scholarly journals The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 338
Author(s):  
Moran Nave ◽  
Mihriban Taş ◽  
John Raupp ◽  
Vijay K. Tiwari ◽  
Hakan Ozkan ◽  
...  
Keyword(s):  
Promoter Region ◽  
Haplotype Analysis ◽  
Common Ancestor ◽  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Wheat Species ◽  
Loss Of Function ◽  
Brittle Rachis ◽  
Gene Level ◽  
Large Panel

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

scholarly journals Association between the HMW-glutenin subunits and gluten strength characteristics in khorassan wheat lines - Short Communications

2009 ◽  
Vol 45 (No. 4) ◽  
pp. 169-172 ◽  
Author(s):  
S. Carmona ◽  
L. Caballero ◽  
J.B. Alvarez
Keyword(s):  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
General Characteristic ◽  
Gluten Strength ◽  
Wheat Species ◽  
Glutenin Subunits ◽  
Subunit Combination ◽  
Sedimentation Volume ◽  
Hmw Glutenin ◽  
Wheat Lines

Khorassan wheat (Triticum turgidum ssp. turanicum Jakubz em. A. Löve & D. Löve) is an ancient tetraploid wheat that was grown in the Mediterranean region and Near East. Sixteen lines differing in the composition of high-molecular-weight glutenin subunits (HMWGs) were evaluated for SDS-sedimentation volume and quality index (QI). The data suggested that the two subunit combinations detected in the examined materials at the Glu-B1 locus showed differences in both characteristics (relatively higher levels at the presence of the subunit combination 7+15 compared to 6+8). Weak gluten is in general characteristic of this wheat species. It could be used in a better way for other baking applications than for the pasta industry.

Map-based analysis of genes affecting the brittle rachis character in tetraploid wheat (Triticum turgidum L.)

2005 ◽  
Vol 112 (2) ◽  
pp. 373-381 ◽  
Author(s):  
Vamsi J. Nalam ◽  
M. Isabel Vales ◽  
Christy J. W. Watson ◽  
Shahryar F. Kianian ◽  
Oscar Riera-Lizarazu
Keyword(s):  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Brittle Rachis

scholarly journals Identification of theTMEM232 gene associated with atopic dermatitis through targeted capture sequencing

2021 ◽  
Author(s):  
Jie Zheng ◽  
Yuan-yuan Wu ◽  
Wen-liang Fang ◽  
Xin-ying Cai ◽  
Zeng-yun-ou Zhang ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Skin Disorder ◽  
Haplotype Analysis ◽  
Susceptibility Gene ◽  
Enrichment Analysis ◽  
Sequencing Analysis ◽  
Loss Of Function ◽  
Gene Level ◽  
Targeted Capture ◽  
Capture Sequencing

AbstractBACKGROUNDAtopic dermatitis (AD) is a common and complex skin disorder, and the 5q22.1 region had been reported to be associated with AD.OBJECTIVETo identify the susceptibility gene for AD in the 5q22.1 region by haplotype and targeted capture sequencing.METHODSThe haplotypes were reconstructed with our previously genotyping data of four SNPs and six deletions from 3055 Chinese Hans AD patients and 4346 controls. The targeted capture sequencing spanning 5q22.1 region was performed in the selected samples. The gene level enrichment analysis was done using loss of function variants.RESULTSA total of 60 haplotypes were found, and the H15 haplotype had the strongest association with AD (P = 2.72×10 −10, OR = 0.14, 95%CI = 0.07-0.28). However, No co-segregation mutation sites were found in the sequencing analysis within the 16 selected samples, while the enrichment analysis indicated that TMEM232 was significantly associated with AD (P = 7.33×10 -5, OR = 0.33, 95% CI = 0.19-0.58).CONCLUSIONSThis study confirms previous findings that the TMEM232 gene is associated with AD by haplotype analysis and targeted capture sequencing.

scholarly journals Function and evolution of allelic variation of Sr13 conferring resistance to stem rust in tetraploid wheat ( Triticum turgidum L.)

2021 ◽  
Author(s):  
Baljeet K. Gill ◽  
Daryl L. Klindworth ◽  
Matthew N. Rouse ◽  
Jinglun Zhang ◽  
Qijun Zhang ◽  
...  
Keyword(s):  
Stem Rust ◽  
Triticum Turgidum ◽  
Allelic Variation ◽  
Tetraploid Wheat

Molecular characterization and chromosome-specific TRAP-marker development for Langdon durum D-genome disomic substitution lines

Genome ◽  
2006 ◽  
Vol 49 (12) ◽  
pp. 1545-1554 ◽  
Author(s):  
J. Li ◽  
D.L. Klindworth ◽  
F. Shireen ◽  
X. Cai ◽  
J. Hu ◽  
...  
Keyword(s):  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Substitution Lines ◽  
Genome Chromosome ◽  
D Genome ◽  
Single Chromosome ◽  
B Genome ◽  
The Individual ◽  
Trap Marker

The aneuploid stocks of durum wheat ( Triticum turgidum L. subsp. durum (Desf.) Husnot) and common wheat ( T. aestivum L.) have been developed mainly in ‘Langdon’ (LDN) and ‘Chinese Spring’ (CS) cultivars, respectively. The LDN-CS D-genome chromosome disomic substitution (LDN-DS) lines, where a pair of CS D-genome chromosomes substitute for a corresponding homoeologous A- or B-genome chromosome pair of LDN, have been widely used to determine the chromosomal locations of genes in tetraploid wheat. The LDN-DS lines were originally developed by crossing CS nulli-tetrasomics with LDN, followed by 6 backcrosses with LDN. They have subsequently been improved with 5 additional backcrosses with LDN. The objectives of this study were to characterize a set of the 14 most recent LDN-DS lines and to develop chromosome-specific markers, using the newly developed TRAP (target region amplification polymorphism)-marker technique. A total of 307 polymorphic DNA fragments were amplified from LDN and CS, and 302 of them were assigned to individual chromosomes. Most of the markers (95.5%) were present on a single chromosome as chromosome-specific markers, but 4.5% of the markers mapped to 2 or more chromosomes. The number of markers per chromosome varied, from a low of 10 (chromosomes 1A and 6D) to a high of 24 (chromosome 3A). There was an average of 16.6, 16.6, and 15.9 markers per chromosome assigned to the A-, B-, and D-genome chromosomes, respectively, suggesting that TRAP markers were detected at a nearly equal frequency on the 3 genomes. A comparison of the source of the expressed sequence tags (ESTs), used to derive the fixed primers, with the chromosomal location of markers revealed that 15.5% of the TRAP markers were located on the same chromosomes as the ESTs used to generate the fixed primers. A fixed primer designed from an EST mapped on a chromosome or a homoeologous group amplified at least 1 fragment specific to that chromosome or group, suggesting that the fixed primers might generate markers from target regions. TRAP-marker analysis verified the retention of at least 13 pairs of A- or B-genome chromosomes from LDN and 1 pair of D-genome chromosomes from CS in each of the LDN-DS lines. The chromosome-specific markers developed in this study provide an identity for each of the chromosomes, and they will facilitate molecular and genetic characterization of the individual chromosomes, including genetic mapping and gene identification.

scholarly journals Mutational Analysis of a Wheat O-methyltransferase Involved in Flavonoid Metabolism

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 164
Author(s):  
Alexander B. Cain ◽  
Shu Yu ◽  
Li Tian
Keyword(s):  
Mutational Analysis ◽  
Tetraploid Wheat ◽  
Hydroxyl Groups ◽  
Loss Of Function ◽  
Soluble Phenolics ◽  
Mutant Lines ◽  
Similar Growth ◽  
Close Homolog ◽  
Lignin Deposition

Methylated flavones, and tricin in particular, have been implicated in protecting wheat plants against a variety of biotic and abiotic stresses. Methylated flavones are produced via O-methylation of the hydroxyl groups in flavones, which is catalyzed by O-methyltransferases (OMTs). To examine the role of wheat OMT2 in methylated flavone biosynthesis and facilitate interrogation of tricin functions in wheat-environment interactions, loss-of-function mutants of OMT2 homoeologs, omt-A2 and omt-B2, were identified from a tetraploid wheat Targeting Induced Local Lesions in Genomes (TILLING) mutant population and crossed to generate the omt-A2omt-B2 double mutant. Although tricin and most other soluble phenolics did not differ in leaves and glumes of TILLING control and the omt-A2, omt-B2, and omt-A2 omt-B2 mutants, chlorogenic acid was increased in glumes of omt-A2 omt-B2 relative to TILLING control, suggesting that it might serve as a substrate for OMT2. The omt2 mutant lines showed similar growth phenotypes as well as comparable lignin deposition in cell walls of stems compared to TILLING control. These results collectively suggest that OMT2 and its close homolog OMT1 may possess overlapping activities in tricin production, with OMT1 compensating for the missing OMT2 activities in the omt2 mutant lines.

scholarly journals A Signature of Nine lncRNA Methylated Genes Predicts Survival in Patients With Glioma

2021 ◽  
Vol 11 ◽  
Author(s):  
Meng Cheng ◽  
Libo Sun ◽  
Kebing Huang ◽  
Xiaoyu Yue ◽  
Jie Chen ◽  
...  
Keyword(s):  
High Risk ◽  
Promoter Region ◽  
Malignant Tumors ◽  
Risk Group ◽  
Glioma Cells ◽  
Low Risk ◽  
The Cancer Genome Atlas ◽  
Migration And Invasion ◽  
Aberrant Methylation ◽  
Loss Of Function

Glioma is one of the most common malignant tumors of the central nervous system, and its prognosis is extremely poor. Aberrant methylation of lncRNA promoter region is significantly associated with the prognosis of glioma patients. In this study, we investigated the potential impact of methylation of lncRNA promoter region in glioma patients to establish a signature of nine lncRNA methylated genes for determining glioma patient prognosis. Methylation data and clinical follow-up data were obtained from The Cancer Genome Atlas (TCGA). The multistep screening strategy identified nine lncRNA methylated genes that were significantly associated with the overall survival (OS) of glioma patients. Subsequently, we constructed a risk signature that containing nine lncRNA methylated genes. The risk signature successfully divided the glioma patients into high-risk and low-risk groups. Compared with the low-risk group, the high-risk group had a worse prognosis, higher glioma grade, and older age. Furthermore, we identified two lncRNAs termed PCBP1-AS1 and LINC02875 that may be involved in the malignant progression of glioma cells by using the TCGA database. Loss-of-function assays confirmed that knockdown of PCBP1-AS1 and LINC02875 inhibited the proliferation, migration, and invasion of glioma cells. Therefore, the nine lncRNA methylated genes signature may provide a novel predictor and therapeutic target for glioma patients.

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