Synergy of Two Reference Genomes for the Grass Family

Messing, Joachim

doi:10.1104/pp.108.128520

Cited by 7 publications

(3 citation statements)

References 64 publications

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“…Gene characterization based on cDNA does not give information about regulatory sequences and it is known that major traits are manifested by non-transcribed sequences (Messing 2009). Furthermore, isolated sugarcane promoters have not generally retained the expected patterns of reporter transgene expression, suggesting that the sugarcane gene silencing machinery is highly efficient (Mudge et al 2009).…”

Section: Gene Discovery and Sugarcane Genomicsmentioning

confidence: 99%

The Biotechnology Roadmap for Sugarcane Improvement

Hotta

Lembke

Domingues

et al. 2010

Tropical Plant Biol.

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Due to the strategic importance of sugarcane to Brazil, FAPESP, the main São Paulo state research funding agency, launched in 2008 the FAPESP Bioenergy Research Program (BIOEN, http://bioenfapesp.org). BIOEN aims to generate new knowledge and human resources for the improvement of the sugarcane and ethanol industry. As part of the BIOEN program, a Workshop on Sugarcane Improvement was held on March 18th and 19th 2009 in São Paulo, Brazil. The aim of the workshop was to explore present and future challenges for sugarcane improvement and its use as a sustainable bioenergy and biomaterial feedstock. The workshop was divided in four sections that represent important challenges for sugarcane improvement: a) gene discovery and sugarcane genomics, b) transgenics and controlled transgene expression, c) sugarcane physiology (photosynthesis, sucrose metabolism, and drought) and d) breeding and statistical genetics. This report summarizes the roadmap for the improvement of sugarcane.

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Section: Gene Discovery and Sugarcane Genomicsmentioning

confidence: 99%

The Biotechnology Roadmap for Sugarcane Improvement

Hotta

Lembke

Domingues

et al. 2010

Tropical Plant Biol.

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“…Collinearity between homoeologous regions of the maize genome is interrupted by inversions and translocations (Wei et al, 2007). In contrast with maize, sorghum (Sorghum bicolor) has experienced uniform expansion by retrotransposon insertions (Messing, 2009;Paterson et al, 2009). In wheat, at the grain hardness locus (Ha), deletions account for a majority of genome rearrangements (Chantret et al, 2005), and at the HMM Glutenin locus, indels (insertions and deletions) are the major contributors to structural differences between the A, B, and D homoeologs (Gu et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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“…A second theme in this issue is the power of genomic approaches to provide not only data in the form of genome sequence and transcriptome profiles but also insights into genome biology (Messing 2009;Wicker et al, 2009). An astounding 47 Poaceae species have transcriptome or genome sequence datasets available (Buell, 2009).…”

Section: Grasses Have Powerful Genomic and Genetic Resourcesmentioning

confidence: 99%