A direct repeat sequence associated with the centromeric retrotransposons in wheat

Genome ◽  
2004 ◽  
Vol 47 (4) ◽  
pp. 747-756 ◽  
Author(s):  
Hidetaka Ito ◽  
Shuhei Nasuda ◽  
Takashi R Endo
Keyword(s):  
Genomic Dna ◽  
Direct Repeat ◽  
Repeat Sequence ◽  
Triticum Monococcum ◽  
Fish Analysis ◽  
Long Terminal Repeats ◽  
D Genome ◽  
B Genome ◽  
Cereal Species ◽  
A Genome

A high-density BAC filter of Triticum monococcum was screened for the presence of a centromeric retrotransposon using the integrase region as a probe. Southern hybridization to the BAC digests using total genomic DNA probes of Triticum monococcum, Triticum aestivum, and Hordeum vulgare detected differentially hybridizing restriction fragments between wheat and barley. The fragments that hybridized to genomic DNA of wheat but not to that of barley were subcloned. Fluorescence in situ hybridization (FISH) analysis indicated that the clone pHind258 hybridized strongly to centromeric regions in wheat and rye and weakly to those in barley. The sequence of pHind258 was homologous to integrase and long terminal repeats of centromeric Ty3-gypsy retrotransposons of cereal species. Additionally, pHind258 has a pair of 192-bp direct repeats. FISH analysis indicated that the 192-bp repeat probe hybridized to centromeres of wheat and rye but not to those of barley. We found differential FISH signal intensities among wheat chromosomes using the 192-bp probe. In general, the A-genome chromosomes possess strong FISH signals, the B-genome chromosomes possess moderate signals, and the D-genome chromosomes possess weak signals. This was consistent with the estimated copy numbers of the 192-bp repeats in the ancestral species of hexaploid wheat.Key words: centromere, Ty3-gypsy retrotransposon, FISH, wheat, repetitive element.

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.

Characterization of six wheat × Thinopyrum intermedium derivatives by GISH, RFLP, and multicolor GISH

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 490-495 ◽  
Author(s):  
F P Han ◽  
G Fedak ◽  
A Benabdelmouna ◽  
K Armstrong ◽  
T Ouellet
Keyword(s):  
Genomic Dna ◽  
Aegilops Tauschii ◽  
Rflp Analysis ◽  
Aegilops Speltoides ◽  
Thinopyrum Intermedium ◽  
B Genome ◽  
A Genome ◽  
Genetic Stocks ◽  
Disomic Addition Lines ◽  
Thinopyrum Elongatum

Restriction fragment length polymorphism (RFLP) analysis and multicolor genomic in situ hybridization (GISH) are useful tools to precisely characterize genetic stocks derived from crosses of wheat (Triticum aestivum) with Thinopyrum intermedium and Thinopyrum elongatum. The wheat × Th. intermedium derived stocks designated Z1, Z2, Z3, Z4, Z5, and Z6 were initially screened by multicolor GISH using Aegilops speltoides genomic DNA for blocking and various combinations of genomic DNA from Th. intermedium, Triticum urartu, and Aegilops tauschii for probes. The probing (GISH) results indicated that lines Z1 and Z3 were alien disomic addition lines with chromosome numbers of 2n = 44. Z2 was a substitution line in which chromosome 2D was substituted by a pair of Th. intermedium chromosomes; this was confirmed by RFLP and muticolour GISH. Z4 (2n = 44) contained two pairs of wheat – Th. intermedium translocated chromosomes; one pair involved A-genome chromosomes, the other involved D- and A-genome chromosomes. Z5 (2n = 44) contained one pair of wheat – Th. intermedium translocated chromosomes involving the D- and A-genome chromosomes of wheat. Z6 (2n = 44) contained one pair of chromosomes derived from Th. intermedium plus another pair of translocated chromosomes involving B-genome chromosomes of wheat. Line Z2 was of special interest because it has some resistance to infection by Fusarium graminearum.Key words: wheat, Thinopyrum intermedium, addition, substitution, and translocation lines, GISH, multicolor GISH, RFLP.

scholarly journals Pervasive hybridizations in the history of wheat relatives

2018 ◽  
Author(s):  
Sylvain Glémin ◽  
Celine Scornavacca ◽  
Jacques Dainat ◽  
Concetta Burgarella ◽  
Véronique Viader ◽  
...  
Keyword(s):  
Methodological Approach ◽  
Diploid Species ◽  
Phylogenomic Analysis ◽  
D Genome ◽  
Species Relationship ◽  
B Genome ◽  
Hybridization Event ◽  
A Genome ◽  
History Of ◽  
Complex Scenario

AbstractBread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

Phylogenetic analysis of C, M, N, and U genomes and their relationships with Triticum and other related genomes as revealed by LMW-GS genes at Glu-3 loci

Genome ◽  
2011 ◽  
Vol 54 (4) ◽  
pp. 273-284 ◽  
Author(s):  
Shunli Wang ◽  
Xiaohui Li ◽  
Ke Wang ◽  
Xiaozheng Wang ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Aegilops Tauschii ◽  
Cysteine Residue ◽  
Aegilops Speltoides ◽  
Low Molecular Weight ◽  
D Genome ◽  
B Genome ◽  
A Genome ◽  
Study Support

Phylogenetic relationships between the C, U, N, and M genomes of Aegilops species and the genomes of common wheat and other related species were investigated by using three types of low-molecular-weight glutenin subunit (LMW-GS) genes at Glu-3 loci. A total of 20 LMW-GS genes from Aegilops and Triticum species were isolated, including 11 LMW-m type and 9 LMW-i type genes. Particularly, four LMW-m type and three LMW-i type subunits encoded by the genes on the C, N, and U genomes possessed an extra cysteine residue at conserved positions, which could provide useful information for understanding phylogenetic relationships among Aegilops and Triticum genomes. Phylogenetic trees constructed by using either LMW-i or the combination of LMW-m and LMW-s, as well as analysis of all the three types of LMW-GS genes together, demonstrated that the C and U genomes were closely related to the A genome, whereas the N and M genomes were closely related to the D genome. Our results support previous findings that the A genome was derived from Triticum uratu, the B genome was from Aegilops speltoides, and the D genome was from Aegilops tauschii. In addition, phylogenetic relationships among different genomes analysed in this study support the concept that Aegilops is not monophyletic.

Tracing B-genome chromatin in Brassica napus × B. juncea interspecific progeny

Genome ◽  
2006 ◽  
Vol 49 (11) ◽  
pp. 1490-1497 ◽  
Author(s):  
C.J. Schelfhout ◽  
R. Snowdon ◽  
W.A. Cowling ◽  
J.M. Wroth
Keyword(s):  
Chromosome Count ◽  
Repeat Sequence ◽  
Chain Reaction ◽  
B Genome ◽  
A Genome ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Pcr Assays ◽  
Selection Of

We used polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) techniques to demonstrate the presence of Brassica B-genome chromosomes and putative B-genome introgressions in B. napus × B. juncea interspecific progeny. The B-genome - specific repeat sequence pBNBH35 was used to generate PCR products and FISH probes. The highest frequencies of viable progeny were obtained when B. napus was the maternal parent of the interspecific hybrid and the first backcross. B-genome - positive PCR assays were found in 34/51 fertile F2 progeny (67%), which was more than double the proportion found in fertile BC1 progeny. Four B-genome - positive F2-derived families and 1 BC1-derived family were fixed or segregating for B. juncea morphology in the F4 and BC1S2, respectively, but in only 2 of these families did B. juncea-type plants exhibit B. juncea chromosome count (2n = 36) and typical B-genome FISH signals on 16 chromosomes. The remaining B. juncea-type plants had B. napus chromosome count (2n = 38) and no B-genome FISH signals, except for 1 exceptional F4-derived line that exhibited isolated and weak B-genome FISH signals on 11 chromosomes and typical A-genome FISH signals. B. juncea morphology was associated with B-genome - positive PCR signals but not necessarily with 16 intact B-genome chromosomes as detected by FISH. B-genome chromosomes tend to be eliminated during selfing or backcrossing after crossing B. juncea with B. napus, and selection of lines containing B-genome chromatin during early generations would be promoted by use of this B-genome repetitive marker.

scholarly journals Novel fluorescent sequence-related amplified polymorphism(FSRAP) markers for the construction of a genetic linkage map of wheat(Triticum aestivum L.)

Genetika ◽  
2017 ◽  
Vol 49 (3) ◽  
pp. 1081-1093 ◽  
Author(s):  
Lingbo Zhao ◽  
Zhang Li ◽  
Jipeng Qu ◽  
Yan Yu ◽  
Lu Lu ◽  
...  
Keyword(s):  
Genetic Linkage Map ◽  
Average Distance ◽  
Triticum Aestivum L ◽  
Genetic Maps ◽  
The Novel ◽  
Linkage Groups ◽  
D Genome ◽  
Wheat Varieties ◽  
B Genome ◽  
A Genome

Novel fluorescent sequence-related amplified polymorphism (FSRAP) markers were developed based on the SRAP molecular marker. Then, the FSRAP markers were used to construct the genetic map of a wheat (Triticum aestivumL.) recombinant inbred line population derived from a Chuanmai 42?Chuannong 16 cross. Reproducibility and polymorphism tests indicated that the FSRAP markers have repeatability and better reflect the polymorphism of wheat varieties compared with SRAP markers. A total of 430 polymorphic loci between Chuanmai 42 and Chuannong 16 were detected with 189 FSRAP primer combinations. A total of 281 FSARP markers and 39 SSR markers re classified into 20 linkage groups. The maps spanned a total length of 2499.3cM with an average distance of 7.81cM between markers. A total of 201 markers were mapped on the B genome and covered a distance of 1013cM. On the A genome, 84 markers were mapped and covered a distance of 849.6cM. On the D genome, however, only 35 markers were mapped and covered a distance of 636.7cM. No FSRAP markers were distributed on the 7D chromosome. The results of the present study revealed that the novel FSRAP markers can be used to generate dense, uniform genetic maps of wheat.

Biochemical data bearing on the relationship between the genome of Triticum urartu and the A and B genomes of the polyploid wheats

Genome ◽  
1988 ◽  
Vol 30 (4) ◽  
pp. 576-581 ◽  
Author(s):  
K. Kerby ◽  
J. Kuspira ◽  
B. L. Jones
Keyword(s):  
Amino Acid ◽  
Triticum Turgidum ◽  
Amino Acid Sequences ◽  
Triticum Monococcum ◽  
Triticum Urartu ◽  
B Genome ◽  
Genome Donor ◽  
A Genome ◽  
The Relationship ◽  
Donor Species

To determine whether the Triticum urartu genome is more closely related to the A or B genome of the polyploid wheats, the amino acid sequence of its purothionin was compared to the amino acid sequences of the purothionins in Triticum monococcum, Triticum turgidum, and Triticum aestivum. The residue sequence of the purothionin from T. urartu differs by five and six amino acid substitutions respectively from the α1 and α2 forms coded for by genes in the B and D genomes, and is identical to the β form specified by a gene in the A genome. Therefore, the T. urartu purothionin is either coded by a gene in the A genome or a chromosome set highly homologous to it. The results demonstrate that at least a portion of the T. urartu and T. monococcum genomes is homologous and probably identical. A variety of other studies have also shown that T. urartu is very closely related to T. monococcum and, in all likelihood, also possesses the A genome. Therefore, it could be argued that either T. urartu and T. monococcum are the same species or that T. urartu rather than T. monococcum is the source of the A genome in T. turgidum and T. aestivum. Except for Johnson's results, our data and that of others suggest a revised origin of polyploid wheats. Specifically, the list of six putative B genome donor species is reduced to five, all members of the Sitopsis section of the genus Aegilops.Key words: Triticum monococcum, Triticum urartu, polyploid wheats, genomes A and B, purothionins.

Hypervariation associated with a 12-nucleotide direct repeat and inferences on intergenomic homogenization of ribosomal RNA gene spacers based on the DNA sequence of a clone from the wheat Nor-D3 locus

Genome ◽  
1987 ◽  
Vol 29 (5) ◽  
pp. 770-781 ◽  
Author(s):  
Michael Lassner ◽  
Olin Anderson ◽  
Jan Dvořák
Keyword(s):  
Dna Sequence ◽  
Ribosomal Rna ◽  
Consensus Sequence ◽  
Direct Repeat ◽  
Triticum Aestivum L ◽  
Sequence Information ◽  
D Genome ◽  
Ribosomal Rna Gene ◽  
Nontranscribed Spacer ◽  
B Genome

A ribosomal RNA gene (rDNA) unit from the Nor-D3 locus (D genome) of Triticum aestivum L. was cloned and the "nontranscribed spacer" (NTS) was sequenced. The DNA sequence was compared with previously reported Nor-B2 locus (B genome) NTS sequences to study the molecular basis of evolution of these repeated genes and to look for evidence of homogenization between B- and D-genome rDNA. The NTS has seven subrepeats with a modal repeat length of 120 nucleotides; the subrepeats are shorter than Nor-B2 subrepeats owing to loss of one element of a 12-bp duplication present in Nor-B2 subrepeats. This 12 nucleotide sequence or its permutation, whose consensus sequence is CACGTACACGGA, is found at all sites where the B- and D-genome rDNA spacers differ by insertions or deletions longer than two nucleotides. The DNA sequence information was used to identify restriction sites unique to each locus that could be used in search of conversions between the B- and D-genome rDNA loci. Despite the coexistence of rDNA of the B- and D-genomes in the same nucleus for a minimum of 8000 years, no evidence for frequent interchromosomal conversion events between chromosomes 1B or 6B and 5D was found. Key words: Triticum, rDNA, concerted evolution, spacer.

SOME CHARACTERISTICS OF HEXAPLOID TRITICALE SUBSTITUTION LINES INVOLVING THE A-, B-, AND D-GENOME CHROMOSOMES OF WHEAT

1981 ◽  
Vol 23 (4) ◽  
pp. 679-689 ◽  
Author(s):  
E. N. Larter ◽  
K. Noda
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Triticum Aestivum L ◽  
Low Fertility ◽  
Specific Chromosome ◽  
Substitution Lines ◽  
D Genome ◽  
Seed Supply ◽  
B Genome ◽  
A Genome ◽  
Definitive Method

Three hexaploid (2n = 6x = 42) triticale lines (× Triticosecale Wittmack) were synthesized in which a specific chromosome of either the A or B genomes was replaced by a homoelogous chromosome of the D genome of wheat (Triticum aestivum L. em Thell.). Two of the substitutions involved the B genome [substitution lines 1D(1B)R-4 and 6D (6B)R-5] and the third involved the A genome [4D(4A)R-1]. Polyacrylamide gel electrophoresis of gliadin proteins produced distinct differences in banding patterns between the three substitutions and provided a definitive method for the identification of specific chromosome substitutions in triticale. Plant and spike characteristics of the substitution triticales were similar to those of the control (unsubstituted) triticale. Substitution 6D(6B)R-5 exhibited extremely low fertility and was difficult to maintain. The substitution 4D(4A), on the other hand, appeared to have no effect on fertility, while substitution 1D(1B) reduced fertility by almost one-half of that of the control triticale. Chromosome pairing in substitution 4D(4A)R-1 was regular whereas 1D(1B)R-4 exhibited an average of five univalents/cell at MI. Limited seed supply prevented a meiotic study of 6D(6B)R-5. Flour proteins of the three substitution triticales ranged from 15.8% for 4D(4A)R-1 to 18.0% for 6D(6B)R-5. A comparison of the three substitutions for amino acid composition indicated that line 6D(6B)R-5 was 25% higher in methionine than the control, while in substitution 4D(4A)R-1 methionine content was reduced by 53%.

Genomic Instability in Wheat Induced by Chromosome 6b(s) of Triticum Speltoides.

Genetics ◽  
1988 ◽  
Vol 120 (4) ◽  
pp. 1085-1094
Author(s):  
R S Kota ◽  
J Dvorak
Keyword(s):  
Chinese Spring ◽  
Wheat Chromosome ◽  
Triticum Aestivum L ◽  
Chromosome Rearrangements ◽  
D Genome ◽  
Dicentric Chromosomes ◽  
B Genome ◽  
Ring Chromosomes ◽  
Chinese Spring Wheat ◽  
A Genome

Abstract A massive restructuring of chromosomes was observed during the production of a substitution of chromosome 6B(s) from Triticum speltoides (Tausch) Gren. ex Richter for chromosome 6B of Chinese Spring wheat (Triticum aestivum L.). Deletions, translocations, ring chromosomes, dicentric chromosomes and a paracentric inversion were observed. Chromosome rearrangements occurred in both euchromatic and heterochromatic regions. Chromosome rearrangements were not observed either in the amphiploid between Chinese Spring and T. speltoides or in Chinese Spring. No chromosome rearrangements were observed in the backcross derivatives; however, after self-pollination of a monosomic substitution (2n = 41) of chromosome 6B(s) for wheat chromosome 6B, 49 of the 138 plants carried chromosome aberrations. Chromosome rearrangements were observed in both wheat and T. speltoides chromosomes. The frequency of chromosome rearrangements was high among the B-genome chromosomes, moderate among the A-genome chromosomes, and low among the D-genome chromosomes. In the B genome, the rearrangements were nonrandom, occurring most frequently in chromosomes 1B and 5B. Chromosome rearrangements were also frequent for the 6B(s) chromosome of T. speltoides. An intriguing aspect of these observations is that they indicate that wheat genomes can be subject to uneven rates of structural chromosome differentiation in spite of being in the same nucleus.

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