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Comparison of two orthologous 20 kb regions including the Bx gene. A dot plot compares the tetraploid Bx region to the same region from hexaploid wheat. A comparison window of 30 bp and 70% identity was used. The light block in the middle of the diagonal is composed of uncharacterized repeat sequences, and the heavy block structure at the right end is caused by the repeat domain in the HMW-glutenin genes. The Bx HMW-glutenin gene regions of the hexaploid and tetraploid wheat are indicated by line A and B, respectively.
Source publication
Two overlapping bacterial artificial chromosome (BAC) clones from the B genome of the tetraploid wheat Triticum turgidum were identified, each of which contains one of the two high-molecular-weight (HMW) glutenin genes, comprising the complex Glu-B1 locus. The complete sequence (285 506 bp of DNA) of this chromosomal region was determined. The two...
Context in source publication
Context 1
... 20.4 kb region of the B-genome was previously reported for the Bx7 gene from the bread wheat cultivar Cheyenne (Anderson et al., 2002), including 16 035 bp 5 to the Bx-coding sequence. A pair-wise comparison of two available Bx region sequences is shown in Figure 4. The only major break in the diagonal is a 404 bp region probably caused by a transposon-related insertion into the hexaploid B genome since the region is bordered by an 8 bp duplication signature. ...
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Citations
... For example, a comparison of the Gli-2 loci between T. dicoccoides Korn and T. aestivum cv. Chinese Spring (CS) showed a large sequence difference between the two A subgenomes and a conservative region between the two B subgenomes [20]. To date, a detailed analysis of other genomes (except for the A, B, and D genomes) on the interval of these loci has not been reported. ...
Background
Prolamins, unique to Gramineae (grasses), play a key role in the human diet. Thinopyrum elongatum (syn. Agropyron elongatum or Lophopyrum elongatum ), a grass of the Triticeae family with a diploid E genome (2n = 2x = 14), is genetically well-characterized, but little is known about its prolamin genes and the relationships with homologous loci in the Triticeae species .
Results
In this study, a total of 19 α-gliadin, 9 γ-gliadin, 19 ω-gliadin, 2 high-molecular-weight glutenin subunit (HMW-GS), and 5 low-molecular-weight glutenin subunit (LMW-GS) genes were identified in the Th. elongatum genome. Micro-synteny and phylogenetic analysis revealed dynamic changes of prolamin gene regions and genetic affinities among Th. elongatum , Triticum aestivum , T. urartu and Aegilops tauschii . The Th. elongatum genome, like the B subgenome of T. aestivum , only contained celiac disease epitope DQ8-glia-α1/DQ8.5-glia-α1, which provided a theoretical basis for the low gluten toxicity wheat breeding. The transcriptome data of Th. elongatum exhibited differential expression in quantity and pattern in the same subfamily or different subfamilies. Dough rheological properties of T. aestivum - Th. elongatum disomic substitution (DS) line 1E(1D) showed higher peak height values than that of their parents, and DS6E(6D) exhibited fewer α-gliadins, which indicates the potential usage for wheat quality breeding.
Conclusions
Overall, this study provided a comprehensive overview of the prolamin gene family in Th. elongatum , and suggested a promising use of this species in the generation of improved wheat breeds intended for the human diet.
... Hexaploid wheat, comprised of the A-, B-and D-genomes, thus contains three HMW glutenin loci; Glu-A1, Glu-B1 and Glu-D1, respectively. Each locus harbors two HMW glutenin genes known as the x and y subunit, which are tightly linked but separated by tens to hundreds of kilobase pairs (kb) [9][10][11] . Each subunit consists of short, unique N and C terminal domains which flank a highly repetitive central region that accounts for 74-84% of the total protein length 12 . ...
Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome of Aegilops tauschii to tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity of Ae. tauschii. We discovered 45 haplotypes in Glu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele 2 + 12 was found in Ae. tauschii Lineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele 5 + 10 allele originated in Lineage 3, a recently characterized lineage of Ae. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity in Ae. tauschii at Glu-D1. Ae. tauschii is thus a reservoir for unique Glu-D1 alleles and provides the genomic resource to begin utilizing new alleles for end-use quality improvement in wheat breeding programs. Delorean et al., along with colleagues from the Open Wild Wheat Consortium, present an analysis of Aegilops tauschii genomes to investigate the origins of the Glu-D1 gene in modern wheats. They discover an abundance of novel Glu-D1 gene alleles that could serve as a reservoir for generating higher quality wheat varieties. This is a companion to the Consortium paper which is available in Nature Biotechnology.
... For example, a comparison of the Gli-2 loci between T. dicoccoides Korn and T. aestivum cv. Chinese Spring (CS) showed a large sequence difference between the two A genomes and a conservative region between the two B genomes [20]. To date, a detailed analysis of other genomes (except for the A, B, and D genomes) on the interval of these loci has not been reported. ...
Background: Prolamins, unique to Gramineae (grasses), play a key role in the human diet. Thinopyrum elongatum (also known as tall wheatgrass, rush wheatgrass, or Eurasian quackgrass) of Elytrigia is genetically well-characterized, but little is known about its prolamin genes and the relationships with homologous loci in the Triticum genus.
Results: In this study, a total of 19 α-gliadin, 9 γ-gliadin, 19 ω-gliadin, 2 high-molecular-weight glutenin subunit (HMW-GS), and 5 low-molecular-weight glutenin subunit (LMW-GS) genes in the Th. elongatum genome were annotated. The transcriptome data of Th. elongatum exhibited differential expression in quantity and pattern in the same subfamily or different subfamilies. In addition, microsynteny and phylogenetic analysis revealed dynamic changes of prolamin gene region and genetic affinities among Th. elongatum, T. aestivum, T. urartu, and Aegilops tauschii. The E genome, like the B genome, only contained DQ8-glia-α1/DQ8.5-glia-α1, which provided a theoretical basis for the study of celiac disease (CD). Dough rheological properties of T. aestivum-Th. elongatum disomic substitution (DS) lines 1E(1A), 1E(1D), and 3E(3A) showed much higher peak height values than that of their parent.
Conclusions: Overall, this study provides a comprehensive overview of the prolamin gene superfamily in Th. elongatum, and suggests a promising use of this species in the generation of improved wheat breeds intended for the human diet.
... Shotgun-sequencing libraries were constructed following Kong et al. (2004). Inserts were sequenced from both directions with T7 and T3 primers via BigDye v3.1 terminator chemistry (Applied Biosystems, Foster City, CA, USA) on an ABI3730 xl DNA Analyzer (Applied Biosystems). ...
Centromeres mediate chromosome attachment to microtubules and maintain the integrity of chromosomes for proper segregation of the sister chromatids during cell division. Advances in the assembly of Triticeae genome sequences combined with the capacity to recover hybrid species derived from very distantly related species provides potential experimental systems for linking retrotransposon amplification and repositioning of centromeres via non‐mendelian inheritance in partial amphiploid breeds. The decaploid tall wheatgrass ( Thinopyrum ponticum ) is one of the most successfully used perennial species in wheat breeding for generating translocation lines with valuable agronomic traits. We found that wheat centromere retrotransposons CRW and Quinta widely occur within the tall wheatgrass genome. In addition, one of the genome donors to Th. ponticum , Pseudoroegneria stipifolia (StSt), has been shown to have Abigail and a satellite repeat, CentSt. We also found two other centromeric retrotransposons, Abia and CL135 in Th . ponticum by ChIP‐seq. Examination of partial amphiploid lines that were generated in the 1970s demonstrated extensive modification in centromere sequences using CentSt , Abigail and Abia as probes. We also detected that St‐genome chromosomes were more enriched with Abigail and CentSt , whereas E‐genome chromosomes were enriched with CRW and Quinta in tall wheatgrass and its closer relatives. It can be concluded that bursts of transposition of retrotransposons and repositioning of centromeres via non‐mendelian segregation are common in partial amphiploids derived from interspecific hybrids. Practically speaking, our study reveals that the existence of homologous centromere functional sequences in both a donor and its receptor can substantially contribute to the successful transfer of alien genes into crop species.
Open Research Badges
This article has earned an Open Data Badge for making publicly available the digitally‐shareable data necessary to reproduce the reported results. The data is available at https://www.ncbi.nlm.nih.gov/sra/SRR9089557 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089558 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089559 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089560 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089561 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089562 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089563 ; https://www.ncbi.nlm.nih.gov/sra/SRR9089564 ; https://www.ncbi.nlm.nih.gov/nuccore/MK999394 ; https://www.ncbi.nlm.nih.gov/nuccore/MK999395 ; https://www.ncbi.nlm.nih.gov/nuccore/MK999396
... Transposons are present throughout the genomes of virtually all eukaryotes and are particularly numerous in plants [2], but in the cereals and other plant species including citrus, retrotransposons are localized in domains that are known as "retrotransposon seas" [20][21][22]. Owing to their dynamic nature and the diversity, transposon-based markers have proven to be more informative than other molecular markers such as AFLP [23,24]. These markers are highly polymorphic as a result of the extensive integration events of transposons, and are more useful than other markers such as RAPD and AFLP for genetic diversity studies [1]. ...
Transposable element-based molecular markers can be utilized to investigate genetic diversity and to create genetic linkage maps. In this study, Class I and class II transposons were employed to obtain a comparative account of genetic diversity between wild and cultivated barley genotypes. Three types of PCR-based techniques were used: IMP (Inter MITE Polymorphism), IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism). Specific primer pairs for IMP, IRAP, and REMAP detected a total of 200 bands with an average of 20 bands per marker. The mean polymorphic information content (PIC) and discrimination power (D) values in all 47 genotypes from these three types of transposon-based polymorphisms were 0.910 and 0.935, respectively. Unweighted Pair Group Method with Arithmetic mean (UPGMA)-based cluster analysis classified all 47 genotypes, both wild and cultivated, into separate groups consistent with their geographical origins. Sequencing followed by chromosome location of polymorphic bands enables precise gene introgression from wild gene pool to cultivated barley. The highly polymorphic nature of these marker systems makes them suitable for use in varietal identification and MAS-based breeding programs in barley and other cereals.
... In wheat, HMW-GSs are encoded by the loci Glu-1A, Glu-1B and Glu-1D on chromosomes 1A, 1B and 1D, respectively (Payne 1987;Shewry et al. 1992). Their duplicate origins have led to the presence of two tightly linked paralogous genes at each locus (x-type and y-type) that are separated by the insertion of retrotransposons (Kong et al. 2004). Although the six HMW-GS genes in wheat have similar primary structures, alleles can be differentiated by separation of gene products by sodium dodecyl sulfate polyacrylamide-gel electrophoresis (SDS-PAGE) or DNA sequence comparison. ...
Key message
This study provides a link between a de novo gene and novel phenotype in wheat–rye hybrids that can be used as a model for induced de novo genetic variation.
Abstract
Wide hybridization can produce de novo DNA variation that may cause novel phenotypes. However, there is still a lack of specific links between changed genes and novel phenotypes in wide hybrids. The well-studied high-molecular-weight glutenin subunit (HMW-GS) genes in tribe Triticeae provide a useful model for addressing this issue. In this study, we investigated the feasibility of a wheat–rye hybridization method for inducing de novo phenotypes using the Glu-1Dx2.2 subunit as an example. We developed three hexaploid wheat lines with normal fertility and a Glu-1Dx2.2 variant, named Glu-1Dx2.2
v
, derived from three F1 hybrids. The wild-type Glu-1Dx2.2 has two direct repeats of 295 bp length separated by an intervening 101 bp in its central repetitive region. In the mutant Glu-1Dx2.2
v
, one copy of the repeats and the intervening sequence were deleted, probably through homology-dependent illegitimate recombination (IR). This study provides a direct link between a de novo allele and novel phenotype. Our results indicate that the wheat–rye method may be a useful tool to induce de novo genetic variations that broaden the genetic diversity for wheat improvement.
... Among LMW-GS, LMW-m type genes could be considered to be the most primitive forms than other LMW-GS genes, and LMW-s and LMW-i type genes were variant forms among the LMW-GS gene families (D'Ovidio and Masci, 2004). The second evolutionary line of wheat prolamins contains only the HMW-GS, and likely arose as a tandem duplication of a globulin gene, with one of the resulting genes evolving into an HMW-GS (Kong et al., 2004 ). A subsequent tandem duplication of a chromosome fragment containing an ancestral HMW-glutenin and globulin genes resulted in the x-and y-type HMW-GS. ...
... Glu-1 loci sequences are recognized by Gu et al. [10], Kong et al. [11], Anderson and Greene [12], Halford et al. [4], and Wan et al. [13]. ...
Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker's results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism).
... The paralogous x-and y-type HMW-GS genes are considered to be generated originally from a lineage-specific duplication event of ancestor globulin that occurred only in Triticeae as well as Brachypodium ( Kong et al. 2004; Fig. 5 Phylogenetic tree constructed by the deduced amino acid sequences of seven typical HMW-GS genes from B. distachyon accessions (Bd21, Bd21-3, Bd3, Bd4, Bd10, Bd14 and Bd347) and 23 previously characterised HMW-GS genes from different Triticum and related species. The HMW-GS from B. distachyon are underlined and D-hordein (AAP31051) from barley was used as a reference of outgroup. ...
Brachypodium distachyon, a small wild grass within the Pooideae family, is a new model organism for exploring the functional genomics of cereal crops. It was shown to have close relationships to wheat, barley and rice. Here, we describe the molecular characterisation and evolutionary relationships of high molecular weight glutenin subunits (HMW-GS) genes from B. distachyon. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), high performance capillary electrophoresis (HPCE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses demonstrated that there was no HMW-GS expression in the Brachypodium grains due to the silencing of their encoding genes. Through allele-specific polymerase chain reaction (AS-PCR) amplification and cloning, a total of 13 HMW-GS encoding genes from diploid, tetraploid and hexaploid Brachypodium species were obtained, and all of them had typical structural features of y-type HMW-GS genes from common wheat and related species, particularly more similar to the 1Dy12 gene. However, the presence of an in-frame premature stop codon (TAG) at position 1521 in the coding region resulted in the conversion of all the genes to pseudogenes. Further, quantitative real-time PCR (qRT-PCR) analysis revealed that HMW-GS genes in B. distachyon displayed a similar trend, but with a low transcriptional expression profile during grain development due to the occurrence of the stop codon. Phylogenetic analysis showed that the highly conserved Glu-1-2 loci were presented in B. distachyon, which displayed close phylogenetic evolutionary relationships with Triticum and related species.
... Among LMW-GS, LMW-m type genes could be considered to be the most primitive forms than other LMW-GS genes, and LMW-s and LMW-i type genes were variant forms among the LMW-GS gene families (D'Ovidio and Masci, 2004). The second evolutionary line of wheat prolamins contains only the HMW-GS, and likely arose as a tandem duplication of a globulin gene, with one of the resulting genes evolving into an HMW-GS (Kong et al., 2004 ). A subsequent tandem duplication of a chromosome fragment containing an ancestral HMW-glutenin and globulin genes resulted in the x-and y-type HMW-GS. ...
Meeting demands for increased cereal production in China is a great challenge and this paper provides updated information on cereal production and the potential adaptation of cropping systems to climate change, as well as on progress in improving yield potential and developing molecular markers and GM cereals in China. Maize production and soybean imports are increasing significantly to meet the strong demand for feed by a rapidly growing livestock industry. Extension of the rice and maize growing seasons in northeastern China and improvement of the cropping system through delayed wheat planting have contributed to improving cereal productivity despite changing climatic conditions. Significant improvements in yield potential of rice, maize, and wheat have been achieved. Comparative genomics has been successfully used to develop and validate functional markers for processing quality traits in wheat, and also for developing new varieties. Although transgenic Bt rice and maize, and maize expressing phytase have been developed, their commercialization has not been officially permitted. International collaboration has contributed significantly to cereal production by providing germplasm and improved crop management practices. Full integration of applied molecular technologies into conventional breeding programs and promotion of lower-input technologies, will play a key role in increasing and sustaining future cereal production.
