Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

Genome ◽  
2009 ◽  
Vol 52 (6) ◽  
pp. 576-587 ◽  
Author(s):  
Humphrey Wanjugi ◽  
Devin Coleman-Derr ◽  
Naxin Huo ◽  
Shahryar F. Kianian ◽  
Ming-Cheng Luo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Transposable Elements ◽  
Repetitive Dna ◽  
Hexaploid Wheat ◽  
Rapid Development ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
Dynamic Evolution ◽  
D Genome ◽  
Repeat Dna

In hexaploid wheat ( Triticum aestivum L.) (AABBDD, C = 17 000 Mb), repeat DNA accounts for ∼90% of the genome, of which transposable elements (TEs) constitute 60%–80%. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs are conserved and collinear between the homologous wheat genomes, based on identical insertion patterns. In this study, we exploited the unique and abundant TE insertion junction regions identified from diploid Aegilops tauschii to develop genome-specific repeat DNA junction markers (RJM) for use in hexaploid wheat. In this study, both BAC end and random shotgun sequences were used to search for RJM. Of the 300 RJM primer pairs tested, 269 (90%) amplified single bands from diploid Ae. tauschii. Of these 269 primer pairs, 260 (97%) amplified hexaploid wheat and 9 (3%) amplified Ae. tauschii only. Among the RJM primers that amplified hexaploid wheat, 88% were successfully assigned to individual chromosomes of the hexaploid D genome. Among the 38 RJM primers mapped on chromosome 6D, 31 (82%) were unambiguously mapped to delineated bins of the chromosome using various wheat deletion lines. Our results suggest that the unique RJM derived from the diploid D genome could facilitate genetic, physical, and radiation mapping of the hexaploid wheat D genome.

The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.)

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1120-1126 ◽  
Author(s):  
Didier Lamoureux ◽  
Daniel G Peterson ◽  
Wanlong Li ◽  
John P Fellers ◽  
Bikram S Gill
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
D Genome ◽  
Genomic Libraries ◽  
Gene Space ◽  
Fold Enrichment ◽  
Gene Enrichment ◽  
Fold Reduction

We report the results of a study on the effectiveness of Cot filtration (CF) in the characterization of the gene space of bread wheat (Triticum aestivum L.), a large genome species (1C = 16 700 Mb) of tremendous agronomic importance. Using published Cot data as a guide, 2 genomic libraries for hexaploid wheat were constructed from the single-stranded DNA collected at Cot values > 1188 and 1639 M·s. Compared with sequences from a whole genome shotgun library from Aegilops tauschii (the D genome donor of bread wheat), the CF libraries exhibited 13.7-fold enrichment in genes, 5.8-fold enrichment in unknown low-copy sequences, and a 3-fold reduction in repetitive DNA. CF is twice as efficient as methylation filtration at enriching wheat genes. This research suggests that, with improvements, CF will be a highly useful tool in sequencing the gene space of wheat.Key words: gene enrichment, renaturation kinetics, gene-rich regions, bread wheat.

scholarly journals Association analysis of grain traits with SSR markers between Aegilops tauschii and hexaploid wheat (Triticum aestivum L.)

2015 ◽  
Vol 14 (10) ◽  
pp. 1936-1948 ◽  
Author(s):  
Jing-lan ZHAO ◽  
Hong-wei WANG ◽  
Xiao-cun ZHANG ◽  
Xu-ye DU ◽  
An-fei LI ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Ssr Markers ◽  
Association Analysis ◽  
Hexaploid Wheat ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L

scholarly journals Genotype-dependent Burst of Transposable Element Expression in Crowns of Hexaploid Wheat (Triticum aestivum L.) during Cold Acclimation

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Debbie Laudencia-Chingcuanco ◽  
D. Brian Fowler
Keyword(s):  
Triticum Aestivum ◽  
Transposable Elements ◽  
Transposable Element ◽  
Hexaploid Wheat ◽  
Expression Profiles ◽  
Cold Treatment ◽  
Triticum Aestivum L ◽  
Dna Transposons ◽  
Specific Induction ◽  
Cold Hardy

The expression of 1,613 transposable elements (TEs) represented in the Affymetrix Wheat Genome Chip was examined during cold treatment in crowns of four hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throughout the experiment in three of the genotypes. In winter Norstar, the most cold-hardy of the four genotypes, a subset of the TEs showed a burst of expression after vernalization saturation was achieved. About 47% of the TEs were expressed, and both Class I (retrotransposons) and Class II (DNA transposons) types were well represented.GypsyandCopiawere the most represented among the retrotransposons whileCACTAandMarinerwere the most represented DNA transposons. The data suggests that theVrn-A1region plays a role in the stage-specific induction of TE expression in this genotype.

Analysis of relationships between Aegilops tauschii and the D genome of wheat utilizing microsatellites

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 661-668 ◽  
Author(s):  
Tamás Lelley ◽  
Maria Stachel ◽  
Heinrich Grausgruber ◽  
Johann Vollmann
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Hexaploid Wheat ◽  
Aegilops Tauschii ◽  
Null Alleles ◽  
The Caspian Sea ◽  
D Genome ◽  
Wheat Varieties ◽  
Center Of Origin ◽  
Primer Sets

Sixty Aegilops tauschii accessions and 60 European hexaploid wheat varieties were analyzed with 14 wheat microsatellite (WMS) primer sets to (i) study the phylogeny of Ae. tauschii, (ii) search for a specific genotype of Ae. tauschii most closely related to the D genome of hexaploid wheat, and (iii) narrow down the presumed birthplace of the latter. An average of 6.5 and 4.0 alleles per locus was detected in Ae. tauschii and in wheat, respectively. The highest genetic diversity of Ae. tauschii was found in Transcaucasia and southeast of the Caspian Sea. Distribution of the 87 alleles (without null alleles) found in Aegilops did not allow differentiation of the species into the two subspecies strangulata and tauschii. Excluding null alleles, 41 alleles occurred parallel in wheat and in Aegilops. Data obtained in this study supports the view of the D genome of hexaploid wheat being a composite of several sources but does not support subsp. strangulata as the possible major source of the D genome. The highest number of region-specific alleles (three) in Ae. tauschii occurring also in the D genome of wheat, and therefore most indicative for its evolution was found in present-day Georgia, where subsp. strangulata is not endemic.Key words: Triticum aestivum, Aegilops tauschii, genetic distance, center of origin, evolution.

Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 979-987 ◽  
Author(s):  
Peng Zhang ◽  
Wanlong Li ◽  
Bernd Friebe ◽  
Bikram S Gill
Keyword(s):  
Triticum Aestivum ◽  
In Situ Hybridization ◽  
Transposable Elements ◽  
Fluorescence In Situ Hybridization ◽  
Hexaploid Wheat ◽  
D Genome ◽  
Bac Clones ◽  
Dispersed Repeat ◽  
Bac Fish

Fluorescence in situ hybridization (FISH) is widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts, making them amenable for FISH mapping. In our BAC-FISH experiments, we selected 56 restriction fragment length polymorphism (RFLP)-locus-specific BAC clones from the libraries of Triticum monococcum and Aegilops tauschii, which are the A- and D-genome donors of wheat (Triticum aestivum, 2n = 6x = 42), respectively. The BAC clone 676D4 from the T. monococcum library contains a dispersed repeat that preferentially hybridizes to A-genome chromosomes, and two BAC clones, 9I10 and 9M13, from the Ae. tauschii library contain a dispersed repeat that preferentially hybridizes to the D-genome chromosomes. These repeats are useful in simultaneously discriminating the three different genomes in hexaploid wheat, and in identifying intergenomic translocations in wheat or between wheat and alien chromosomes. Sequencing results show that both of these repeats are transposable elements, indicating the importance of transposable elements, especially retrotransposons, in the genome evolution of wheat.Key words: bacterial artificial chromosome (BAC), fluorescence in situ hybridization (FISH), transposable elements (TEs), wheat, Triticum aestivum.

The biology and ecology of hexaploid wheat (Triticum aestivum L.) and its implications for trait confinement

2008 ◽  
Vol 88 (5) ◽  
pp. 997-1013 ◽  
Author(s):  
C. J. Willenborg ◽  
R. C. Van Acker
Keyword(s):  
Triticum Aestivum ◽  
Gene Flow ◽  
Hexaploid Wheat ◽  
Triticum Turgidum ◽  
Cropping Systems ◽  
Pollen Viability ◽  
Triticum Aestivum L ◽  
Genetically Engineered ◽  
Wide Range ◽  
Trait Confinement

This review summarizes the biological and ecological factors of hexaploid wheat (Triticum aestivum L.) that contribute to trait movement including the ability to volunteer, germination and establishment characteristics, breeding system, pollen movement, and hybridization potential. Although wheat has a short-lived seedbank with a wide range of temperature and moisture requirements for germination and no evidence of secondary dormancy, volunteer wheat populations are increasing in relative abundance and some level of seed persistence in the soil has been observed. Hexaploid wheat is predominantly self-pollinating with cleistogamous flowers and pollen viability under optimal conditions of only 0.5 h, yet observations indicate that pollen-mediated gene flow can and will occur at distances up to 3 km and is highly dependent on prevailing wind patterns. Hybridization with wild relatives such as A. cylindrica Host., Secale cereale L., and Triticum turgidum L. is a serious concern in regions where these species grow in field margins and unmanaged lands, regardless of which genome the transgene is located on. More research is needed to determine the long-term population dynamics of volunteer wheat populations before conclusions can be drawn with regard to their role in trait movement. Seed movement has the potential to create adventitious presence (AP) on a larger scale than pollen, and studies tracing the movement of wheat seed in the grain handling system are needed. Finally, the development of mechanistic models that predict landscape-level trait movement are required to identify transgene escape routes and critical points for gene containment in various cropping systems. Key words: Triticum, coexistence, gene flow, genetically-engineered, herbicide-resistant, trait confinement

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