Comparative Genomics of Grasses Promises a Bountiful Harvest

Paterson, Andrew H.; Bowers, John E.; Feltus, F. Alex; Tang, Haibao; Lin, Lifeng; Wang, Xiyin

doi:10.1104/pp.108.129262

Cited by 43 publications

(25 citation statements)

References 80 publications

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“…), and sugarcane (Saccharum officinarum), which are globally some of the most agriculturally and economically important crops (FAOSTAT, 2007). Understanding complex interactions underlying agronomic traits within these species, therefore, is of great significance, in particular to help with crop improvements to meet the challenges of plant and human health but also for basic understanding of complex biological systems.In addition to their pivotal role in agriculture, grasses offer a powerful model system in that their genomes are closely conserved and functional genomic knowledge gained in one species can be hypothesized to occur in another syntenic region (translational functional genomics; Paterson et al, 2009). In cases of grass species with poorly resolved, polyploid genomes such as sugarcane, where genomic resources are not as far progressed as in other grasses (e.g.…”

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confidence: 99%

“…In addition to their pivotal role in agriculture, grasses offer a powerful model system in that their genomes are closely conserved and functional genomic knowledge gained in one species can be hypothesized to occur in another syntenic region (translational functional genomics; Paterson et al, 2009). In cases of grass species with poorly resolved, polyploid genomes such as sugarcane, where genomic resources are not as far progressed as in other grasses (e.g.…”

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confidence: 99%

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Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

2011

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One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.The combination of genomics, genetics, and systemslevel computational methods provides a powerful approach toward insight into complex biological systems. Of particular significance is the discovery of genetic interactions that lead to desirable agricultural and economic traits in the Poaceae family (grasses). The Poaceae includes valuable crops such as rice (Oryza sativa), maize (Zea mays), wheat (Triticum spp.), and sugarcane (Saccharum officinarum), which are globally some of the most agriculturally and economically important crops (FAOSTAT, 2007). Understanding complex interactions underlying agronomic traits within these species, therefore, is of great significance, in particular to help with crop improvements to meet the challenges of plant and human health but also for basic understanding of complex biological systems.In addition to their pivotal role in agriculture, grasses offer a powerful model system in that their genomes are closely conserved and functional genomic knowledge gained in one species can be hypothesized to occur in another syntenic region (translational functional genomics; Paterson et al., 2009). In cases of grass species with poorly resolved, polyploid genomes such as sugarcane, where genomic resources are not as far progressed as in other grasses (e.g. rice, sorghum [Sorghum bicolor], maize, etc.), translational functional genomics methods may be the most cost-effective strategy for crop improvement as well as for unraveling the functional consequences of polyploidy. Additionally, crops rich in genetically mapped loci deposited in sites like Gramene (Jaiswal, 2011) provide a rich source of systems genetic hypotheses that could in principle accelerate the translation of interacting gene sets ass...

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Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

2011

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“…Comparative mapping studies conducted in several plant families have consistently shown that closely related species exhibit high synteny and colinearity (Paterson et al 2000;Paterson et al 2009;Tang et al 2008). However, chromosome segment duplications, mobility of DNA sequences, gene deletion and localised chromosomal rearrangements may create deviations from colinearity (Paterson et al 2000).…”

Section: Introductionmentioning

confidence: 99%

High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping

Hudson

Kullan

Freeman

et al. 2011

Tree Genetics & Genomes

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Understanding genome differentiation is important to compare and transfer genomic information between taxa, such as from model to non-model organisms. Comparative genetic mapping can be used to assess genome differentiation by identifying similarities and differences in chromosome organisation. Following release of the assembled Eucalyptus grandis genome sequence (January 2011; http://www.phytozome.net/), a better understanding of genome differentiation between E. grandis and other commercially important species belonging to the subgenus Symphyomyrtus is required. In this study, comparative genetic mapping analyses were conducted between E. grandis, E. urophylla and E. globulus using high density linkage maps constructed from Diversity Array Technology and microsatellite molecular markers. There were 236 -393 common markers between maps, providing the highest resolution yet achieved for comparative mapping in Eucalyptus. In two intra-section comparisons (section Maidenaria -E. globulus and sectionLatoangulatae -E. grandis vs. E. urophylla), ~1% of common markers were non-syntenic and within chromosomes 4.7-6.8% of markers were non-colinear. Consistent with increasing taxonomic distance, lower synteny (6.6% non-syntenic markers) was observed in an inter-section comparison between E. globulus and E. grandis x E. urophylla consensus linkage maps. Two small chromosomal translocations, or duplications, were identified in this comparison representing possible genomic differences between E. globulus and section Latoangulatae species. Despite these differences, the overall high level of synteny and colinearity observed between section Maidenaria -Latoangulatae suggests that the genomes of these species are highly conserved indicating that sequence information from the E. grandis genome will be highly transferable to related Symphyomyrtus species.

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“…The sorghum genome is approximately 740 Mb. The sequence of the grain sorghum BTx623 has been released (Paterson et al 2009a). The sorghum genome is appreciably smaller and less complex than the maize genome, and as a member of the Saccharinae subtribe, it is the ideal model for its fellow members sugarcane and Miscanthus , both of which are polyploids that do not succumb easily to genetic studies due to sterility issues.…”

Section: Three Bioenergy Grasses: All For One One For Allmentioning

confidence: 99%

Survey of Genomics Approaches to Improve Bioenergy Traits in Maize, Sorghum and SugarcaneFree Access

Vermerris

2011

Journal of Integrative Plant Biology

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Bioenergy crops currently provide the only source of alternative energy with the potential to reduce the use of fossil transportation fuels in a way that is compatible with existing engine technology, including in developing countries. Even though bioenergy research is currently receiving considerable attention, many of the concepts are not new, but rather build on intense research efforts from 30 years ago. A major difference with that era is the availability of genomics tools that have the potential to accelerate crop improvement significantly. This review is focused on maize, sorghum and sugarcane as representatives of bioenergy grasses that produce sugar and/or lignocellulosic biomass. Examples of how genetic mapping, forward and reverse genetics, highthroughput expression profiling and comparative genomics can be used to unravel and improve bioenergy traits will be presented.Vermerris W (2011) Survey of genomics approaches to improve bioenergy traits in maize, sorghum and sugarcane. J. Integr. Plant Biol. 53(2), 105-119. Back to the Future: Energy from Plant BiomassDuring most of the history of modern humans, plant biomass was the primary source of energy for heating and cooking. This changed with the discovery of large reserves of coal, natural gas and oil, which have rapidly transformed societies and global exchange of people, goods and ideas, at the cost of pollution and emissions of vast amounts of greenhouse gases. The desire to curb the net release of greenhouse gases associated with the combustion of these fossil fuels, the fact that many countries desire to become less dependent on imported fuels, and the prospect of improving rural economies by producing bioenergy crops appear to have resulted in the pendulum swinging back towards the use of biomass. This is evidenced by the development of three Bioenergy Centers funded by the U.S. (Davison et al. 2009;Scheller et al. 2010;Slater et al. 2010), the call for large-scale, multi-institutional regional bioenergy projects funded through the U.S. Department of Agriculture's National Institute of Food and Agriculture, and similar initiatives in the European Union, India and many other countries across the globe. Even though bio-based fuels are currently the only alternative source of liquid transportation fuels compatible with the existing fleet of automobiles, there is an emerging sense that bioenergy production is only feasible if it can be produced in a sustainable manner, whereby soil quality (Wilhelm et al. 2004(Wilhelm et al. , 2007, invasiveness and landscape diversity (Firbank 2008), displacement of carbon-sequestering native vegetation (Fargione et al. 2008), and water use are given ample consideration. Bioenergy can be generated in a variety of ways. The oldest form, referenced above, is to simply burn biomass for heat. Open fires are notoriously inefficient, but newly developed boilers that burn wood pellets provide efficient means to heat residential homes (Fiedler 2004; Johansson et al. 2004). Alternatively, the biomass can be burned ...

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Comparative Genomics of Grasses Promises a Bountiful Harvest

Cited by 43 publications

References 80 publications

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice

High synteny and colinearity among Eucalyptus genomes revealed by high-density comparative genetic mapping

Survey of Genomics Approaches to Improve Bioenergy Traits in Maize, Sorghum and SugarcaneFree Access

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