits to satisfy the needs of small grain stakeholders.

This Research Topic will provide an excellent platform to bring together new knowledge related to genetics and genomics of small grain crops to improve their resistance to biotic and abiotic stresses and the composition, nutritional quality, and processing properties through molecular breeding approaches. The Topic will also deliver valuable information on agronomically important genes, across the small grain crops at the chromosomal and DNA levels.

Dr. Vijay Tiwari
Dr. Nicholas Santantonio
Guest Editors

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Keywords

  • Genome
  • Sequencing
  • QTL
  • Exome
  • Gene
  • Transposons
  • Yield
  • Diseases
  • Resistance
  • Breeding
  • Genomics
  • Phenomics
  • Translocations
  • Heat
  • Drought

Published Papers (3 papers)

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Research

21 pages, 1987 KiB  
Article
Genome-Wide Identification, Characterization and Expression Pattern Analysis of the γ-Gliadin Gene Family in the Durum Wheat (Triticum durum Desf.) Cultivar Svevo
by Roberta Paris, Giuseppe Petruzzino, Michele Savino, Vanessa De Simone, Donatella B. M. Ficco and Daniela Trono
Genes 2021, 12(11), 1743; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111743 - 29 Oct 2021
Cited by 2 | Viewed by 2054
Abstract
Very recently, the genome of the modern durum wheat cv. Svevo was fully sequenced, and its assembly is publicly available. So, we exploited the opportunity to carry out an in-depth study for the systematic characterization of the γ-gliadin gene family in the cv. [...] Read more.
Very recently, the genome of the modern durum wheat cv. Svevo was fully sequenced, and its assembly is publicly available. So, we exploited the opportunity to carry out an in-depth study for the systematic characterization of the γ-gliadin gene family in the cv. Svevo by combining a bioinformatic approach with transcript and protein analysis. We found that the γ-gliadin family consists of nine genes that include seven functional genes and two pseudogenes. Three genes, Gli-γ1a, Gli-γ3a and Gli-γ4a, and the pseudogene Gli-γ2a* mapped on the A genome, whereas the remaining four genes, Gli-γ1b, Gli-γ2b, Gli-γ3b and Gli-γ5b, and the pseudogene Gli-γ4b* mapped on the B genome. The functional γ-gliadins presented all six domains and eight-cysteine residues typical of γ-gliadins. The Gli-γ1b also presented an additional cysteine that could possibly have a role in the formation of the gluten network through binding to HMW glutenins. The γ-gliadins from the A and B genome differed in their celiac disease (CD) epitope content and composition, with the γ-gliadins from the B genome showing the highest frequency of CD epitopes. In all the cases, almost all the CD epitopes clustered in the central region of the γ-gliadin proteins. Transcript analysis during seed development revealed that all the functional γ-gliadin genes were expressed with a similar pattern, although significant differences in the transcript levels were observed among individual genes that were sometimes more than 60-fold. A progressive accumulation of the γ-gliadin fraction was observed in the ripening seeds that reached 34% of the total gliadin fraction at harvest maturity. We believe that the insights generated in the present study could aid further studies on gliadin protein functions and future breeding programs aimed at the selection of new healthier durum wheat genotypes. Full article
(This article belongs to the Special Issue Genetics and Breeding of Triticeae: Improving Small Grain Crop Plants)
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9 pages, 3823 KiB  
Article
The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene
by Moran Nave, Mihriban Taş, John Raupp, Vijay K. Tiwari, Hakan Ozkan, Jesse Poland, Iago Hale, Takao Komatsuda and Assaf Distelfeld
Genes 2021, 12(3), 338; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030338 - 25 Feb 2021
Cited by 7 | Viewed by 2778
Abstract
Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes [...] Read more.
Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species. Full article
(This article belongs to the Special Issue Genetics and Breeding of Triticeae: Improving Small Grain Crop Plants)
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24 pages, 5754 KiB  
Article
The AP2/ERF Gene Family in Triticum durum: Genome-Wide Identification and Expression Analysis under Drought and Salinity Stresses
by Sahar Faraji, Ertugrul Filiz, Seyed Kamal Kazemitabar, Alessandro Vannozzi, Fabio Palumbo, Gianni Barcaccia and Parviz Heidari
Genes 2020, 11(12), 1464; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121464 - 07 Dec 2020
Cited by 78 | Viewed by 6092
Abstract
Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) [...] Read more.
Members of the AP2/ERF transcription factor family play critical roles in plant development, biosynthesis of key metabolites, and stress response. A detailed study was performed to identify TtAP2s/ERFs in the durum wheat (Triticum turgidum ssp. durum) genome, which resulted in the identification of 271 genes distributed on chromosomes 1A-7B. By carrying 27 genes, chromosome 6A had the highest number of TtAP2s/ERFs. Furthermore, a duplication assay of TtAP2s/ERFs demonstrated that 70 duplicated gene pairs had undergone purifying selection. According to RNA-seq analysis, the highest expression levels in all tissues and in response to stimuli were associated with DRF and ERF subfamily genes. In addition, the results revealed that TtAP2/ERF genes have tissue-specific expression patterns, and most TtAP2/ERF genes were significantly induced in the root tissue. Additionally, 13 TtAP2/ERF genes (six ERFs, three DREBs, two DRFs, one AP2, and one RAV) were selected for further analysis via qRT-PCR of their potential in coping with drought and salinity stresses. The TtAP2/ERF genes belonging to the DREB subfamily were markedly induced under both drought-stress and salinity-stress conditions. Furthermore, docking simulations revealed several residues in the pocket sites of the proteins associated with the stress response, which may be useful in future site-directed mutagenesis studies to increase the stress tolerance of durum wheat. This study could provide valuable insights for further evolutionary and functional assays of this important gene family in durum wheat. Full article
(This article belongs to the Special Issue Genetics and Breeding of Triticeae: Improving Small Grain Crop Plants)
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