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Advanced Research in Wheat Genome and Breeding
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Advanced Research in Wheat Genome and Breeding

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 7492

Special Issue Editor

Dr. Maria Oszvald

E-Mail Website
Guest Editor
Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
Interests: plant tissue culture; molecular biology; biotechnology; plant biotechnology; agricultural biotechnology; plant genetics

Special Issue Information

Dear Colleagues,

Wheat is one of the most important crops, providing a source of dietary protein and calories for the majority of the world’s population.

Wheat production is challenged by biotic and abiotic stresses, causing significant yield losses in global wheat production environments that can lead to food insecurity. There is also a need for a healthier diet, which, for instance, includes higher fibre intake.

The above being the case, developing effective resistance genes in wheat breeding programs is essential. Understanding the genetic background of grain development could help to identify, characterize, and deploy effective genes from diverse sources into pre-breeding lines and future wheat varieties.

Next-generation sequencing (NGS) platforms and associated bioinformatics tools have revolutionized wheat genomics. The full wheat genome sequence alignment is the most important landmark that enables the identification of marker–trait associations, candidate genes, and enhanced breeding values in genomic selection studies. High-throughput genotyping platforms have an essential role in the estimation of genetic diversity, the construction of high-density genetic maps, dissecting polygenic traits, better understanding their interactions through GWAS and QTL mapping, and the isolation of different genes. The application of breeder-friendly KASP assays in wheat breeding programs has expedited the identification and pyramiding of resistance- or quality-related alleles/genes in elite lines.

Dr. Maria Oszvald
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 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 genome
  • candidate genes
  • QTL mapping
  • breeding
  • genetic traits

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Published Papers (5 papers)

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Research

19 pages, 2839 KiB  
Article
Diversity of Expression Patterns of Lr34, Lr67, and Candidate Genes towards Lr46 with Analysis of Associated miRNAs in Common Wheat Hybrids in Response to Puccinia triticina Fungus
by Julia Spychała, Agnieszka Tomkowiak, Aleksandra Noweiska, Roksana Bobrowska, Jan Bocianowski, Aleksandra Sobiech and Michał Tomasz Kwiatek
Curr. Issues Mol. Biol. 2024, 46(6), 5511-5529; https://doi.org/10.3390/cimb46060329 - 31 May 2024
Viewed by 787
Abstract
Leaf rust caused by Puccinia triticina (Pt) is one of the most dangerous diseases causing significant losses in common wheat crops. In adult plants resistant to rust, a horizontal adult plant resistance (APR) type is observed, which protects the plant against multiple pathogen [...] Read more.
Leaf rust caused by Puccinia triticina (Pt) is one of the most dangerous diseases causing significant losses in common wheat crops. In adult plants resistant to rust, a horizontal adult plant resistance (APR) type is observed, which protects the plant against multiple pathogen races and is distinguished by greater persistence under production conditions. Crucial pleiotropic slow-rust genes such as Lr34, Lr46, Lr67, and Lr68, in combination with other genes of lesser influence, continue to increase durable resistance to rust diseases. Based on our previous results, we selected four candidate genes for Lr46 out of ten candidates and analysed them for expression before and after inoculation by P. triticina. As part of our study, we also investigated the expression patterns of miRNA molecules complementary to Lr34 and the candidate genes. The aim of the study was to analyse the expression profiles of candidate genes for the Lr46 gene and the Lr34 and Lr67 genes responsible for the differential leaf-rust resistance of hybrid forms of the F1 generation resulting from crosses between the Glenlea cultivar and cultivars from Polish breeding companies. In addition, the expression of five miRNAs (tae-miR9653b, tae-miR5384-3p, tae-miR9780, tae-miR9775 and tae-miR164), complementary to Lr34, and selected candidate genes were analysed using stem-loop RT-PCR and ddPCR. Biotic stress was induced in adult plants by inoculation with Pt fungal spores, under controlled conditions. Plant material was collected before and 6, 12, 24, and 48 h after inoculation (hpi). Differences in expression patterns of Lr34, Lr67, and candidate genes (for Lr46) were analysed by qRT-PCR and showed that gene expression changed at the analysed time points. Identification of molecular markers coupled to the Lr genes studied was also carried out to confirm the presence of these genes in wheat hybrids. qRT-PCR was used to examine the expression levels of the resistance genes. The highest expression of Lr46/Yr29 genes (Lr46-Glu2, Lr46-RLK1, Lr46-RLK2, and Lr46-RLK3) occurred at 12 and 24 hpi, and such expression profiles were obtained for only one candidate gene among the four genes analysed (Lr46-Glu2), indicating that it may be involved in resistance mechanisms of response to Pt infection. Full article
(This article belongs to the Special Issue Advanced Research in Wheat Genome and Breeding)
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20 pages, 5048 KiB  
Article
An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress
by Xin Liu, Selvakumar Sukumaran, Esteri Viitanen, Nupur Naik, Sameer Hassan and Henrik Aronsson
Curr. Issues Mol. Biol. 2024, 46(5), 4417-4436; https://doi.org/10.3390/cimb46050268 - 7 May 2024
Viewed by 1014
Abstract
Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many [...] Read more.
Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat’s salt tolerance. Full article
(This article belongs to the Special Issue Advanced Research in Wheat Genome and Breeding)
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21 pages, 3381 KiB  
Article
Phenotyping and Exploitation of Kompetitive Allele-Specific PCR Assays for Genes Underpinning Leaf Rust Resistance in New Spring Wheat Mutant Lines
by Saule Kenzhebayeva, Shynarbek Mazkirat, Sabina Shoinbekova, Saule Atabayeva, Alfia Abekova, Nargul Omirbekova, Gulina Doktyrbay, Saltant Asrandina, Dinara Zharassova, Aigul Amirova and Albrecht Serfling
Curr. Issues Mol. Biol. 2024, 46(1), 689-709; https://doi.org/10.3390/cimb46010045 - 12 Jan 2024
Cited by 1 | Viewed by 1455
Abstract
Leaf rust (Puccinia triticina Eriks) is a wheat disease causing substantial yield losses in wheat production globally. The identification of genetic resources with permanently effective resistance genes and the generation of mutant lines showing increased levels of resistance allow the efficient incorporation [...] Read more.
Leaf rust (Puccinia triticina Eriks) is a wheat disease causing substantial yield losses in wheat production globally. The identification of genetic resources with permanently effective resistance genes and the generation of mutant lines showing increased levels of resistance allow the efficient incorporation of these target genes into germplasm pools by marker-assisted breeding. In this study, new mutant (M3 generation) lines generated from the rust-resistant variety Kazakhstanskaya-19 were developed using gamma-induced mutagenesis through 300-, 350-, and 400-Gy doses. In field trials after leaf rust inoculation, 75 mutant lines showed adult plant resistance. These lines were evaluated for resistance at the seedling stage via microscopy in greenhouse experiments. Most of these lines (89.33%) were characterized as resistant at both developmental stages. Hyperspectral imaging analysis indicated that infected leaves of wheat genotypes showed increased relative reflectance in visible and near-infrared light compared to the non-infected genotypes, with peak means at 462 and 644 nm, and 1936 and 2392 nm, respectively. Five spectral indexes, including red edge normalized difference vegetation index (RNDVI), structure-insensitive pigment index (SIPI), ratio vegetation index (RVSI), water index (WI), and normalized difference water index (NDWI), demonstrated significant potential for determining disease severity at the seedling stage. The most significant differences in reflectance between susceptible and resistant mutant lines appeared at 694.57 and 987.51 nm. The mutant lines developed were also used for the development and validation of KASP markers for leaf rust resistance genes Lr1, Lr2a, Lr3, Lr9, Lr10, and Lr17. The mutant lines had high frequencies of “a” resistance alleles (0.88) in all six Lr genes, which were significantly associated with seedling resistance and suggest the potential of favorable haplotype introgression through functional markers. Nine mutant lines characterized by the presence of “b” alleles in Lr9 and Lr10—except for one line with allele “a” in Lr9 and three mutant lines with allele “a” in Lr10—showed the progressive development of fungal haustorial mother cells 72 h after inoculation. One line from 300-Gy-dosed mutant germplasm with “b” alleles in Lr1, Lr2a, Lr10, and Lr17 and “a” alleles in Lr3 and Lr9 was characterized as resistant based on the low number of haustorial mother cells, suggesting the contribution of the “a” alleles of Lr3 and Lr9. Full article
(This article belongs to the Special Issue Advanced Research in Wheat Genome and Breeding)
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31 pages, 9129 KiB  
Article
Physiological and Transcriptomic Analyses Reveal Commonalities and Specificities in Wheat in Response to Aluminum and Manganese
by Daozhen Luo, Chunnuan Xian, Wenjie Zhang, Ying Qin, Qing Li, Muhammad Usman, Shiheng Sun, Yongxiu Xing and Dengfeng Dong
Curr. Issues Mol. Biol. 2024, 46(1), 367-397; https://doi.org/10.3390/cimb46010024 - 2 Jan 2024
Cited by 3 | Viewed by 1647
Abstract
Aluminum (Al) and manganese (Mn) toxicity are the top two constraints of crop production in acid soil. Crops have evolved common and specific mechanisms to tolerate the two stresses. In the present study, the responses (toxicity and tolerance) of near-isogenic wheat lines (ET8 [...] Read more.
Aluminum (Al) and manganese (Mn) toxicity are the top two constraints of crop production in acid soil. Crops have evolved common and specific mechanisms to tolerate the two stresses. In the present study, the responses (toxicity and tolerance) of near-isogenic wheat lines (ET8 and ES8) and their parents (Carazinho and Egret) to Al and Mn were compared by determining the physiological parameters and conducting transcriptome profiling of the roots. The results showed the following: (1) Carazinho and ET8 exhibited dual tolerance to Al and Mn compared to Egret and ES8, indicated by higher relative root elongation and SPAD. (2) After entering the roots, Al was mainly distributed in the roots and fixed in the cell wall, while Mn was mainly distributed in the cell sap and then transported to the leaves. Both Al and Mn stresses decreased the contents of Ca, Mg, and Zn; Mn stress also inhibited the accumulation of Fe, while Al showed an opposite effect. (3) A transcriptomic analysis identified 5581 differentially expressed genes (DEGs) under Al stress and 4165 DEGs under Mn stress. Among these, 2774 DEGs were regulated by both Al and Mn stresses, while 2280 and 1957 DEGs were exclusively regulated by Al stress and Mn stress, respectively. GO and KEGG analyses indicated that cell wall metabolism responds exclusively to Al, while nicotianamine synthesis exclusively responds to Mn. Pathways such as signaling, phenylpropanoid metabolism, and metal ion transport showed commonality and specificity to Al and Mn. Transcription factors (TFs), such as MYB, WRKY, and AP2 families, were also regulated by Al and Mn, and a weighted gene co-expression network analysis (WGCNA) identified PODP7, VATB2, and ABCC3 as the hub genes for Al tolerance and NAS for Mn tolerance. The identified genes and pathways can be used as targets for pyramiding genes and breeding multi-tolerant varieties. Full article
(This article belongs to the Special Issue Advanced Research in Wheat Genome and Breeding)
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17 pages, 2098 KiB  
Article
Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by 1-FEH w3
by Nusrat Khan, Jingjuan Zhang, Shahidul Islam, Rudi Appels and Bernard Dell
Curr. Issues Mol. Biol. 2023, 45(8), 6634-6650; https://doi.org/10.3390/cimb45080419 - 11 Aug 2023
Viewed by 1681
Abstract
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived [...] Read more.
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding. Full article
(This article belongs to the Special Issue Advanced Research in Wheat Genome and Breeding)
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