Research

16 pages, 3302 KiB

Open AccessArticle

The Evolution, Expression Patterns, and Domestication Selection Analysis of the Annexin Gene Family in the Barley Pan-Genome

by Liqin Chen, Kunxiang Chen, Xi Xi, Xianghong Du, Xinyi Zou, Yujia Ma, Yingying Song, Changquan Luo and Song Weining

Int. J. Mol. Sci. 2024, 25(7), 3883; https://doi.org/10.3390/ijms25073883 - 30 Mar 2024

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Abstract

Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, [...] Read more.

Plant annexins constitute a conserved protein family that plays crucial roles in regulating plant growth and development, as well as in responses to both biotic and abiotic stresses. In this study, a total of 144 annexin genes were identified in the barley pan-genome, comprising 12 reference genomes, including cultivated barley, landraces, and wild barley. Their chromosomal locations, physical–chemical characteristics, gene structures, conserved domains, and subcellular localizations were systematically analyzed to reveal the certain differences between wild and cultivated populations. Through a cis-acting element analysis, co-expression network, and large-scale transcriptome analysis, their involvement in growth, development, and responses to various stressors was highlighted. It is worth noting that HvMOREXann5 is only expressed in pistils and anthers, indicating its crucial role in reproductive development. Based on the resequencing data from 282 barley accessions worldwide, genetic variations in thefamily were investigated, and the results showed that 5 out of the 12 identified HvMOREXanns were affected by selection pressure. Genetic diversity and haplotype frequency showed notable reductions between wild and domesticated barley, suggesting that a genetic bottleneck occurred on the annexin family during the barley domestication process. Finally, qRT-PCR analysis confirmed the up-regulation of HvMOREXann7 under drought stress, along with significant differences between wild accessions and varieties. This study provides some insights into the genome organization and genetic characteristics of the annexin gene family in barley at the pan-genome level, which will contribute to better understanding its evolution and function in barley and other crops. Full article

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

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12 pages, 5633 KiB

Open AccessCommunication

Global Analysis of Lysine Lactylation of Germinated Seeds in Wheat

by Junke Zhu, Weiwei Guo and Yubin Lan

Int. J. Mol. Sci. 2023, 24(22), 16195; https://doi.org/10.3390/ijms242216195 - 11 Nov 2023

Viewed by 873

Abstract

Protein lactylation is a newly discovered posttranslational modification (PTM) and is involved in multiple biological processes, both in mammalian cells and rice grains. However, the function of lysine lactylation remains unexplored in wheat. In this study, we performed the first comparative proteomes and [...] Read more.

Protein lactylation is a newly discovered posttranslational modification (PTM) and is involved in multiple biological processes, both in mammalian cells and rice grains. However, the function of lysine lactylation remains unexplored in wheat. In this study, we performed the first comparative proteomes and lysine lactylomes during seed germination of wheat. In total, 8000 proteins and 927 lactylated sites in 394 proteins were identified at 0 and 12 h after imbibition (HAI). Functional enrichment analysis showed that glycolysis- and TCA-cycle-related proteins were significantly enriched, and more differentially lactylated proteins were enriched in up-regulated lactylated proteins at 12 HAI vs. 0 HAI through the KEGG pathway and protein domain enrichment analysis compared to down-regulated lactylated proteins. Meanwhile, ten particularly preferred amino acids near lactylation sites were found in the embryos of germinated seeds: AA*K^laT, A***K^laD********A, K^laA**T****K, K******A*K^la, K*K^la********K, K^laA******A, K^la*A, KD****K^la, K********K^la and K^laG. These results supplied a comprehensive profile of lysine lactylation of wheat and indicated that protein lysine lactylation played important functions in several biological processes. Full article

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

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14 pages, 1952 KiB

Open AccessArticle

Evaluation of the Allelic Variations in Vernalisation (VRN1) and Photoperiod (PPD1) Genes and Genetic Diversity in a Spanish Spelt Wheat Collection

by Carmen Palomino and Adoración Cabrera

Int. J. Mol. Sci. 2023, 24(22), 16041; https://doi.org/10.3390/ijms242216041 - 07 Nov 2023

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Abstract

Allelic variation within genes controlling the vernalisation requirement (VRN1) and photoperiod response (PPD1) determines the adaptation of wheat to different environmental growing conditions as well as influences other traits related to grain yield. This study aimed to screen a [...] Read more.

Allelic variation within genes controlling the vernalisation requirement (VRN1) and photoperiod response (PPD1) determines the adaptation of wheat to different environmental growing conditions as well as influences other traits related to grain yield. This study aimed to screen a Spanish spelt wheat collection using gene-specific molecular markers for VRN-A1, VRN-B1, VRN-D1, and PPD-D1 loci and to phenotype for heading date (HD) in both field and greenhouse experiments under a long photoperiod and without vernalisation. Fifty-five spelt genotypes (91.7%) exhibited a spring growth habit, and all of them carried at least one dominant VRN1 allele, whereas five (8.3%) genotypes had a winter growth habit, and they carried the triple recessive allele combination. The Vrn-D1s was the most frequent allele in the studied set of spelt accessions, and it was found in combination with both the dominant Vrn-A1b and/or Vrn-B1a alleles in 88.3% of the spelt accessions tested. All spelt accessions carried the photoperiod-sensitive Ppd-D1b allele, which may explain the late heading of spelt germplasm compared to the commercial spring bread wheat Setenil used as a control. The least significant difference test showed significant differences between allelic combinations, the earliest accessions being those carrying two or three dominant alleles, followed by the one-gene combinations. In addition, the genetic diversity was evaluated through capillary electrophoresis using 15 wheat simple sequence repeat (SSR) markers. Most markers had high levels of polymorphism, producing 95 different alleles which ranged between 53 and 279 bp in size. Based on the polymorphic information content values obtained (from 0.51 to 0.97), 12 out of the 15 SSRs were catalogued as informative markers (values > 0.5). According to the dendrogram generated, the spelt accessions clustered as a separate group from the commercial bread wheat Setenil. Knowledge of VRN1 and PPD1 alleles, heading time, and genetic variability using SSR markers is valuable for spelt wheat breeding programs. Full article

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

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15 pages, 4575 KiB

Open AccessArticle

Identification and Expressional Analysis of siRNAs Responsive to Fusarium graminearum Infection in Wheat

by Kai Fu, Qianhui Wu, Ning Jiang, Sijia Hu, Hongyan Ye, Yi Hu, Lei Li, Tao Li and Zhengxi Sun

Int. J. Mol. Sci. 2023, 24(21), 16005; https://doi.org/10.3390/ijms242116005 - 06 Nov 2023

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Abstract

The outbreak of Fusarium head blight (FHB) poses a serious threat to wheat production as it leads to both significant yield losses and accumulation of several mycotoxins including deoxynivalenol (DON) in the grains, which are harmful to human and livestock. To date, hundreds [...] Read more.

The outbreak of Fusarium head blight (FHB) poses a serious threat to wheat production as it leads to both significant yield losses and accumulation of several mycotoxins including deoxynivalenol (DON) in the grains, which are harmful to human and livestock. To date, hundreds of FHB-resistance-related quantitative trait loci (QTLs) have been reported, but only a few of them have been cloned and used for breeding. Small interfering RNAs (siRNA) have been reported in plants to mediate host defense against pathogens, but they have rarely been reported in wheat-FHB interaction. In order to identify the key siRNAs that can potentially be used in the improvement of resistance to FHB, siRNAs from the spikes of an FHB-resistant variety Sumai 3 and an FHB-susceptible variety of Chinese Spring (CS) were sequenced after F. graminearum infection and mock inoculation, respectively. The expression patterns of the siRNAs of interest were analyzed. A total of 4019 siRNAs of high-confidence were identified, with 131 being CS-specific, 309 Sumai 3-specific and 3071 being common in both varieties. More than 87% of these siRNAs were 24 nt in length. An overall down-regulation trend was found for siRNAs in the spikes of both varieties after being infected with F. graminearum. The expression patterns for Triticum aestivum Dicer-like 3 (TaDCL3) that synthesizes 24 nt siRNAs were validated by qRT-PCR, which were positively correlated with those of the siRNAs. A total of 85% of the differentially expressed genes putatively targeted by the siRNAs were significantly up-regulated after infection, showing a negative correlation with the overall down-regulated expression of siRNAs. Interestingly, the majority of the up-regulated genes are annotated as disease resistance. These results suggested that the inhibition of siRNA by F. graminearum up-regulated the disease resistance genes, which were putatively suppressed by siRNAs through RNA-directed DNA methylation (RdDM). Consequently, the resistant capability to F. graminearum infection was enhanced. This study provides novel clues for investigating the function of siRNA in wheat-F. graminearum interaction. Full article

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

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17 pages, 2712 KiB

Open AccessArticle

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

by Yi Yuan, Xiaohui Yin, Xiaowen Han, Shuo Han, Yiting Li, Dongfang Ma, Zhengwu Fang, Junliang Yin and Shuangjun Gong

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

Cited by 4 | Viewed by 1319

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 [...] Read more.

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)

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16 pages, 4222 KiB

Open AccessArticle

Evolution and Expression of the Expansin Genes in Emmer Wheat

by Ming Li, Tao Liu, Rui Cao, Qibin Cao, Wei Tong and Weining Song

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

Cited by 1 | Viewed by 1003

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 [...] Read more.

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)

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16 pages, 3362 KiB

Open AccessArticle

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

by 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

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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 [...] Read more.

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)

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14 pages, 2563 KiB

Open AccessArticle

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

by Yi Dai, Jinfeng Li, Juntao Shi, Yujiao Gao, Haigang Ma, Yonggang Wang and Hongxiang Ma

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

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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. [...] Read more.

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)

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14 pages, 1182 KiB

Open AccessArticle

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

by Xiaoqing Li, Anton P. Wasson, Alexander B. Zwart, Alex Whan, Peter R. Ryan, Kerrie Forrest, Matthew Hayden, Sabrina Chin, Richard Richards and Emmanuel Delhaize

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

Viewed by 930

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 [...] Read more.

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)

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18 pages, 5440 KiB

Open AccessArticle

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

by Tianbao Li, Chuizheng Kong, Pingchuan Deng, Chengdao Li, Guangyao Zhao, Hongjie Li, Lifeng Gao, Dangqun Cui and Jizeng Jia

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

Cited by 1 | Viewed by 1302

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 [...] Read more.

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)

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16 pages, 4099 KiB

Open AccessArticle

Epigenetic Landscape Is Largely Shaped by Diversiform Transposons in Aegilops tauschii

by Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu and Jizeng Jia

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

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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 [...] Read more.

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)

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