Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Special Issue "Wheat Genetics and Genomics 2.0"

Special Issue Editors
Special Issue Information
Keywords
Related Special Issue
Published Papers

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 June 2024 | Viewed by 3624

Share This Special Issue

Special Issue Editor

Dr. Xiaojun Nie

E-Mail Website
Guest Editor

College of Agronomy, Northwest A&F University, Yangling 712100, China
Interests: plant genomics; mining elite germplasm with stress resistance
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 accounts for more than 20% of total global calorie and protein consumption. With the huge challenges posed by 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 are thus available for application to its progenitors, providing a new platform for the exploitation of gene resources and genome-associated crop improvement. Developing a better understanding of the mechanism underlying its adaptability, yield, and quality is of great significance for promoting improvements in wheat genetics and molecular breeding. This Special Issue of IJMS, entitled “Wheat Genetics and Genomics”, will include papers containing new research data and timely review articles that focus on the study of wheat genomics; these will include, but are not limited to, the exploration of genome variation (pan-genome, re-sequencing, etc.) and the mining of key functional genes (via 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 that cover any of the related topics.

This special issue is supervised by Dr. Xiaojun Nie, assisted by our Topical Advisory Panel Member Dr. Hongxing Ma（Yangzhou University).

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
genetics
molecular breeding
genome variation
multiomics

Related Special Issue

Wheat Genetics and Genomics in International Journal of Molecular Sciences (12 articles)

Published Papers (7 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Open AccessArticle

Genome-Wide Identification, Characterization and Expression Analysis of the TaDUF724 Gene Family in Wheat (Triticum aestivum)

and

Int. J. Mol. Sci. 2023, 24(18), 14248; https://doi.org/10.3390/ijms241814248 - 18 Sep 2023

Viewed by 282

Abstract

Unknown functional domain (DUF) proteins constitute a large number of functionally uncharacterized protein families in eukaryotes. DUF724s play crucial roles in plants. However, the insight understanding of wheat TaDUF724s is currently lacking. To explore the possible function of TaDUF724s in wheat growth and development and stress response, the family members were systematically identified and characterized. In total, 14 TaDUF724s were detected from a wheat reference genome; they are unevenly distributed across the 11 chromosomes, and, according to chromosome location, they were named TaDUF724-1 to TaDUF724-14. Evolution analysis revealed that TaDUF724s were under negative selection, and fragment replication was the main reason for family expansion. All TaDUF724s are unstable proteins; most TaDUF724s are acidic and hydrophilic. They were predicted to be located in the nucleus and chloroplast. The promoter regions of TaDUF724s were enriched with the cis-elements functionally associated with growth and development, as well as being hormone-responsive. Expression profiling showed that TaDUF724-9 was highly expressed in seedings, roots, leaves, stems, spikes and grains, and strongly expressed throughout the whole growth period. The 12 TaDUF724 were post-transcription regulated by 12 wheat MicroRNA (miRNA) through cleavage and translation. RT-qPCR showed that six TaDUF724s were regulated by biological and abiotic stresses. Conclusively, TaDUF724s were systematically analyzed using bioinformatics methods, which laid a theoretical foundation for clarifying the function of TaDUF724s in wheat. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Evolution and Expression of the Expansin Genes in Emmer Wheat

and

Int. J. Mol. Sci. 2023, 24(18), 14120; https://doi.org/10.3390/ijms241814120 - 15 Sep 2023

Viewed by 261

Abstract

Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 TdEXPs and 49 TtEXPs from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide “T” in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Local and Bayesian Survival FDR Estimations to Identify Reliable Associations in Whole Genome of Bread Wheat

Mohammad Bahman Sadeqi

Agim Ballvora

and

Jens Léon

Int. J. Mol. Sci. 2023, 24(18), 14011; https://doi.org/10.3390/ijms241814011 - 12 Sep 2023

Viewed by 331

Abstract

Estimating the FDR significance threshold in genome-wide association studies remains a major challenge in distinguishing true positive hypotheses from false positive and negative errors. Several comparative methods for multiple testing comparison have been developed to determine the significance threshold; however, these methods may be overly conservative and lead to an increase in false negative results. The local FDR approach is suitable for testing many associations simultaneously based on the empirical Bayes perspective. In the local FDR, the maximum likelihood estimator is sensitive to bias when the GWAS model contains two or more explanatory variables as genetic parameters simultaneously. The main criticism of local FDR is that it focuses only locally on the effects of single nucleotide polymorphism (SNP) in tails of distribution, whereas the signal associations are distributed across the whole genome. The advantage of the Bayesian perspective is that knowledge of prior distribution comes from other genetic parameters included in the GWAS model, such as linkage disequilibrium (LD) analysis, minor allele frequency (MAF) and call rate of significant associations. We also proposed Bayesian survival FDR to solve the multi-collinearity and large-scale problems, respectively, in grain yield (GY) vector in bread wheat with large-scale SNP information. The objective of this study was to obtain a short list of SNPs that are reliably associated with GY under low and high levels of nitrogen (N) in the population. The five top significant SNPs were compared with different Bayesian models. Based on the time to events in the Bayesian survival analysis, the differentiation between minor and major alleles within the association panel can be identified. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Molecular Characterization and Marker Development of the HMW-GS Gene from Thinopyrum elongatum for Improving Wheat Quality

and

Int. J. Mol. Sci. 2023, 24(13), 11072; https://doi.org/10.3390/ijms241311072 - 04 Jul 2023

Viewed by 499

Abstract

The quality of wheat primarily depends on its storage protein quality, especially in regards to gluten content and high-molecular-weight glutenin subunits (HMW-GS). The number of HMW-GS alleles is limited in bread wheat (Triticum aestivum L.), whereas it is abundant in wheat relatives. Therefore, HMW-GS alleles from wheat relatives could provide a potential for improving quality in wheat breeding. Thinopyrum elongatum (EE) is one of the relatives of wheat. The E genome is closely related to the ABD genome in wheat; therefore, Th. elongatum is often used as an excellent exogenous gene donor for wheat genetic improvement. In this study, the high-molecular glutenin subunit gene was cloned and sequenced from Th. elongatum. A specific molecular marker for identifying the Glu-1Ey subunit gene was developed and applied to detected wheat-Th. elongatum alien introgression lines. Quality analysis indicated that the substitution and addition lines containing Th. elongatum alleles significantly (p < 0.05) increased grain protein content by 3.76% to 5.11%, wet-gluten content by 6.55% to 8.73%, flour 8-MW by 0.25% to 6.35%, and bread volume value by 33.77 mL to 246.50 mL, in comparing it with Chinese Spring. The GMP content and lactic acid SRC showed significant positive correlations with flour processing quality and might be used as indicators for wheat quality. The results were expected to provide a novel route for improving processing quality in wheat quality breeding. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Physical Mapping of QTLs for Root Traits in a Population of Recombinant Inbred Lines of Hexaploid Wheat

and

Int. J. Mol. Sci. 2023, 24(13), 10492; https://doi.org/10.3390/ijms241310492 - 22 Jun 2023

Viewed by 500

Abstract

Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F_6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat

and

Int. J. Mol. Sci. 2023, 24(12), 10217; https://doi.org/10.3390/ijms241210217 - 16 Jun 2023

Viewed by 623

Abstract

Crop genetic diversity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele diversity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog diversity, intra-varietal diversity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional diversity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous diversity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Figure 1

Open AccessArticle

Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii

and

Int. J. Mol. Sci. 2023, 24(11), 9349; https://doi.org/10.3390/ijms24119349 - 27 May 2023

Viewed by 680

Abstract

Transposons (TEs) account for more than 80% of the wheat genome, the highest among all known crop species. They play an important role in shaping the elaborate genomic landscape, which is the key to the speciation of wheat. In this study, we analyzed the association between TEs, chromatin states, and chromatin accessibility in Aegilops tauschii, the D genome donor of bread wheat. We found that TEs contributed to the complex but orderly epigenetic landscape as chromatin states showed diverse distributions on TEs of different orders or superfamilies. TEs also contributed to the chromatin state and openness of potential regulatory elements, affecting the expression of TE-related genes. Some TE superfamilies, such as hAT-Ac, carry active/open chromatin regions. In addition, the histone mark H3K9ac was found to be associated with the accessibility shaped by TEs. These results suggest the role of diversiform TEs in shaping the epigenetic landscape and in gene expression regulation in Aegilops tauschii. This has positive implications for understanding the transposon roles in Aegilops tauschii or the wheat D genome. Full article

(This article belongs to the Special Issue Wheat Genetics and Genomics 2.0)

► Show Figures

Journal Menu

Journal Browser

Special Issue "Wheat Genetics and Genomics 2.0"

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Related Special Issue

Published Papers (7 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI