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Genetic and Genomic Approaches for Breeding in Wheat
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Genetic and Genomic Approaches for Breeding in Wheat

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

Deadline for manuscript submissions: closed (25 August 2023) | Viewed by 4618

Special Issue Editors

Dr. Alireza Pour-Aboughadareh

E-Mail Website
Guest Editor
Department of Cereal Research, Seed and Plant Improvement Institute, Karaj, Iran
Interests: molecular breeding; abiotic stresses; genetic diversity; wheat and barley germplasms; plant physiology
Special Issues, Collections and Topics in MDPI journals
Dr. Jan Bocianowski

E-Mail Website
Guest Editor
Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
Interests: biometry; quantitative genetics; regression analysis; multivariate regression; plant breeding
Dr. Parviz Heidari

E-Mail Website
Guest Editor
Faculty of Agricultural, Shahrood University of Technology, Shahrood, Iran
Interests: cell signaling; abiotic stresses; functional analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Among cereal crops, wheat is the most important source of dietary protein and plays a critical role in supplying food worldwide. Although in the second half of the 20th century, a significant increase in the production of high-yield wheat has been observed due to an initiative known as the Green Revolution, the changing climate has made its sustainable production incredibly difficult. Wheat production faces a lot of environmental stresses that limit its growth and, ultimately, yield performance. In this situation, conventional breeding strategies are time-consuming and ineffective in attaining high-yield goals under changing climates. Hence, the use of new breeding approaches in wheat breeding is necessary to achieve sustainable production. Progress in biotechnological tools has led to the appearance of several genomic tools that can accelerate breeding programs. Several genomic approaches, such as genomic selection, recurrent selection through QTL and meta-QTL analysis, the use of genome-wide markers for gene mapping, marker-assisted selection in haploid breeding, and heterosis breeding are currently used as novel approaches for developing climate-resilient wheat cultivars. The recent development and application of high-throughput approaches such as NGS have shifted the research focus from individual genes to networks of genes with a common function. This has deepened our knowledge of the underlying genetic bases of complex agronomic traits in wheat.

This Special Issue welcomes original research articles and reviews discussing the latest advances related to genetic and genomic approaches for breeding in wheat. We believe that wheat breeders will find this compilation helpful.

Dr. Alireza Pour-Aboughadareh
Dr. Jan Bocianowski
Dr. Parviz Heidari
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • wheat
  • wheat germplasm
  • genetic diversity
  • molecular markers
  • genomic selection
  • marker–trait association
  • genetic mapping
  • association analysis
  • transcriptomics
  • gene editing

Published Papers (3 papers)

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Research

22 pages, 15190 KiB  
Article
Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study
by S Ramappa, Monika A. Joshi, Hari Krishna, Vijay Dunna, Neelu Jain, Rohini Sreevathsa and Narayana Bhat Devate
Genes 2023, 14(10), 1902; https://doi.org/10.3390/genes14101902 - 30 Sep 2023
Viewed by 1040
Abstract
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat’s capacity [...] Read more.
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat’s capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (−0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance −log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress. Full article
(This article belongs to the Special Issue Genetic and Genomic Approaches for Breeding in Wheat)
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15 pages, 1172 KiB  
Article
Expression Profiling of the Slow Rusting Resistance Genes Lr34/Yr18 and Lr67/Yr46 in Common Wheat (Triticum aestivum L.) and Associated miRNAs Patterns
by Julia Spychała, Agnieszka Tomkowiak, Aleksandra Noweiska, Roksana Bobrowska, Jan Bocianowski, Michał Książkiewicz, Aleksandra Sobiech and Michał Tomasz Kwiatek
Genes 2023, 14(7), 1376; https://doi.org/10.3390/genes14071376 - 29 Jun 2023
Cited by 2 | Viewed by 1404
Abstract
The main efforts in common wheat (Triticum aestivum L.) breeding focus on yield, grain quality, and resistance to biotic and abiotic stresses. One of the major threats affecting global wheat cultivation and causing significant crop production losses are rust diseases, including leaf [...] Read more.
The main efforts in common wheat (Triticum aestivum L.) breeding focus on yield, grain quality, and resistance to biotic and abiotic stresses. One of the major threats affecting global wheat cultivation and causing significant crop production losses are rust diseases, including leaf rust caused by a biotrophic fungus Puccinia triticina Eriks. Genetically determined resistance to leaf rust has been characterized in young plants (seedling resistance) as well as in plants at the adult plant stage. At the seedling stage, resistance is controlled vertically by major R genes, conferring a race-specific response that is highly effective but usually short-lived due to the rapid evolution of potentially virulent fungi. In mature plants, horizontal adult plant resistance (APR) was described, which provides long-term protection against multiple races of pathogens. A better understanding of molecular mechanisms underlying the function of APR genes would enable the development of new strategies for resistance breeding in wheat. Therefore, in the present study we focused on early transcriptomic responses of two major wheat APR genes, Lr34 and Lr67, and three complementary miRNAs, tae-miR9653b, tae-miR9773 and tae-miR9677b, to inoculation with P. triticina. Plant material consisted of five wheat reference varieties, Artigas, NP846, Glenlea, Lerma Rojo and TX89D6435, containing the Lr34/Yr18 and Lr67/Yr46 resistance genes. Biotic stress was induced by inoculation with fungal spores under controlled conditions in a phytotron. Plant material consisted of leaf tissue sampled before inoculation as well as 6, 12, 24 and 48 h postinoculation (hpi). The APR gene expression was quantified using real-time PCR with two reference genes, whereas miRNA was quantified using droplet digital PCR. This paper describes the resistance response of APR genes to inoculation with races of leaf rust-causing fungi that occur in central Europe. The study revealed high variability of expression profiles between varieties and time-points, with the prevalence of downregulation for APR genes and upregulation for miRNAs during the development of an early defense response. Nevertheless, despite the downregulation initially observed, the expression of Lr34 and Lr67 genes in studied cultivars was significantly higher than in a control line carrying wild (susceptible) alleles. Full article
(This article belongs to the Special Issue Genetic and Genomic Approaches for Breeding in Wheat)
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17 pages, 1191 KiB  
Article
Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers
by Aras Türkoğlu, Kamil Haliloğlu, Seyyed Abolgahasem Mohammadi, Ali Öztürk, Parisa Bolouri, Güller Özkan, Jan Bocianowski, Alireza Pour-Aboughadareh and Bita Jamshidi
Genes 2023, 14(6), 1182; https://doi.org/10.3390/genes14061182 - 29 May 2023
Cited by 4 | Viewed by 1612
Abstract
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were [...] Read more.
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon’s information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses. Full article
(This article belongs to the Special Issue Genetic and Genomic Approaches for Breeding in Wheat)
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