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Wheat Breeding through Genetic and Physical Mapping 2.0

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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 August 2021) | Viewed by 31422

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Prof. Dr. Agata Gadaleta

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Department of Agriculture & Environmental Sciences, University of Bari Aldo Moro, Via G Amendola 165-A, I-70126 Bari, Italy
Interests: wheat; molecular marker; QTL analysis; genetic map; nitrogen metabolism; genetic trasformation; wheat quality; biotic stress tolerance
Special Issues, Collections and Topics in MDPI journals

Dr. Domenica Nigro

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Università degli Studi di Bari Aldo Moro, Bari, Italy
Interests: wheat; molecular marker; QTL analysis; genetic map; nitrogen metabolism; genetic trasformation; wheat quality; biotic stress tolerance

Dr. Ilaria Marcotuli

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Guest Editor

Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy
Interests: genetics, plant biotechnology, cereal, fibre, molecular biology, GWAS, linkage analysis, phylogeny

Special Issue Information

Dear Colleagues,

You are invited to contribute to the Special Issue “Wheat breeding through genetic and physical mapping”, focused on the genetic and physical mapping of QTLs, candidate genes, and regulatory sequences involved in the control of wheat’s important agronomic traits, such as grain yield and quality, nutrient-use efficiency, and biotic and abiotic stress resistance.
This Special Issue will aim to report novel research and reviews exploiting the recent advances in wheat genome sequencing and associated studies related to the topic.

Prof. Agata Gadaleta
Dr. Domenica Nigro
Guest Editors

Manuscript Submission Information

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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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

Bread wheat
Durum wheat
Molecular markers
Genetic mapping
Physical mapping
Breeding
GWAS

Published Papers (10 papers)

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Editorial

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3 pages, 169 KiB

Open AccessEditorial

Wheat Breeding through Genetic and Physical Mapping 2

by Agata Gadaleta

Int. J. Mol. Sci. 2021, 22(24), 13359; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413359 - 12 Dec 2021

Viewed by 1657

Abstract

Following the success of the first topic, the special issue of “Wheat breeding through genetic and physical mapping 2” has been re-proposed in order to keep current the recent advancement in research on genetic and physical mapping of candidate genes for agronomically important [...] Read more.

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

Research

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33 pages, 11476 KiB

Open AccessArticle

by Jingjuan Zhang, Maoyun She, Rongchang Yang, Yanjie Jiang, Yebo Qin, Shengnan Zhai, Sadegh Balotf, Yun Zhao, Masood Anwar, Zaid Alhabbar, Angéla Juhász, Jiansheng Chen, Hang Liu, Qier Liu, Ting Zheng, Fan Yang, Junkang Rong, Kefei Chen, Meiqin Lu, Shahidul Islam and Wujun Ma Show full author list Hide full author list

Int. J. Mol. Sci. 2021, 22(21), 11934; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111934 - 03 Nov 2021

Cited by 9 | Viewed by 2601

Abstract

In the present study, four large-scale field trials using two doubled haploid wheat populations were conducted in different environments for two years. Grain protein content (GPC) and 21 other yield-related traits were investigated. A total of 227 QTL were mapped on 18 chromosomes, which formed 35 QTL clusters. The potential candidate genes underlying the QTL clusters were suggested. Furthermore, adding to the significant correlations between yield and its related traits, correlation variations were clearly shown within the QTL clusters. The QTL clusters with consistently positive correlations were suggested to be directly utilized in wheat breeding, including 1B.2, 2A.2, 2B (4.9–16.5 Mb), 2B.3, 3B (68.9–214.5 Mb), 4A.2, 4B.2, 4D, 5A.1, 5A.2, 5B.1, and 5D. The QTL clusters with negative alignments between traits may also have potential value for yield or GPC improvement in specific environments, including 1A.1, 2B.1, 1B.3, 5A.3, 5B.2 (612.1–613.6 Mb), 7A.1, 7A.2, 7B.1, and 7B.2. One GPC QTL (5B.2: 671.3–672.9 Mb) contributed by cultivar Spitfire was positively associated with nitrogen use efficiency or grain protein yield and is highly recommended for breeding use. Another GPC QTL without negatively pleiotropic effects on 2A (50.0–56.3 Mb), 2D, 4D, and 6B is suggested for quality wheat breeding. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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20 pages, 5165 KiB

Open AccessArticle

Alternative Splicing of TaGS3 Differentially Regulates Grain Weight and Size in Bread Wheat

by Xiaoli Ren, Liya Zhi, Lei Liu, Deyuan Meng, Qiannan Su, Aamana Batool, Jun Ji, Liqiang Song, Na Zhang, Lin Guo, Xigang Liu, Junming Li and Wei Zhang

Int. J. Mol. Sci. 2021, 22(21), 11692; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111692 - 28 Oct 2021

Cited by 7 | Viewed by 2270

Abstract

The heterotrimeric G-protein mediates growth and development by perceiving and transmitting signals in multiple organisms. Alternative splicing (AS), a vital process for regulating gene expression at the post-transcriptional level, plays a significant role in plant adaptation and evolution. Here, we identified five splicing variants of G_γ subunit gene TaGS3 (TaGS3.1 to TaGS3.5), which showed expression divergence during wheat polyploidization, and differential function in grain weight and size determination. TaGS3.1 overexpression significantly reduced grain weight by 5.89% and grain length by 5.04%, while TaGS3.2–3.4 overexpression did not significantly alter grain size compared to wild type. Overexpressing TaGS3.5 significantly increased the grain weight by 5.70% and grain length by 4.30%. Biochemical assays revealed that TaGS3 isoforms (TaGS3.1–3.4) with an intact OSR domain interact with WGB1 to form active G_βγ heterodimers that further interact with WGA1 to form inactive G_αβγ heterotrimers. Truncated isoforms TaGS3.2–3.4 , which lack the C-terminal Cys-rich region but have enhanced binding affinity to WGB1, antagonistically compete with TaGS3.1 to bind WGB1, while TaGS3.5 with an incomplete OSR domain does not interact with WGB1. Taking these observations together, we proposed that TaGS3 differentially regulates grain size via AS, providing a strategy by which the grain size is fine-tuned and regulated at the post-transcriptional level. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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14 pages, 2883 KiB

Open AccessArticle

TaWAK2A-800, a Wall-Associated Kinase, Participates Positively in Resistance to Fusarium Head Blight and Sharp Eyespot in Wheat

by Feilong Guo, Tianci Wu, Gangbiao Xu, Haijun Qi, Xiuliang Zhu and Zengyan Zhang

Int. J. Mol. Sci. 2021, 22(21), 11493; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222111493 - 25 Oct 2021

Cited by 9 | Viewed by 1796

Abstract

Fusarium head blight (FHB) and sharp eyespot are important diseases of the cereal plants, including bread wheat (Triticum aestivum) and barley. Both diseases are predominately caused by the pathogenic fungi, Fusarium graminearum and Rhizoctonia cerealis. The roles of the wheat-wall-associated kinases (WAKs) in defense against both F. graminearum and R. cerealis have remained largely unknown. This research reports the identification of TaWAK2A-800, a wheat WAK-coding gene located on chromosome 2A, and its functional roles in wheat resistance responses to FHB and sharp eyespot. TaWAK2A-800 transcript abundance was elevated by the early infection of R. cerealis and F. graminearum, or treatment with exogenous chitin. The gene transcript seemed to correspond to the resistance of wheat. Further functional analyses showed that silencing TaWAK2A-800 compromised the resistance of wheat to both FHB (F. graminearum) and sharp eyespot (R. cerealis). Moreover, the silencing reduced the expression levels of six defense-related genes, including the chitin-triggering immune pathway-marker genes, TaCERK1, TaRLCK1B, and TaMPK3. Summarily, TaWAK2A-800 participates positively in the resistance responses to both F. graminearum and R. cerealis, possibly through a chitin-induced pathway in wheat. TaWAK2A-800 will be useful for breeding wheat varieties with resistance to both FHB and sharp eyespot. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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13 pages, 3146 KiB

Open AccessArticle

The Wall-Associated Receptor-Like Kinase TaWAK7D Is Required for Defense Responses to Rhizoctonia cerealis in Wheat

by Haijun Qi, Xiuliang Zhu, Feilong Guo, Liangjie Lv and Zengyan Zhang

Int. J. Mol. Sci. 2021, 22(11), 5629; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115629 - 26 May 2021

Cited by 15 | Viewed by 3437

Abstract

Sharp eyespot, caused by necrotrophic fungus Rhizoctonia cerealis, is a serious fungal disease in wheat (Triticum aestivum). Certain wall-associated receptor kinases (WAK) mediate resistance to diseases caused by biotrophic/hemibiotrophic pathogens in several plant species. Yet, none of wheat WAK genes with positive effect on the innate immune responses to R. cerealis has been reported. In this study, we identified a WAK gene TaWAK7D, located on chromosome 7D, and showed its positive regulatory role in the defense response to R. cerealis infection in wheat. RNA-seq and qRT-PCR analyses showed that TaWAK7D transcript abundance was elevated in wheat after R. cerealis inoculation and the induction in the stem was the highest among the tested organs. Additionally, TaWAK7D transcript levels were significantly elevated by pectin and chitin treatments. The knock-down of TaWAK7D transcript impaired resistance to R. cerealis and repressed the expression of five pathogenesis-related genes in wheat. The green fluorescent protein signal distribution assays indicated that TaWAK7D localized on the plasma membrane in wheat protoplasts. Thus, TaWAK7D, which is induced by R. cerealis, pectin and chitin stimuli, positively participates in defense responses to R. cerealis through modulating the expression of several pathogenesis-related genes in wheat. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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18 pages, 1527 KiB

Open AccessArticle

Development of an Australian Bread Wheat Nested Association Mapping Population, a New Genetic Diversity Resource for Breeding under Dry and Hot Climates

by Charity Chidzanga, Delphine Fleury, Ute Baumann, Dan Mullan, Sayuri Watanabe, Priyanka Kalambettu, Robert Pontre, James Edwards, Kerrie Forrest, Debbie Wong, Peter Langridge, Ken Chalmers and Melissa Garcia

Int. J. Mol. Sci. 2021, 22(9), 4348; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094348 - 21 Apr 2021

Cited by 6 | Viewed by 3244

Abstract

Genetic diversity, knowledge of the genetic architecture of the traits of interest and efficient means of transferring the desired genetic diversity into the relevant genetic background are prerequisites for plant breeding. Exotic germplasm is a rich source of genetic diversity; however, they harbor undesirable traits that limit their suitability for modern agriculture. Nested association mapping (NAM) populations are valuable genetic resources that enable incorporation of genetic diversity, dissection of complex traits and providing germplasm to breeding programs. We developed the OzNAM by crossing and backcrossing 73 diverse exotic parents to two Australian elite varieties Gladius and Scout. The NAM parents were genotyped using the iSelect wheat 90K Infinium SNP array, and the progeny were genotyped using a custom targeted genotyping-by-sequencing assay based on molecular inversion probes designed to target 12,179 SNPs chosen from the iSelect wheat 90K Infinium SNP array of the parents. In total, 3535 BC₁F_4:6 RILs from 125 families with 21 to 76 lines per family were genotyped and we found 4964 polymorphic and multi-allelic haplotype markers that spanned the whole genome. A subset of 530 lines from 28 families were evaluated in multi-environment trials over three years. To demonstrate the utility of the population in QTL mapping, we chose to map QTL for maturity and plant height using the RTM-GWAS approach and we identified novel and known QTL for maturity and plant height. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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25 pages, 5069 KiB

Open AccessArticle

Structural and Functional Characterization of the ABA-Water Deficit Stress Domain from Wheat and Barley: An Intrinsically Disordered Domain behind the Versatile Functions of the Plant Abscissic Acid, Stress and Ripening Protein Family

by Ines Yacoubi, Karama Hamdi, Patrick Fourquet, Christophe Bignon and Sonia Longhi

Int. J. Mol. Sci. 2021, 22(5), 2314; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052314 - 26 Feb 2021

Cited by 9 | Viewed by 2541

Abstract

The ASR protein family has been discovered thirty years ago in many plant species and is involved in the tolerance of various abiotic stresses such as dehydration, salinity and heat. Despite its importance, nothing is known about the conserved ABA-Water Deficit Stress Domain (ABA-WDS) of the ASR gene family. In this study, we characterized two ABA-WDS domains, isolated from durum wheat (TtABA-WDS) and barley (HvABA-WDS). Bioinformatics analysis shows that they are both consistently predicted to be intrinsically disordered. Hydrodynamic and circular dichroism analysis indicate that both domains are largely disordered but belong to different structural classes, with HvABA-WDS and TtABA-WDS adopting a PreMolten Globule-like (PMG-like) and a Random Coil-like (RC-like) conformation, respectively. In the presence of the secondary structure stabilizer trifluoroethanol (TFE) or of increasing glycerol concentrations, which mimics dehydration, the two domains acquire an α-helical structure. Interestingly, both domains are able to prevent heat- and dehydration-induced inactivation of the enzyme lactate dehydrogenase (LDH). Furthermore, heterologous expression of TtABA-WDS and HvABA-WDS in the yeast Saccharomyces cerevisiae improves its tolerance to salt, heat and cold stresses. Taken together our results converge to show that the ABA-WDS domain is an intrinsically disordered functional domain whose conformational plasticity could be instrumental to support the versatile functions attributed to the ASR family, including its role in abiotic stress tolerance. Finally, and after validation in the plant system, this domain could be used to improve crop tolerance to abiotic stresses. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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17 pages, 994 KiB

Open AccessArticle

Functional Validation of Glutamine synthetase and Glutamate synthase Genes in Durum Wheat near Isogenic Lines with QTL for High GPC

by Domenica Nigro, Stefania Fortunato, Stefania Lucia Giove, Elisabetta Mazzucotelli and Agata Gadaleta

Int. J. Mol. Sci. 2020, 21(23), 9253; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21239253 - 04 Dec 2020

Cited by 12 | Viewed by 2458

Abstract

Durum wheat (Triticum turgidum L. ssp. durum) is a minor crop grown on about 17 million hectares of land worldwide. Several grain characteristics determine semolina’s high end-use quality, such as grain protein content (GPC) which is directly related to the final products’ nutritional and technological values. GPC improvement could be pursued by considering a candidate gene approach. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a bottleneck in the first step of nitrogen assimilation. QTL for GPC have been located on all chromosomes, and several major ones have been reported on 2A and 2B chromosomes, where GS2 and Fd-GOGAT genes have been mapped. A useful and efficient method to validate a putative QTL is the constitution of near-isogenic lines (NILs) by using the marker found to be associated to that QTL. Here, we present the development of two distinct sets of heterogeneous inbred family (HIF)- based NILs segregating for GS2 and Fd-GOGAT genes obtained from heterozygous lines at those loci, as well as their genotypic and phenotypic characterizations. The results allow the validation of the previously identified GPC QTL on 2A and 2B chromosomes, along with the role of these key genes in GPC control. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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Review

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22 pages, 2533 KiB

Open AccessReview

Dissection of Molecular Processes and Genetic Architecture Underlying Iron and Zinc Homeostasis for Biofortification: From Model Plants to Common Wheat

by Jingyang Tong, Mengjing Sun, Yue Wang, Yong Zhang, Awais Rasheed, Ming Li, Xianchun Xia, Zhonghu He and Yuanfeng Hao

Int. J. Mol. Sci. 2020, 21(23), 9280; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21239280 - 05 Dec 2020

Cited by 23 | Viewed by 4711

Abstract

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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29 pages, 3239 KiB

Open AccessReview

Molecular Control and Application of Male Fertility for Two-Line Hybrid Rice Breeding

by Muhammad Furqan Ashraf, Guoqing Peng, Zhenlan Liu, Ali Noman, Saad Alamri, Mohamed Hashem, Sameer H. Qari and Omar Mahmoud al Zoubi

Int. J. Mol. Sci. 2020, 21(21), 7868; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21217868 - 23 Oct 2020

Cited by 10 | Viewed by 5462

Abstract

The significance of the climate change may involve enhancement of plant growth as well as utilization of the environmental alterations in male fertility (MF) regulation via male sterility (MS) systems. We described that MS systems provide a fundamental platform for improvement in agriculture production and have been explicated for creating bulk germplasm of the two-line hybrids (EGMS) in rice as compared to the three-line, to gain production sustainability and exploit its immense potential. Environmental alterations such as photoperiod and/or temperature and humidity regulate MS in EGMS lines via genetic and epigenetic changes, regulation of the noncoding RNAs, and RNA-metabolism including the transcriptional factors (TFs) implication. Herein, this article enlightens a deep understanding of the molecular control of MF in EGMS lines and exploring the regulatory driving forces that function efficiently during plant adaption under a changing environment. We highlighted a possible solution in obtaining more stable hybrids through apomixis (single-line system) for seed production. Full article

(This article belongs to the Special Issue Wheat Breeding through Genetic and Physical Mapping 2.0)

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