Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes

Yan, Liuling; Echenique, Viviana; Busso, Carlos S.; SanMiguel, Phillip; Ramakrishna, Wusirika; Bennetzen, Jeffrey L.; Harrington, Sandra E.; Dubcovsky, Jorge

doi:10.1007/s00438-002-0765-3

Cited by 18 publications

(16 citation statements)

References 32 publications

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“…Ten of these were comparatively sequenced for five orthologous regions of the wheat A genome at the diploid, tetraploid, and/ or hexaploid levels and were partially overlapping (Wicker et al 2003b;Chantret et al 2005;Isidore et al 2005;Dvorak et al 2006;Gu et al 2006), while others were determined at only one ploidy level (mostly diploid) Yan et al 2002Yan et al , 2003Miller et al 2006). Comparisons show that no shared TE insertions were observed between orthologous regions (from two ploidy levels), except in the region of the high-molecular-weight (HMW) glutenin gene, the sequences of which were nearly identical at the tetraploid and hexaploid levels (Gu et al 2006).…”

Section: Resultsmentioning

confidence: 99%

“…Publicly available genomic sequences from the wheat A genome: The retained publicly available A-genome sequences consist of 19 sequenced and well annotated BAC clones or contigs Yan et al 2002Yan et al , 2003Wicker et al 2003b;Chantret et al 2005;Isidore et al 2005;Dvorak et al 2006;Gu et al 2006;Miller et al 2006), representing .3.5 Mb. Accession numbers for the analyzed BAC sequences are the following: diploid A genome-AF326781, AF488415, AY146588, AY188331, AY188332, AY188333, AY491681, AY951944, AY951945, DQ267106, AF459639; tetraploid A genome-AY146587, AY485644, AY663391, CT009587, DQ267105; hexaploid A genome-AY663392, CT009586, DQ537335.…”

Section: Methodsmentioning

confidence: 99%

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Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

Charles¹,

Belcram²,

Just³

et al. 2008

Genetics

122

128

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Transposable elements (TEs) constitute .80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, ,0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

Charles¹,

Belcram²,

Just³

et al. 2008

Genetics

122

128

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“…RNA from leaves, undifferentiated apices, and young spikes was extracted by using the Trizol method (Invitrogen). RT-PCR procedures were performed as described (22). Quantitative PCR experiments were performed in an Applied Biosystems ABI 7700 by using three TaqMan systems for T. monococcum AP1 and for actin and ubiquitin as endogenous controls (Appendix 3, which is published as supporting information on the PNAS web site).…”

Section: Methodsmentioning

confidence: 99%

Positional cloning of the wheat vernalization gene VRN1

Yan

Loukoianov

Tranquilli

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

1,234

1,181

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Winter wheats require several weeks at low temperature to flower. This process, vernalization, is controlled mainly by the VRN1 gene. Using 6,190 gametes, we found VRN1 to be completely linked to MADS-box genes AP1 and AGLG1 in a 0.03-centimorgan interval flanked by genes Cysteine and Cytochrome B5. No additional genes were found between the last two genes in the 324-kb Triticum monococcum sequence or in the colinear regions in rice and sorghum. Wheat AP1 and AGLG1 genes were similar to Arabidopsis meristem identity genes AP1 and AGL2, respectively. AP1 transcription was regulated by vernalization in both apices and leaves, and the progressive increase of AP1 transcription was consistent with the progressive effect of vernalization on flowering time. Vernalization was required for AP1 transcription in apices and leaves in winter wheat but not in spring wheat. AGLG1 transcripts were detected during spike differentiation but not in vernalized apices or leaves, suggesting that AP1 acts upstream of AGLG1. No differences were detected between genotypes with different VRN1 alleles in the AP1 and AGLG1 coding regions, but three independent deletions were found in the promoter region of AP1. These results suggest that AP1 is a better candidate for VRN1 than AGLG1. The epistatic interactions between vernalization genes VRN1 and VRN2 suggested a model in which VRN2 would repress directly or indirectly the expression of AP1. A mutation in the promoter region of AP1 would result in the lack of recognition of the repressor and in a dominant spring growth habit.

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“…2). 13 Environmental conditions of the trials carried out in this study were very diverse 14 (supplementary Table 1). Lack of enough CDD quite possibly led to insufficient 15 vernalization (trials SPVA01 and SPVA99).…”

Section: Heading Time 10mentioning

confidence: 99%

Heading date QTL in a spring × winter barley cross evaluated in Mediterranean environments

et al. 2007

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Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes

Cited by 18 publications

References 32 publications

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

Positional cloning of the wheat vernalization gene VRN1

Heading date QTL in a spring × winter barley cross evaluated in Mediterranean environments

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