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Wheat Genetics and Genomics: 3rd Edition
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Wheat Genetics and Genomics: 3rd Edition

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: 20 September 2025 | Viewed by 2516

Special Issue Editor

Prof. Dr. Xiaojun Nie

E-Mail Website
Guest Editor
College of Agronomy, Northwest A&F University, Xianyang 712100, China
Interests: plant genomics; molecular mechanism underlying abiotic stress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As one of the most successful crops since the dawn of agriculture, wheat is now one of the major world crop and provides more than 20% of the total calories and protein consumed. With the huge challenges of population expansion and climate change, wheat production must be sustainably increased to ensure global food security. The genomes and pan-genomes for wheat have recently been released and become available for application to its progenitors, providing a new platform for exploitation of gene resources and genome-associated crop improvement. Better understanding the mechanism underlying its adaptability, yield, and quality is of great significance to promote improvements in wheat genetics and molecular breeding. A Special Issue “Wheat Genetics and Genomics” is being planned for IJMS and will include papers with new research data and timely review articles focusing on the study of wheat genomics, including but not limited to the exploration of genome variation (pan-genome, re-sequencing, etc.) and the mining of key functional genes (by QTL mapping, genome-wide association studies, transcriptome-wide association studies, etc.) as well as multiomics studies (RNA-seq, sRNA, proteome, metabolome, phenomics, etc.). We welcome novel research and reviews covering any of the related topics.

This Special Issue is supervised by Prof. Dr. Xiaojun Nie, assisted by our Topical Advisory Panel Member Dr. Pingchuan Deng (College of Agronomy, Northwest A & F University).

Prof. Dr. Xiaojun Nie
Guest Editor

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

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Keywords

  • wheat
  • genetics
  • molecular breeding
  • genome variation
  • multiomics

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Related Special Issues

Published Papers (4 papers)

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Research

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17 pages, 9471 KiB  
Article
Characterization and Fine Mapping of the Stay-Green-Related Spot Leaf Gene TaSpl1 with Enhanced Stripe Rust and Powdery Mildew Resistance in Wheat
by Xiaomin Xu, Xin Du, Yanlong Jin, Yanzhen Wang, Zhenyu Wang, Jixin Zhao, Changyou Wang, Xinlun Liu, Chunhuan Chen, Pingchuan Deng, Tingdong Li and Wanquan Ji
Int. J. Mol. Sci. 2025, 26(9), 4002; https://doi.org/10.3390/ijms26094002 - 23 Apr 2025
Viewed by 156
Abstract
Lesion mimic phenotypes, characterized by leaf spots formed in the absence of pathogens or pests, are often associated with reactive oxygen species (ROS) accumulation and cell necrosis. This study identified a novel and stable homozygous spotted phenotype (HSP) from the F8 population [...] Read more.
Lesion mimic phenotypes, characterized by leaf spots formed in the absence of pathogens or pests, are often associated with reactive oxygen species (ROS) accumulation and cell necrosis. This study identified a novel and stable homozygous spotted phenotype (HSP) from the F8 population of common wheat (XN509 × N07216). The yellow spots that appeared at the booting stage were light-sensitive, and accompanied by cell necrosis and H2O2 accumulation. Compared with homozygous normal plants (HNPs), HSPs exhibited enhanced resistance to stripe rust and powdery mildew without compromising yield. RNA-Seq analysis at three stages revealed that differentially expressed genes (DEGs) between HSPs and HNPs were significantly enriched in KEGG pathways related to photosynthesis and photosynthesis-antenna proteins. GO analysis highlighted chloroplast and light stimulus-related down-regulated DEGs. Fine mapping identified TaSpl1 within a 0.91 Mb interval on chromosome 3DS, flanked by the markers KASP188 and KASP229, using two segregating populations comprising 1117 individuals. The candidate region contained 42 annotated genes, including 14 DEGs based on previous BSR-Seq data. PCR amplification and qRT-PCR verification identified the expression of TraesCS3D02G022100 was consistent with RNA-Seq data. Gene homology analysis and silencing experiments confirmed that TraesCS3D02G022100 was associated with stay-green traits. These findings provide new insights into the genetic regulation of lesion mimics, photosynthesis, and disease resistance in wheat. Full article
(This article belongs to the Special Issue Wheat Genetics and Genomics: 3rd Edition)
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15 pages, 2395 KiB  
Article
Identification of QTL for Grain Traits and Plant Height Using the Recombinant Inbred Line Population Derived from the Cross of Zhongke 331 × Nongda 399
by Yi Liu, Yongxing Chen, Yijun Yang, Dan Qiu, Huaizhi Zhang, Jinghuang Hu, Guanghao Guo, Keyu Zhu, Hongkui Fu, Hongjie Li, Zhiyong Liu, Ruihui Wang and Qiuhong Wu
Int. J. Mol. Sci. 2025, 26(8), 3526; https://doi.org/10.3390/ijms26083526 - 9 Apr 2025
Viewed by 267
Abstract
Improving wheat yield is essential to meet the increasing demand for food production. This study aims to identify quantitative trait loci (QTL) associated with grain traits and plant height (PH) in winter wheat, using a recombinant inbred line (RIL) population derived from a [...] Read more.
Improving wheat yield is essential to meet the increasing demand for food production. This study aims to identify quantitative trait loci (QTL) associated with grain traits and plant height (PH) in winter wheat, using a recombinant inbred line (RIL) population derived from a cross between Zhongke 331 and Nongda 399. The RIL population was genotyped using the 16K GenoBaits Wheat single nucleotide polymorphism (SNP) array. A genetic linkage map was established, comprising 14,868 SNPs and spanning 3846.91 cM, with an average interval of 1.11 cM between markers. These SNPs were categorized into 3463 SNP bin markers, with 1653, 1508, and 302 located in the A, B, and D sub-genomes, respectively. QTL analysis for thousand-grain weight (TGW), grain length (GL), grain width (GW), and PH revealed 61 QTL influencing these traits across six environments. Loci qPH-4B.1 and qPH-4D.1 were consistently detected in five environments. QTL clusters with pleiotropic effects that regulate multiple grain traits were identified on chromosomes 4B and 4D. Furthermore, the combination of qPH-4B.1 and qPH-4D.1 resulted in a reduced plant height compared to the presence of either locus alone, indicating an additive effect between these loci. Full article
(This article belongs to the Special Issue Wheat Genetics and Genomics: 3rd Edition)
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19 pages, 14661 KiB  
Article
Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat (Triticum aestivum L.)
by Yang Zhang, Yanmin Xu, Yulu Mao, Xiaodi Tan, Yuan Tian, Xiaofei Ma, Hutai Ji and Dingyi Zhang
Int. J. Mol. Sci. 2025, 26(1), 133; https://doi.org/10.3390/ijms26010133 - 27 Dec 2024
Viewed by 730
Abstract
The NF-YA gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA [...] Read more.
The NF-YA gene family is a highly conserved transcription factor that plays a crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies in multiple plants, there has been a dearth of focused and systematic analysis on NF-YA genes in wheat grains. In this study, we carried out a comprehensive bioinformatics analysis of the NF-YA gene family in wheat, using the latest genomic data from the Chinese Spring. A total of 19 TaNF-YA genes were identified. An analysis of conserved domains, phylogenetic relationships, and gene structure indicated a significant degree of conservation among TaNF-YAs. A gene collinearity analysis demonstrated that fragment duplication was the predominant mechanism driving the amplification of TaNF-YAs. Furthermore, cis-acting elements within the promoters of TaNF-YAs were found to be implicated in grain development. Subsequently, SNP analysis revealed the genetic variation in the NF-YA gene family in different wheat. Moreover, published RNA-seq data were used and RNA-seqs of Pinyu8155, Yaomai30, Yaomai36, and Pinyu8175 were performed to identify TaNF-YAs influencing grain development. Finally, it was found that NF-YAs had no self-activating activity in wheat. This study provides key candidate genes for the exploration of grain development in the wheat filling stage and also lays a foundation for further research on the regulation of starch and protein synthesis and accumulation. Full article
(This article belongs to the Special Issue Wheat Genetics and Genomics: 3rd Edition)
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Review

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47 pages, 4501 KiB  
Review
Micronutrient Biofortification in Wheat: QTLs, Candidate Genes and Molecular Mechanism
by Adnan Nasim, Junwei Hao, Faiza Tawab, Ci Jin, Jiamin Zhu, Shuang Luo and Xiaojun Nie
Int. J. Mol. Sci. 2025, 26(5), 2178; https://doi.org/10.3390/ijms26052178 - 28 Feb 2025
Viewed by 872
Abstract
Micronutrient deficiency (hidden hunger) is one of the serious health problems globally, often due to diets dominated by staple foods. Genetic biofortification of a staple like wheat has surfaced as a promising, cost-efficient, and sustainable strategy. Significant genetic diversity exists in wheat and [...] Read more.
Micronutrient deficiency (hidden hunger) is one of the serious health problems globally, often due to diets dominated by staple foods. Genetic biofortification of a staple like wheat has surfaced as a promising, cost-efficient, and sustainable strategy. Significant genetic diversity exists in wheat and its wild relatives, but the nutritional profile in commercial wheat varieties has inadvertently declined over time, striving for better yield and disease resistance. Substantial efforts have been made to biofortify wheat using conventional and molecular breeding. QTL and genome-wide association studies were conducted, and some of the identified QTLs/marker-trait association (MTAs) for grain micronutrients like Fe have been exploited by MAS. The genetic mechanisms of micronutrient uptake, transport, and storage have also been investigated. Although wheat biofortified varieties are now commercially cultivated in selected regions worldwide, further improvements are needed. This review provides an overview of wheat biofortification, covering breeding efforts, nutritional evaluation methods, nutrient assimilation and bioavailability, and microbial involvement in wheat grain enrichment. Emerging technologies such as non-destructive hyperspectral imaging (HSI)/red, green, and blue (RGB) phenotyping; multi-omics integration; CRISPR-Cas9 alongside genomic selection; and microbial genetics hold promise for advancing biofortification. Full article
(This article belongs to the Special Issue Wheat Genetics and Genomics: 3rd Edition)
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