Variability in wheat based on low-copy DNA sequence comparisons

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 951-957 ◽  
Author(s):  
L. E. Talbert ◽  
N. K. Blake ◽  
E. W. Storlie ◽  
M. Lavin
Keyword(s):  
Dna Sequence ◽  
Diploid Species ◽  
Sequence Variability ◽  
D Genome ◽  
Sequence Comparisons ◽  
Molecular Analyses ◽  
B Genome ◽  
Hybridization Event ◽  
Copy Dna ◽  
Diploid Ancestor

The chromosomes of the B genome of hexaploid wheat (AABBDD) do not pair completely with those of any of the diploid species with genomes similar to B. Various biochemical and molecular analyses have suggested that each of the five diploid species in section Sitopsis of Triticum are ancestral to B. These observations have led to the hypothesis that the B genome may be polyphyletic, descending from more than one diploid ancestor. This hypothesis may account for differences between the wheat B genome and the diploids and also for variability that currently exists among different wheat accessions. In this study, we cloned and compared nucleotide sequences for three low-copy DNA fragments from the B and D genomes of several wheat accessions and from diploid relatives of the B and D genomes. Our results suggested that the amount of DNA sequence variability in wheat is low, although somewhat more variability existed in the B genome than in the D genome. The B genome of wheat was significantly diverged from all the Sitopsis diploid species, and Triticum speltoides was closer to B than to other members of this section. The D genome of wheat was very similar to that of its progenitor, Triticum tauschii. No evidence for a polyphyletic origin of the B genome was found. A more parsimonious hypothesis is that the wheat B genome diverged from its diploid ancestor after the original hybridization event occurred.Key words: wheat, low-copy DNA, phylogenetics.

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.

scholarly journals Pervasive hybridizations in the history of wheat relatives

2019 ◽  
Vol 5 (5) ◽  
pp. eaav9188 ◽  
Author(s):  
Sylvain Glémin ◽  
Celine Scornavacca ◽  
Jacques Dainat ◽  
Concetta Burgarella ◽  
Véronique Viader ◽  
...  
Keyword(s):  
Methodological Approach ◽  
Diploid Species ◽  
Phylogenomic Analysis ◽  
D Genome ◽  
B Genome ◽  
Hybridization Event ◽  
History Of ◽  
Complex Scenario ◽  
Ancient Hybridization

Cultivated wheats are derived from an intricate history of three genomes, A, B, and D, present in both diploid and polyploid species. It was recently proposed that the D genome originated from an ancient hybridization between the A and B lineages. However, this result has been questioned, and a robust phylogeny of wheat relatives is still lacking. Using transcriptome data from all diploid species and a new methodological approach, our comprehensive phylogenomic analysis revealed that more than half of the species descend from an ancient hybridization event but with a more complex scenario involving a different parent than previously thought—Aegilops mutica, an overlooked wild species—instead of the B genome. We also detected other extensive gene flow events that could explain long-standing controversies in the classification of wheat relatives.

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.

Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: The B genome of wheat

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 351-360 ◽  
Author(s):  
Nancy K Blake ◽  
Ben R Lehfeldt ◽  
Matt Lavin ◽  
Luther E Talbert
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Diploid Species ◽  
Single Copy ◽  
Wheat Evolution ◽  
Polyploid Evolution ◽  
B Genome ◽  
Genome Donor ◽  
Copy Dna

Study of bread wheat (Triticum aestivum) may help to resolve several questions related to polyploid evolution. One such question regards the possibility that the component genomes of polyploids may themselves be polyphyletic, resulting from hybridization and introgression among different polyploid species sharing a single genome. We used the B genome of wheat as a model system to test hypotheses that bear on the monophyly or polyphyly of the individual constituent genomes. By using aneuploid wheat stocks, combined with PCR-based cloning strategies, we cloned and sequenced two single-copy-DNA sequences from each of the seven chromosomes of the wheat B genome and the homologous sequences from representatives of the five diploid species in section Sitopsis previously suggested as sister groups to the B genome. Phylogenetic comparisons of sequence data suggested that the B genome of wheat underwent a genetic bottleneck and has diverged from the diploid B genome donor. The extent of genetic diversity among the Sitopsis diploids and the failure of any of the Sitopsis species to group with the wheat B genome indicated that these species have also diverged from the ancestral B genome donor. Our results support monophyly of the wheat B genome.Key words: wheat evolution, phylogenetics, DNA sequencing.

Molecular evidence for the origin and evolution of chromosome 4A in polyploidy wheats

1985 ◽  
Vol 27 (2) ◽  
pp. 246-250 ◽  
Author(s):  
A. Lane Rayburn ◽  
B. S. Gill
Keyword(s):  
In Situ Hybridization ◽  
Chinese Spring ◽  
Diploid Species ◽  
Aegilops Speltoides ◽  
Molecular Evidence ◽  
Wheat Evolution ◽  
D Genome ◽  
Origin And Evolution ◽  
B Genome

The chromosomes of polyploid Triticum species and the putative donor diploid species were analyzed by in situ hybridization with a repeated DNA sequence clone pSc 119 isolated from rye and also found in wheat. In Triticum aestivum cv. Chinese Spring, chromosome 4A showed one terminal site in the short arm and one terminal and two interstitial sites of hybridization in the long arm. Triticum turgidum contained a 4A chromosome identical to 'Chinese Spring' with respect to hybridization sites. Chromosome 4A of the timopheevi wheats differed from 4A of 'Chinese Spring' in that the site of the sequence on the short arm was subterminal rather than terminal. Of the A-, B-, and D-genome progenitor species, only potential B-genome donors Aegilops speltoides and Aegilops sharonensis each showed a chromosome with hybridization sites similar to 4A. This suggested that 4A belongs to the B genome. Moreover, with regard to this sequence, chromosome 4A has undergone only minor changes during the evolution of the polyploid wheats.Key words: wheat evolution, in situ hybridization, biotin labeling.

Organization and evolution of two repetitive sequences, 18-24J and 12-13P, in the genome of Chenopodium (Amaranthaceae)

Genome ◽  
2018 ◽  
Vol 61 (9) ◽  
pp. 643-652 ◽  
Author(s):  
Maja Orzechowska ◽  
Maciej Majka ◽  
Hanna Weiss-Schneeweiss ◽  
Ales Kovařík ◽  
Natalia Borowska-Zuchowska ◽  
...  
Keyword(s):  
Repetitive Sequences ◽  
Diploid Species ◽  
Chromosomal Marker ◽  
Polyploid Species ◽  
Chromosomal Distribution ◽  
Chromosomal Organization ◽  
Molecular Analyses ◽  
B Genome ◽  
A Genome ◽  
Eurasian Species

The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels. The 12-13P repeat contains a tandemly arranged 40 bp minisatellite element forming a large proportion of the genome of Chenopodium (up to 3.5%). FISH revealed its localization to the pericentromeric regions of the chromosomes. The chromosomal distribution of 12-13P delivered additional chromosomal marker for B-genome diploids. The 18-24J repeat showed a dispersed organization in all of the chromosomes of the analyzed diploid species and the Eurasian tetraploids. In the American allotetraploids (C. quinoa, C. berlandieri) and Eurasian allohexaploids (e.g., C. album) very intense hybridization signals of 18-24J were observed only on 18 chromosomes that belong to the B subgenome of these polyploids. Combined cytogenetic and molecular analyses suggests that reorganization of these two repeats accompanied the diversification and speciation of diploid (especially A genome) and polyploid species of Chenopodium s.s.

Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 479-486 ◽  
Author(s):  
Kiyotaka Nagaki ◽  
Hisashi Tsujimoto ◽  
Kazuhiro Isono ◽  
Tetsuo Sasakuma
Keyword(s):  
Dna Sequence ◽  
Repetitive Dna ◽  
Repetitive Sequences ◽  
Diploid Species ◽  
Restriction Enzymes ◽  
D Genome ◽  
Triticeae Species ◽  
Repetitive Dna Sequence ◽  
Aegilops Squarrosa ◽  
Digestion Pattern

We have characterized a so-called D genome specific repetitive DNA sequence (pAs1) of Aegilops squarrosa L. (2n = 14, genome DD) with respect to its DNA sequence and its distribution among Triticeae species. The clone consisted of three units of a repetitive DNA sequence of 336 or 337 base pairs, and was AT rich (65.2%). DNA analyses revealed the presence of the pAs1-like sequences in other genomes of Triticeae species, although the repetition was greatly (as much as 100-fold) variable among the genomes. The repetitive sequences from 10 diploid species were amplified using PCR with specific primers, and the sequential variability was analyzed by the digestion pattern obtained with five restriction enzymes. Since the AfaI site was the most conservatively present in the unit of the repetitive sequences, we named them "Afa family." The analysis clearly displayed the variation of the repetitive sequences regardless of the uniformity of the size of the amplified product. These results indicated that plural amplification events of these repetitive sequences happened independently in the genome evolution of Triticeae.Key words: Triticeae, Aegilops squarrosa, repetitive DNA sequence, CAPS analysis, Afa family.

Chromosomal organization of a sequence related to LTR-like elements of Ty1-copia retrotransposons in Avena species

Genome ◽  
1999 ◽  
Vol 42 (4) ◽  
pp. 706-713 ◽  
Author(s):  
Concha Linares ◽  
Antonio Serna ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Diploid Species ◽  
D Genome ◽  
Specific Sequence ◽  
Chromosomal Organization ◽  
Intergenomic Translocations ◽  
A Genome ◽  
Slot Blot Analysis ◽  
Copia Retrotransposons

A repetitive sequence, pAs17, was isolated from Avena strigosa (As genome) and characterized. The insert was 646 bp in length and showed 54% AT content. Databank searches revealed its high homology to the long terminal repeat (LTR) sequences of the specific family of Ty1-copia retrotransposons represented by WIS2-1A and Bare. It was also found to be 70% identical to the LTR domain of the WIS2-1A retroelement of wheat and 67% identical to the Bare-1 retroelement of barley. Southern hybridizations of pAs17 to diploid (A or C genomes), tetraploid (AC genomes), and hexaploid (ACD genomes) oat species revealed that it was absent in the C diploid species. Slot-blot analysis suggested that both diploid and tetraploid oat species contained 1.3 × 104 copies, indicating that they are a component of the A-genome chromosomes. The hexaploid species contained 2.4 × 104 copies, indicating that they are a component of both A- and D-genome chromosomes. This was confirmed by fluorescent in situ hybridization analyses using pAs17, two ribosomal sequences, and a C-genome specific sequence as probes. Further, the chromosomes involved in three C-A and three C-D intergenomic translocations in Avena murphyi (AC genomes) and Avena sativa cv. Extra Klock (ACD genomes), respectively, were identified. Based on its physical distribution and Southern hybridization patterns, a parental retrotransposon represented by pAs17 appears to have been active at least once during the evolution of the A genome in species of the Avena genus.Key words: chromosomal organization, in situ hybridization, intergenomic translocations, LTR sequence, oats.

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.

The genomic inheritance of aluminum tolerance in 'Atlas 66' wheat

Genome ◽  
1992 ◽  
Vol 35 (4) ◽  
pp. 689-693 ◽  
Author(s):  
William A. Berzonsky
Keyword(s):  
Root Growth ◽  
Aluminum Tolerance ◽  
Triticum Aestivum L ◽  
Nuclear Genes ◽  
D Genome ◽  
Hard Red Spring Wheat ◽  
Al Stress ◽  
Soft Red Winter Wheat ◽  
B Genome ◽  
Segregation Ratios

Toxicity to aluminum (Al) limits wheat (Triticum aestivum L. em. Thell.) yields. 'Atlas 66', a soft red winter wheat classified as tolerant (root growth ≥ 0.5 cm after Al stress) to 0.44 mM Al, was hybridized with tetraploid (4x) and hexaploid (6x) 'Canthatch', a hard red spring wheat classified as sensitive (root growth < 0.5 cm after Al stress) to 0.44 mM Al. Progenies produced from these hybridizations were tested for tolerance to 0.44 mM Al in solution to ascertain the number of genes and the genomes of 'Atlas 66', which determine tolerance to aluminum. Tests of 'Atlas 66', 6x-'Canthatch', and the F1's resulting from hybridizations between the parents indicated that dominant, nuclear genes carried by 'Atlas 66' determine tolerance to 0.44 mM Al. Segregation ratios for the F2 significantly differed from ratios expected for a dominant, duplicate genetic mechanism. F1 backcross segregation ratios did not significantly differ from ratios expected for dominant, duplicate nuclear genes for tolerance to aluminum. The expression of genes for tolerance to 0.44 mM Al for 'Atlas 66' appears to be more complex than is predicted by the existence of two dominant genes. A crossing scheme, which involved hybridizing 4x-'Canthatch' with 'Atlas 66', was executed to produce 42-chromosome plants having recombinant A- and B-genome chromosomes and D-genome chromosomes derived exclusively from 'Atlas 66'. Eleven F6 and F7 lines, developed from these plants, were selfed and plants in the F6 generation were backcrossed to 'Atlas 66' and 6x-'Canthatch'. The F6 and F7 lines were subjected to 0.44 mM Al in solution as were the backcrosses. While none of the lines had more than 50% of their seedlings classified as sensitive to Al in the F6 generation, four lines exhibited such a response in the F7 generation. In general, backcrossing the F6 lines to 6x-'Canthatch' increased sensitivity to Al, while backcrossing to 'Atlas 66' increased tolerance. Results suggest that genes for tolerance to Al in 'Atlas 66' wheat are not all located on D-genome chromosomes.Key words: aluminum tolerance, genomic inheritance, Triticum.

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