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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 December 2022) | Viewed by 27981

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Dr. Xiaojun Nie

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College of Agronomy, Northwest A&F University, Yangling 712100, China
Interests: plant genomics; evolutionary genomics; molecular mechanism underlying abiotic stresses
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Weining Song

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College of Agronomy, Northwest A&F University, Yangling, China
Interests: wheat genomics

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.

Dr. Xiaojun Nie
Prof. Dr. Weining Song
Guest Editors

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Related Special Issue

Wheat Genetics and Genomics 2.0 in International Journal of Molecular Sciences (11 articles)

Published Papers (12 papers)

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18 pages, 11024 KiB

Open AccessArticle

Proteomic Analysis of Roots Response to Potassium Deficiency and the Effect of TaHAK1-4A on K⁺ Uptake in Wheat

by Ke Xu, Yong Zhao, Yaxin Yu, Ruoxi Sun, Weiwei Wang, Shuhua Zhang and Xueju Yang

Int. J. Mol. Sci. 2022, 23(21), 13504; https://doi.org/10.3390/ijms232113504 - 4 Nov 2022

Cited by 3 | Viewed by 1423

Abstract

Potassium (K⁺) is essential for plant growth and stress responses. A deficiency in soil K⁺ contents can result in decreased wheat quality and productivity. Thus, clarifying the molecular mechanism underlying wheat responses to low-K⁺ (LK) stress is critical. In this study, a tandem mass tag (TMT)-based quantitative proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in roots of the LK-tolerant wheat cultivar “KN9204” at the seedling stage after exposure to LK stress. A total of 104 DAPs were identified in the LK-treated roots. The DAPs related to carbohydrate and energy metabolism, transport, stress responses and defense, and post-translational modifications under LK conditions were highlighted. We identified a high-affinity potassium transporter (TaHAK1-4A) that was significantly up-regulated after the LK treatment. Additionally, TaHAK1-4A was mainly expressed in roots, and the encoded protein was localized in the plasma membrane. The complementation assay in yeast suggested that TaHAK1-4A mediates K⁺ uptake under extreme LK conditions. The overexpression of TaHAK1-4A increased the fresh weight and root length of Arabidopsis under LK conditions and improved the growth of Arabidopsis athak5 mutant seedlings, which grow poorly under LK conditions. Moreover, silencing of TaHAK1-4A in wheat roots treated with LK stress decreased the root length, dry weight, K⁺ concentration, and K⁺ influx. Accordingly, TaHAK1-4A is important for the uptake of K⁺ by roots exposed to LK stress. Our results reveal the protein metabolic changes in wheat induced by LK stress. Furthermore, we identified a candidate gene potentially relevant for developing wheat lines with increased K⁺ use efficiency. Full article

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

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18 pages, 10466 KiB

Open AccessArticle

Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)

by Kuijun She, Wenqiu Pan, Ying Yan, Tingrui Shi, Yingqi Chu, Yue Cheng, Bo Ma and Weining Song

Int. J. Mol. Sci. 2022, 23(21), 13027; https://doi.org/10.3390/ijms232113027 - 27 Oct 2022

Cited by 7 | Viewed by 2250

Abstract

The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10⁻³ and 0.391 × 10⁻³, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops. Full article

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

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19 pages, 3678 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling Analysis of the Long-Chain Acyl-CoA Synthetases Reveal Their Potential Roles in Wheat Male Fertility

by Yongjie Liu, Zihan Liu, Huishu Zhang, Shaohua Yuan, Yanmei Li, Tianbao Zhang, Jianfang Bai and Liping Zhang

Int. J. Mol. Sci. 2022, 23(19), 11942; https://doi.org/10.3390/ijms231911942 - 8 Oct 2022

Cited by 2 | Viewed by 1409

Abstract

Long-chain acyl-CoA synthetase (LACS), responsible for the conversion of free FAs into acyl-CoAs, is involved in multiple pathways of lipid metabolism. Although LACS genes in Arabidopsis have been well characterized, no detailed information concerning this family is available for wheat. In the present study, a systematic analysis was carried out for the wheat LACS family. As a result, 30 putative TaLACSs were identified. Expression analysis revealed that 22 Takacs were expressed in wheat anthers. Two orthologs of AtLACS1, TaLACS2 and TaLACS3, were repressed at the vacuolated stage in the cold-treated BS366 (a temperature-sensitive genic male-sterile line). Thus, TaLACS2 and TaLACS3 may function like AtLACS1 in wax biosynthesis in anthers, and the repression of both genes may be correlated with the male sterility of BS366. TaLACS5 is an ortholog of AtLACS5, which was expressed exclusively in anthers. TaLACS5 was repressed in the cold-treated BS366 at the tetrad, uninucleate, and vacuolated stages. The negative correlation between TaLACS5 and TaGAMYB-B, and the MYB domain found in the promoter sequence suggested that TaLACS5 may be negatively regulated by TaGAMYB-B to participate in wheat fertility. These findings will provide a valuable foundation for the understanding of the wheat LACS gene family in male fertility. Full article

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

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16 pages, 19445 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Fusarium graminearum Infection in Wheat

by Guang Yang, Yan Pan, Qinlong Zhao, Jiaqian Huang, Wenqiu Pan, Licao Cui, Weining Song, Therese Ouellet, Youlian Pan and Xiaojun Nie

Int. J. Mol. Sci. 2022, 23(14), 7982; https://doi.org/10.3390/ijms23147982 - 20 Jul 2022

Cited by 2 | Viewed by 1804

Abstract

RNA/DNA difference (RDD) is a post-transcriptional modification playing a crucial role in regulating diverse biological processes in eukaryotes. Although it has been extensively studied in plant chloroplast and mitochondria genomes, RDDs in plant nuclear genomes are not well studied at present. Here, we investigated the RDDs associated with fusarium head blight (FHB) through a novel method by comparing the RNA-seq data between Fusarium-infected and control samples of four wheat genotypes. A total of 187 high-confidence unique RDDs in 36 genes were identified, representing the first landscape of the FHB-responsive RDD in wheat. The majority (26) of these 36 RDD genes were correlated either positively or negatively with FHB levels. Effects of these RDDs on RNA and protein sequences have been identified, their editing frequency and the expression level of the corresponding genes provided, and the prediction of the effect on the minimum folding free energy of mRNA, miRNA binding, and colocation of RDDs with conserved domains presented. RDDs were predicted to induce modifications in the mRNA and protein structures of the corresponding genes. In two genes, TraesCS1B02G294300 and TraesCS3A02G263900, editing was predicted to enhance their affinity with tae-miR9661-5p and tae-miR9664-3p, respectively. To our knowledge, this study is the first report of the association between RDD and FHB in wheat; this will contribute to a better understanding of the molecular basis underlying FHB resistance, and potentially lead to novel strategies to improve wheat FHB resistance through epigenetic methods. Full article

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

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18 pages, 7500 KiB

Open AccessArticle

Characterization of the WAK Gene Family Reveals Genes for FHB Resistance in Bread Wheat (Triticum aestivum L.)

by Xiaobo Xia, Xu Zhang, Yicong Zhang, Lirong Wang, Qi An, Qiang Tu, Lei Wu, Peng Jiang, Peng Zhang, Lixuan Yu, Gang Li and Yi He

Int. J. Mol. Sci. 2022, 23(13), 7157; https://doi.org/10.3390/ijms23137157 - 28 Jun 2022

Cited by 7 | Viewed by 2024

Abstract

Wall-associated kinases (WAKs) are important receptor-like proteins that play major roles in plant defense against pathogens. Fusarium head blight (FHB), one of the most widespread and devastating crop diseases, reduces wheat yield and leads to quality deterioration. Although WAK gene families have been studied in many plants, systematic research on bread wheat (Triticum aestivum) and its role in FHB resistance, in particular, is lacking. In this study, we identified and characterized 320 genes of the TaWAK family in wheat distributed across all chromosomes except 4B and divided them into three phylogenetic groups. Duplication and synteny analyses provided valuable information on the evolutionary characteristics of the TaWAK genes. The gene expression pattern analysis suggested that TaWAK genes play diverse roles in plant biological processes and that at least 30 genes may be involved in the response to Fusarium infection in wheat spikes, with most of the genes contributing to pectin- and chitin-induced defense pathways. Furthermore, 45 TaWAK genes were identified within 17 hcmQTLs that are related to wheat FHB resistance. Our findings provide potential candidate genes for improving FHB resistance and insights into the future functional analysis of TaWAK genes in wheat. Full article

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

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21 pages, 4536 KiB

Open AccessArticle

Genome Wide Identification and Characterization of Wheat GH9 Genes Reveals Their Roles in Pollen Development and Anther Dehiscence

by Liqing Luo, Jianfang Bai, Shaohua Yuan, Liping Guo, Zihan Liu, Haoyu Guo, Tianbao Zhang, Wenjing Duan, Yanmei Li, Changping Zhao, Xiyue Song and Liping Zhang

Int. J. Mol. Sci. 2022, 23(11), 6324; https://doi.org/10.3390/ijms23116324 - 5 Jun 2022

Cited by 7 | Viewed by 2115

Abstract

Glycoside hydrolase family 9 (GH9) is a key member of the hydrolase family in the process of cellulose synthesis and hydrolysis, playing important roles in plant growth and development. In this study, we investigated the phenotypic characteristics and gene expression involved in pollen fertility conversion and anther dehiscence from a genomewide level. In total, 74 wheat GH9 genes (TaGH9s) were identified, which were classified into Class A, Class B and Class C and unevenly distributed on chromosomes. We also investigated the gene duplication and reveled that fragments and tandem repeats contributed to the amplification of TaGH9s. TaGH9s had abundant hormone-responsive elements and light-responsive elements, involving JA–ABA crosstalk to regulate anther development. Ten TaGH9s, which highly expressed stamen tissue, were selected to further validate their function in pollen fertility conversion and anther dehiscence. Based on the cell phenotype and the results of the scanning electron microscope at the anther dehiscence period, we found that seven TaGH9s may target miRNAs, including some known miRNAs (miR164 and miR398), regulate the level of cellulose by light and phytohormone and play important roles in pollen fertility and anther dehiscence. Finally, we proposed a hypothesis model to reveal the regulation pathway of TaGH9 on fertility conversion and anther dehiscence. Our study provides valuable insights into the GH9 family in explaining the male sterility mechanism of the wheat photo-thermo-sensitive genetic male sterile (PTGMS) line and generates useful male sterile resources for improving wheat hybrid breeding. Full article

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

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16 pages, 3126 KiB

Open AccessArticle

Integrate Small RNA and Degradome Sequencing to Reveal Drought Memory Response in Wheat (Triticum aestivum L.)

by Hong Yue, Haobin Zhang, Ning Su, Xuming Sun, Qi Zhao, Song Weining, Xiaojun Nie and Wenjie Yue

Int. J. Mol. Sci. 2022, 23(11), 5917; https://doi.org/10.3390/ijms23115917 - 25 May 2022

Cited by 14 | Viewed by 2122

Abstract

Drought has gradually become one of the most severe abiotic stresses on plants. Plants that experience stress training can exhibit enhanced stress tolerance. According to MicroRNA (miRNA) sequencing data, this study identified 195 candidate drought memory-related miRNAs in wheat, and targets of 64 (32.8%) candidate miRNAs were validated by degradome sequencing. Several drought memory-related miRNAs such as tae-miR9676-5p, tae-MIR9676-p3_1ss21GA, tae-miR171a, tae-miR531_L-2, tae-miR408_L-1, PC-3p-5049_3565, tae-miR396c-5p, tae-miR9778, tae-miR164a-5p, and tae-miR9662a-3p were validated as having a strong response to drought memory by regulating the expression of their target genes. In addition, overexpression of drought memory-related miRNA, tae-miR531_L-2, can remarkably improve the drought tolerance of transgenic Arabidopsisthaliana. Drought memory can regulate plant cellular signal transduction, plant biosynthetic processes, and other biological processes to cope with drought via transcriptional memory. In addition, drought memory-related miRNAs can promote starch and sucrose catabolism and soluble sugar accumulation and regulate proline homeostasis to improve plant drought resistance. Our results could contribute to an understanding of drought memory in wheat seedlings and may provide a new strategy for drought-resistant breeding. Full article

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

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16 pages, 2413 KiB

Open AccessArticle

Genome-Wide Investigation and Functional Verification of the ZIP Family Transporters in Wild Emmer Wheat

by Fangyi Gong, Tiangang Qi, Yanling Hu, Yarong Jin, Jia Liu, Wenyang Wang, Jingshu He, Bin Tu, Tao Zhang, Bo Jiang, Yi Wang, Lianquan Zhang, Youliang Zheng, Dengcai Liu, Lin Huang and Bihua Wu

Int. J. Mol. Sci. 2022, 23(5), 2866; https://doi.org/10.3390/ijms23052866 - 5 Mar 2022

Cited by 7 | Viewed by 2556

Abstract

The zinc/iron-regulated transporter-like protein (ZIP) family has a crucial role in Zn homeostasis of plants. Although the ZIP genes have been systematically studied in many plant species, the significance of this family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of ZIPs genes based on the wild emmer reference genome was conducted, and 33 TdZIP genes were identified. Protein structure analysis revealed that TdZIP proteins had 1 to 13 transmembrane (TM) domains and most of them were predicted to be located on the plasma membrane. These TdZIPs can be classified into three clades in a phylogenetic tree. They were annotated as being involved in inorganic ion transport and metabolism. Cis-acting analysis showed that several elements were involved in hormone, stresses, grain-filling, and plant development. Expression pattern analysis indicated that TdZIP genes were highly expressed in different tissues. TdZIP genes showed different expression patterns in response to Zn deficiency and that 11 genes were significantly induced in either roots or both roots and shoots of Zn-deficient plants. Yeast complementation analysis showed that TdZIP1A-3, TdZIP6B-1, TdZIP6B-2, TdZIP7A-3, and TdZIP7B-2 have the capacity to transport Zn. Overexpression of TdZIP6B-1 in rice showed increased Zn concentration in roots compared with wild-type plants. The expression levels of TdZIP6B-1 in transgenic rice were upregulated in normal Zn concentration compared to that of no Zn. This work provides a comprehensive understanding of the ZIP gene family in wild emmer wheat and paves the way for future functional analysis and genetic improvement of Zn deficiency tolerance in wheat. Full article

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

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20 pages, 2539 KiB

Open AccessArticle

Genome-Wide Association Study on Root System Architecture and Identification of Candidate Genes in Wheat (Triticum aestivum L.)

by Jianhui Ma, Dongyang Zhao, Xiaoxiao Tang, Meng Yuan, Daijing Zhang, Mengyuan Xu, Yingze Duan, Haiyue Ren, Qingdong Zeng, Jianhui Wu, Dejun Han, Tian Li and Lina Jiang

Int. J. Mol. Sci. 2022, 23(3), 1843; https://doi.org/10.3390/ijms23031843 - 6 Feb 2022

Cited by 13 | Viewed by 2856

Abstract

The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of −log₁₀ (p-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes, TraesCS2A01G516200 and TraesCS7B01G036900, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat. Full article

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

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14 pages, 2533 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of RNA/DNA Differences Associated with Drought Response in Wheat

by Yan Pan, Mengqi Li, Jiaqian Huang, Wenqiu Pan, Tingrui Shi, Qifan Guo, Guang Yang and Xiaojun Nie

Int. J. Mol. Sci. 2022, 23(3), 1405; https://doi.org/10.3390/ijms23031405 - 26 Jan 2022

Cited by 4 | Viewed by 2657

Abstract

RNA/DNA difference (RDD) is a post-transcriptional RNA modification to enrich genetic information, widely involved in regulating diverse biological processes in eukaryotes. RDDs in the wheat nuclear genome, especially those associated with drought response or tolerance, were not well studied up to now. In this study, we investigated the RDDs related to drought response based on the RNA-seq data of drought-stressed and control samples in wheat. In total, 21,782 unique RDDs were identified, of which 265 were found to be drought-induced, representing the first drought-responsive RDD landscape in the wheat nuclear genome. The drought-responsive RDDs were located in 69 genes, of which 35 were differentially expressed under drought stress. Furthermore, the effects of RNA/DNA differences were investigated, showing that they could result in changes of RNA secondary structure, miRNA-target binding as well as protein conserved domains in the RDD-containing genes. In particular, the A to C mutation in TraesCS2A02G053100 (orthology to OsRLCK) led to the loss of tae-miR9657b-5p targeting, indicating that RNA/DNA difference might mediate miRNA to regulate the drought-response process. This study reported the first drought-responsive RDDs in the wheat nuclear genome. It sheds light on the roles of RDD in drought tolerance, and may also contribute to wheat genetic improvement based on epi-transcriptome methods. Full article

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

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20 pages, 8681 KiB

Open AccessArticle

The Landscape of Autophagy-Related (ATG) Genes and Functional Characterization of TaVAMP727 to Autophagy in Wheat

by Wenjie Yue, Haobin Zhang, Xuming Sun, Ning Su, Qi Zhao, Zhaogui Yan, Song Weining and Hong Yue

Int. J. Mol. Sci. 2022, 23(2), 891; https://doi.org/10.3390/ijms23020891 - 14 Jan 2022

Cited by 2 | Viewed by 2304

Abstract

Autophagy is an indispensable biological process and plays crucial roles in plant growth and plant responses to both biotic and abiotic stresses. This study systematically identified autophagy-related proteins (ATGs) in wheat and its diploid and tetraploid progenitors and investigated their genomic organization, structure characteristics, expression patterns, genetic variation, and regulation network. We identified a total of 77, 51, 29, and 30 ATGs in wheat, wild emmer, T. urartu and A. tauschii, respectively, and grouped them into 19 subfamilies. We found that these autophagy-related genes (ATGs) suffered various degrees of selection during the wheat’s domestication and breeding processes. The genetic variations in the promoter region of Ta2A_ATG8a were associated with differences in seed size, which might be artificially selected for during the domestication process of tetraploid wheat. Overexpression of TaVAMP727 improved the cold, drought, and salt stresses resistance of the transgenic Arabidopsis and wheat. It also promoted wheat heading by regulating the expression of most ATGs. Our findings demonstrate how ATGs regulate wheat plant development and improve abiotic stress resistance. The results presented here provide the basis for wheat breeding programs for selecting varieties of higher yield which are capable of growing in colder, drier, and saltier areas. Full article

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

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Review

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18 pages, 659 KiB

Open AccessReview

Linking Multi-Omics to Wheat Resistance Types to Fusarium Head Blight to Reveal the Underlying Mechanisms

by Fan Wu, Yao Zhou, Yingying Shen, Zhengxi Sun, Lei Li and Tao Li

Int. J. Mol. Sci. 2022, 23(4), 2280; https://doi.org/10.3390/ijms23042280 - 18 Feb 2022

Cited by 10 | Viewed by 3141

Abstract

Fusarium head blight (FHB) caused by Fusarium graminearum is a worldwide disease which has destructive effects on wheat production, resulting in severe yield reduction and quality deterioration, while FHB-infected wheat grains are toxic to people and animals due to accumulation of fungal toxins. Although impressive progress towards understanding host resistance has been achieved, our knowledge of the mechanism underlying host resistance is still quite limited due to the complexity of wheat–pathogen interactions. In recent years, disease epidemics, the resistance germplasms and components, the genetic mechanism of FHB, and disease management and control, etc., have been well reviewed. However, the resistance mechanism of FHB is quite complex with Type I, II to V resistances. In this review, we focus on the potential resistance mechanisms by linking different resistance types to multi-omics and emphasize the pathways or genes that may play significant roles in the different types of resistance. Deciphering the complicated mechanism of FHB resistance types in wheat at the integral levels based on multi-omics may help discover the genes or pathways that are critical for different FHB resistance, which could then be utilized and manipulated to improve FHB resistance in wheat breeding programs by using transgenic approaches, gene editing, or marker assisted selection strategies. Full article

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

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