scholarly journals Genome-Scale Analysis of Homologous Genes among Subgenomes of Bread Wheat (Triticum aestivum L.)

2020 ◽  
Vol 21 (8) ◽  
pp. 3015
Author(s):  
Caie Zhou ◽  
Zhaonian Dong ◽  
Ting Zhang ◽  
Jianhui Wu ◽  
Shizhou Yu ◽  
...  
Keyword(s):  
Chromosome Rearrangement ◽  
Triticum Aestivum L ◽  
Crop Evolution ◽  
Average Density ◽  
Wheat Genome ◽  
Functional Enrichment ◽  
Homologous Gene ◽  
Primary Metabolite ◽  
Homologous Genes ◽  
Genome Scale

Determining the distribution and correspondence of genome-scale homologous genes in wheat are effective ways to uncover chromosome rearrangement that has occurred during crop evolution and domestication, which can contribute to improvements in crop breeding. High-resolution and comprehensive analysis of the wheat genome by the International Wheat Genome Sequencing Consortium (IWGSC) revealed a total of 88,733 high-confidence homologous genes of four major types (1:1:1, 1:1:0, 0:1:1 and 1:0:1) among the A, B and D subgenomes of wheat. This data was used to compare homologous gene densities among chromosomes, clarify their distribution and correspondence relationship, and compare their functional enrichment. The average density of 1:1:1 homologous genes was about 10 times more than the density of the other three types of homologous genes, although the homologous gene densities of the various chromosomes were similar within each homologous type. Three regions of exceptional density were detected in 1:1:1 homologous genes, the isolate peak on the tail of chromosome 4A, and the desert regions at the start of chromosome 7A and 7D. The correspondence between homologous genes of the wheat subgenomes demonstrated translocation between the tail segments of chromosome 4A and 5A, and the inversion of the segment of original 5A and 7B into the tail of 4A. The homologous genes on the inserting segments of 5A and 7B to 4A were highly enriched in nitrogen, primary metabolite and small molecular metabolism processes, compared with genes on other regions of the original 4A chromosome. This study provides a refined genome-scale reference of homologous genes for wheat molecular research and breeding, which will help to broaden the application of the wheat genome and can be used as a template for research on other polyploid plants.

scholarly journals A Microsatellite Map of Wheat

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 2007-2023 ◽  
Author(s):  
Marion S Röder ◽  
Victor Korzun ◽  
Katja Wendehake ◽  
Jens Plaschke ◽  
Marie-Hélène Tixier ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Reference Population ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
D Genome ◽  
B Genome ◽  
Microsatellite Map ◽  
A Genome ◽  
Polymorphic Microsatellite ◽  
Primer Sets

Abstract Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.

scholarly journals F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1154
Author(s):  
Min Jeong Hong ◽  
Jin-Baek Kim ◽  
Yong Weon Seo ◽  
Dae Yeon Kim
Keyword(s):  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Post Translational Modification ◽  
Genome Wide ◽  
A Genome ◽  
High Sequence Homology ◽  
Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

scholarly journals Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ruibin Wang ◽  
Jingfei Ma ◽  
Qian Zhang ◽  
Chunlai Wu ◽  
Hongyan Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Segmental Duplication ◽  
Expression Profiling ◽  
Abiotic Stresses ◽  
Glutathione Transferase ◽  
Purifying Selection ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Qrt Pcr ◽  
Duplication Events

Abstract Background Glutathione transferases (GSTs), the ancient, ubiquitous and multi-functional proteins, play significant roles in development, metabolism as well as abiotic and biotic stress responses in plants. Wheat is one of the most important crops, but the functions of GST genes in wheat were less studied. Results A total of 330 TaGST genes were identified from the wheat genome and named according to the nomenclature of rice and Arabidopsis GST genes. They were classified into eight classes based on the phylogenetic relationship among wheat, rice, and Arabidopsis, and their gene structure and conserved motif were similar in the same phylogenetic class. The 43 and 171 gene pairs were identified as tandem and segmental duplication genes respectively, and the Ka/Ks ratios of tandem and segmental duplication TaGST genes were less than 1 except segmental duplication gene pair TaGSTU24/TaGSTU154. The 59 TaGST genes were identified to have syntenic relationships with 28 OsGST genes. The expression profiling involved in 15 tissues and biotic and abiotic stresses suggested the different expression and response patterns of the TaGST genes. Furthermore, the qRT-PCR data showed that GST could response to abiotic stresses and hormones extensively in wheat. Conclusions In this study, a large GST family with 330 members was identified from the wheat genome. Duplication events containing tandem and segmental duplication contributed to the expansion of TaGST family, and duplication genes might undergo extensive purifying selection. The expression profiling and cis-elements in promoter region of 330 TaGST genes implied their roles in growth and development as well as adaption to stressful environments. The qRT-PCR data of 14 TaGST genes revealed that they could respond to different abiotic stresses and hormones, especially salt stress and abscisic acid. In conclusion, this study contributed to the further functional analysis of GST genes family in wheat.

scholarly journals Expansion and Functional Diversification of SKP1-Like Genes in Wheat (Triticum aestivum L.)

2019 ◽  
Vol 20 (13) ◽  
pp. 3295
Author(s):  
Imen HajSalah El Beji ◽  
Said Mouzeyar ◽  
Mohammed-Fouad Bouzidi ◽  
Jane Roche
Keyword(s):  
Triticum Aestivum ◽  
Physcomitrella Patens ◽  
Expression Patterns ◽  
Protein S ◽  
Triticum Aestivum L ◽  
Wheat Genome ◽  
Genome Database ◽  
E3 Ligases ◽  
Expression Platform ◽  
Public Data

The ubiquitin proteasome 26S system (UPS), involving monomeric and multimeric E3 ligases is one of the most important signaling pathways in many organisms, including plants. The SCF (SKP1/Cullin/F-box) multimeric complex is particularly involved in response to development and stress signaling. The SKP1 protein (S-phase kinase-associated protein 1) is the core subunit of this complex. In this work, we firstly identified 92 and 87 non-redundant Triticum aestivum SKP1-like (TaSKP) genes that were retrieved from the latest release of the wheat genome database (International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0) and the genome annotation of the TGAC v1 respectively. We then investigated the structure, phylogeny, duplication events and expression patterns of the SKP1-like gene family in various tissues and environmental conditions using a wheat expression platform containing public data. TaSKP1-like genes were expressed differentially in response to stress conditions, displaying large genomic variations or short insertions/deletions which suggests functional specialization within TaSKP1-like genes. Finally, interactions between selected wheat FBX (F-box) proteins and putative ancestral TaSKP1-like proteins were tested using the yeast two-hybrid (Y2H) system to examine the molecular interactions. These observations suggested that six Ta-SKP1 genes are likely to be ancestral genes, having similar functions as ASK1 and ASK2 in Arabidopsis, OSK1 and OSK20 in rice and PpSKP1 and PpSKP2 in Physcomitrella patens.

Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat

2019 ◽  
Vol 60 (8) ◽  
pp. 1761-1777 ◽  
Author(s):  
Lijiang Hou ◽  
Aihua Zhang ◽  
Ruochen Wang ◽  
Peng Zhao ◽  
Dongzhi Zhang ◽  
...  
Keyword(s):  
Root Development ◽  
Hexaploid Wheat ◽  
Glycogen Synthase ◽  
Abiotic Stress Tolerance ◽  
Point Mutations ◽  
Triticum Aestivum L ◽  
Wheat Root ◽  
Homologous Gene ◽  
Evolutionary Divergence ◽  
Biotic And Abiotic Stress

Abstract Brassinosteroid (BR) plays an important role in plant development and biotic and abiotic stress tolerance, but its specific function remains largely unknown in wheat (Triticum aestivum L.), preventing its utilization in this important crop. In this study, the function of BR and its underlying cytological role in wheat root development were comprehensively investigated. Our findings demonstrated that BR has a conserved function in regulating root length in wheat, and novel roles in regulating lateral root emergence and root diameter were uncovered. Analyses of BR homologous gene composition and evolutionary divergence demonstrated that the genetic framework of the wheat BR pathway was close to that of rice, but contained highly redundant homologous copies of genes from the subgenome A, B and D. These homologous copies showed active expression and shared a conserved BR response. The expression of wheat DWF4 and glycogen synthase kinase (GSK) genes in Arabidopsis confirmed that multiple homologous copies maintained their conserved function in regulating root development, highlighting their redundant status and indicating that a special challenge exists in wheat gene modification to deal with this high redundancy. However, our results suggested that the hypermorphic effect of T. aestivum GSK (TaGSK) genes with point mutations may be an effective approach to overcome this redundancy in the manipulation of BR signaling in wheat. Our study provides fundamental data uncovering the function of BR in wheat root development, the underlying genetic basis and a possible strategy to manipulate BR signaling in hexaploid wheat.

Random chromosome elimination in synthetic Triticum–Aegilops amphiploids leads to development of a stable partial amphiploid with high grain micro- and macronutrient content and powdery mildew resistance

Genome ◽  
2010 ◽  
Vol 53 (12) ◽  
pp. 1053-1065 ◽  
Author(s):  
Vijay K. Tiwari ◽  
Nidhi Rawat ◽  
Kumari Neelam ◽  
Sundip Kumar ◽  
Gursharn S. Randhawa ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Powdery Mildew ◽  
Powdery Mildew Resistance ◽  
Chromosome Elimination ◽  
Triticum Aestivum L ◽  
Crop Evolution ◽  
High Fertility ◽  
Mildew Resistance ◽  
Partial Amphiploids

Synthetic amphiploids are the immortal sources for studies on crop evolution, genome dissection, and introgression of useful variability from related species. Cytological analysis of synthetic decaploid wheat ( Triticum aestivum L.) –   Aegilops kotschyi Boiss. amphiploids (AABBDDUkUkSkSk) showed some univalents from the C1 generation onward followed by chromosome elimination. Most of the univalents came to metaphase I plate after the reductional division of paired chromosomes and underwent equational division leading to their elimination through laggards and micronuclei. Substantial variation in the chromosome number of pollen mother cells from different tillers, spikelets, and anthers of some plants also indicated somatic chromosome elimination. Genomic in situ hybridization, fluorescence in situ hybridization, and simple sequence repeat markers analysis of two amphiploids with reduced chromosomes indicated random chromosome elimination of various genomes with higher sensitivity of D followed by the Sk and Uk genomes to elimination, whereas 1D chromosome was preferentially eliminated in both the amphiploids investigated. One of the partial amphiploids, C4 T. aestivum ‘Chinese Spring’ – Ae. kotschyi 396 (2n = 58), with 34 T. aestivum, 14 Uk, and 10 Sk had stable meiosis and high fertility. The partial amphiploids with white glumes, bold seeds, and tough rachis with high grain macro- and micronutrients and resistance to powdery mildew could be used for T. aestivum biofortification and transfer of powdery mildew resistance.

scholarly journals Clustering and Differentiation of glr-3 Gene Function and Its Homologous Proteins

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Yue Ma ◽  
Tiantian Guo ◽  
Yihe Wang ◽  
Xinna Li ◽  
Jingyu Zhang
Keyword(s):  
Secondary Structure ◽  
Protein Glycosylation ◽  
Random Coil ◽  
Homologous Gene ◽  
Phosphorylation Sites ◽  
Homologous Proteins ◽  
Homologous Genes ◽  
Glycosylation Sites ◽  
Α Helix ◽  
Cold Sensing

In order to adapt to the low temperature environment, organisms transmitexcitement to the central system through the thermal sensing system, whichis a classic reflex reaction. The cold receptor GLR-3 perceives cold and produces cold avoidance behavior through peripheral sensory neurons ASER.In order to further understand the gene encoding of the cold sensing glr-3gene and the evolution of its homologous gene group function and proteinfunction, the nucleotide sequence and amino acid sequence of the glr-3gene and its homologous gene in 24 species were obtained and compared.By clustering with the GRIK2 gene sequence of Rana chensinensis, the bioinformatics method was used to predict and sequence analyze the change ofgene, evolution rate, physical and chemical properties of protein, glycosylation sites, phosphorylation sites, secondary structure and tertiary structureof protein. The analysis results show that the glr-3 gene and its homologousgene have obvious positive selection effect. The protein prediction analysisshowed that the glr-3 gene and its homologous genes encoded proteinsin these 25 species were hydrophilic proteins, and the proportion of sidechains of aliphatic amino acids was high. The transmembrane helix waswidespread and there were more N-glycosylation sites and O-glycosylationsites. The protein phosphorylation sites encoded were serine, threonine andtyrosine phosphorylation sites. Secondary structure prediction showed thatthe secondary structure units of the encoded protein were α-helix, β-turn,random coil and extended chain, and the proportion of α-helix was the largest. This study provides useful information on the evolution and function ofthe cold sensing gene glr-3 and its homologous genes.

scholarly journals Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks

2016 ◽  
Author(s):  
Anastasia Baryshnikova
Keyword(s):  
Spatial Analysis ◽  
Biological Networks ◽  
Biological Process ◽  
Genetic Interaction ◽  
Chemical Compounds ◽  
Functional Enrichment ◽  
Relative Positioning ◽  
Chemical Genomic ◽  
Genome Scale ◽  
Novel Drug

Summary/AbstractSpatial Analysis of Functional Enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions are represented in a network, which parts of the network they are associated with and how they are potentially related to one another.Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network fromSaccharomyces cerevisiaewith Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes-of-action of chemical compounds and potentially identify novel drug mechanisms.

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