New Tools For Discovering DNA Variations In Crop Genomes
The study of human genetics has been a successful venture for researchers in recent years. Several million single-nucleotide polymorphisms (SNPs) have been identified from the whole-genome resequencing of multiple individuals, which have served as genetic markers to pinpoint genes controlling common human diseases. In contrast, the genome of a single cultivar or line has yet to be sequenced in its entirety for most crops of economic or societal importance. This slow pace of genomic progress can be mostly explained by the high costs and technical difficulties associated with sequencing crop genomes, which tend to be large in size and complex—containing a high amount of repetitive DNA and duplicated genes that are highly similar in sequence.
With the advent of high-throughput DNA sequencing technologies, it is now possible to cheaply and rapidly sequence hundreds of millions of bases in a matter of hours. A team of scientists at Cornell University (Ithaca, NY), the United States Department of Agriculture-Agriculture Research Service (USDA-ARS), Cold Spring Harbor Laboratory (Cold Spring Harbor, NY), Roche Applied Science Corp. (Indianapolis, IN) and 454 Life Sciences (Branford, CT), have developed molecular and computational tools for the efficient and accurate identification of gene-enriched SNPs in crops. The large, complex genome of maize was used to evaluate these tools.
The study was funded by the National Science Foundation (NSF), Roche Applied Science Corp., and the USDA-ARS. Results from the study were published in the July 2009 issue of The Plant Genome.
In this research collaboration, an existing molecular technique was modified to enable gene-enrichment and resequencing of maize inbred lines B73 and Mo17 with massively parallel pyrosequencing. In addition, a custom computational pipeline was developed to analyze and assemble short reads, identify correctly mapped reads, and call high quality SNPs. With the implementation of these methods, the authors identified 126,683 gene-enriched SNPs between B73 and Mo17 at high accuracy.
“Next-generation sequencing technologies will greatly accelerate the resequencing of multiple to numerous individuals for every major crop species,” says Michael Gore, first co-author of the study. “Such efforts will facilitate the construction of SNP datasets on the order of millions that can be used in whole-genome association studies to assess the contribution of SNPs—common or rare—to complex traits. What we have learned from this pilot study will help us to construct a community SNP resource in maize that is comparable in scale to that of the human haplotype map”.
Although the majority of SNPs do not contribute to phenotypic variation, plant breeders and geneticists alike are interested in using SNPs as genetic markers. As a genetic marker, SNPs can be used for studies of genetic diversity and in the selection of superior plants. The SNPs identified in this study can be used for high-resolution genetic mapping of agronomic traits, which could eventually lead to the development of improved commercial maize hybrids.
Wednesday, July 15, 2009
Wood Burning Stoves have been Reevaluated
The stress of rising natural gas prices is leading many consumers to rethink how they heat their homes. For some this means moving towards modern alternative energy options, while others have been turning to a more traditional method for a solution to these rising costs. In Canada and the United States, wood burning stoves have been reevaluated as a potentially viable option for home heating.
The case for modern woodstoves has developed with the improvement of the products on the market, as wood heating technology has substantially advanced in recent years. With the advanced secondary combustion systems on Environmental Protection Agency certified woodstoves, they are now 95% more efficient than their predecessors.
Dr. Paul Grogan, a plant and ecosystem ecologist and Canadian Research Chair (II) at Queen’s University in Kingston, Ontario conducted a case study on the benefits of woodstoves with the help of final-year undergraduate and first year graduate students. He determined that adding a woodstove to the home can help both consumers heating costs as well as the environment.
The environmental sustainability of woodstove use is dependent upon the consumption of wood from sustainably managed woodlots, as the carbon released is reused as the next generation of trees grows. Annual gross CO2 emissions did in fact increase from 12,610 kg (i.e., ~2.5 metric tons CO2/person per year) to 17,330 kg after the installation of the wood stove. But while this gross amount did increase, the net carbon released by the combustion is negligible, the only surplus coming from the harvest and transport. Based on an average growing time of 130 years before harvest for local Ontario tree species, a woodlot or forest 3.5 hectares in size would provide an indefinite supply of wood heat for a household without a net increase in carbon emissions.
In the case study, adding a woodstove to the ground floor of a 3200ft2 home reduced the mean annual gas cost by 60%; from $2260 to $880. The annual cost of the wood fuel for the woodstove amounted to $1330 for 5 full cords (a cord is 8 feet long by 4 feet high by 4 feet wide - 128ft3 ). This was a yearly savings of $50 at market fossil fuel prices of 2005-2007 without taking into account rising fossil fuel prices or the impending carbon tax. Should these variables come into play Dr. Grogan estimated that the domestic heating costs would be reduced by 25%. This translates into a potential savings of $920 in the first 3 years.
The stress of rising natural gas prices is leading many consumers to rethink how they heat their homes. For some this means moving towards modern alternative energy options, while others have been turning to a more traditional method for a solution to these rising costs. In Canada and the United States, wood burning stoves have been reevaluated as a potentially viable option for home heating.
The case for modern woodstoves has developed with the improvement of the products on the market, as wood heating technology has substantially advanced in recent years. With the advanced secondary combustion systems on Environmental Protection Agency certified woodstoves, they are now 95% more efficient than their predecessors.
Dr. Paul Grogan, a plant and ecosystem ecologist and Canadian Research Chair (II) at Queen’s University in Kingston, Ontario conducted a case study on the benefits of woodstoves with the help of final-year undergraduate and first year graduate students. He determined that adding a woodstove to the home can help both consumers heating costs as well as the environment.
The environmental sustainability of woodstove use is dependent upon the consumption of wood from sustainably managed woodlots, as the carbon released is reused as the next generation of trees grows. Annual gross CO2 emissions did in fact increase from 12,610 kg (i.e., ~2.5 metric tons CO2/person per year) to 17,330 kg after the installation of the wood stove. But while this gross amount did increase, the net carbon released by the combustion is negligible, the only surplus coming from the harvest and transport. Based on an average growing time of 130 years before harvest for local Ontario tree species, a woodlot or forest 3.5 hectares in size would provide an indefinite supply of wood heat for a household without a net increase in carbon emissions.
In the case study, adding a woodstove to the ground floor of a 3200ft2 home reduced the mean annual gas cost by 60%; from $2260 to $880. The annual cost of the wood fuel for the woodstove amounted to $1330 for 5 full cords (a cord is 8 feet long by 4 feet high by 4 feet wide - 128ft3 ). This was a yearly savings of $50 at market fossil fuel prices of 2005-2007 without taking into account rising fossil fuel prices or the impending carbon tax. Should these variables come into play Dr. Grogan estimated that the domestic heating costs would be reduced by 25%. This translates into a potential savings of $920 in the first 3 years.
Wednesday, July 01, 2009
First DNA-based Reconstruction of the Giant Extinct Moa Bird
Scientists have performed the first DNA-based reconstruction of the giant extinct moa bird, using prehistoric feathers recovered from caves and rock shelters in New Zealand.
Researchers from the University of Adelaide and Landcare Research in New Zealand have identified four different moa species after retrieving ancient DNA from moa feathers believed to be at least 2500 years old.
The giant birds – measuring up to 2.5 metres and weighing 250 kilograms – were the dominant animals in New Zealand’s pre-human environment but were quickly exterminated after the arrival of the Maori around 1280AD.
PhD student Nicolas Rawlence from the University’s Australian Centre for Ancient DNA says until now, the scientific community has not known what the 10 different species of moa looked like. ”By using ancient DNA we have been able to connect feathers to four different moa species,” he says.
The researchers compared the feathers to others found in the sediments from red-crowned parakeets that are still living today, determining they had not faded or changed in colour. They then reconstructed the appearance of the stout-legged moa, heavy-footed moa, upland moa and the South Island giant moa.
Their findings were published today in the Proceedings of the Royal Society of London Series B.
“The surprising thing is that while many of the species had a similar, relatively plain brown plumage for camouflage, some had white-tipped feathers to create a speckled appearance,” Mr Rawlence says.
A co-author of the study, Dr Jamie Wood from Landcare Research, says it is likely that the drab colouring was driven by selection to avoid predation by the extinct Haast’s eagle, the largest and most powerful eagle in the world.
The research team also demonstrated that it is possible to retrieve DNA from all parts of the ancient feathers, not just the tip of the quill, as previously thought.
“This important finding opens the way to study DNA from museum bird skins while causing almost no damage to these valuable specimens, just by clipping a small part of a single feather,” says Dr Kyle Armstrong from the Australian Centre for Ancient DNA (ACAD).
ACAD Director Professor Alan Cooper says this finding suggests it may be possible to reconstruct the appearance of other extinct birds using feathers from fossil deposits.
“There are so many enigmatic extinct species that it would be great to see ‘clothed’," Professor Cooper says.
Scientists have performed the first DNA-based reconstruction of the giant extinct moa bird, using prehistoric feathers recovered from caves and rock shelters in New Zealand.
Researchers from the University of Adelaide and Landcare Research in New Zealand have identified four different moa species after retrieving ancient DNA from moa feathers believed to be at least 2500 years old.
The giant birds – measuring up to 2.5 metres and weighing 250 kilograms – were the dominant animals in New Zealand’s pre-human environment but were quickly exterminated after the arrival of the Maori around 1280AD.
PhD student Nicolas Rawlence from the University’s Australian Centre for Ancient DNA says until now, the scientific community has not known what the 10 different species of moa looked like. ”By using ancient DNA we have been able to connect feathers to four different moa species,” he says.
The researchers compared the feathers to others found in the sediments from red-crowned parakeets that are still living today, determining they had not faded or changed in colour. They then reconstructed the appearance of the stout-legged moa, heavy-footed moa, upland moa and the South Island giant moa.
Their findings were published today in the Proceedings of the Royal Society of London Series B.
“The surprising thing is that while many of the species had a similar, relatively plain brown plumage for camouflage, some had white-tipped feathers to create a speckled appearance,” Mr Rawlence says.
A co-author of the study, Dr Jamie Wood from Landcare Research, says it is likely that the drab colouring was driven by selection to avoid predation by the extinct Haast’s eagle, the largest and most powerful eagle in the world.
The research team also demonstrated that it is possible to retrieve DNA from all parts of the ancient feathers, not just the tip of the quill, as previously thought.
“This important finding opens the way to study DNA from museum bird skins while causing almost no damage to these valuable specimens, just by clipping a small part of a single feather,” says Dr Kyle Armstrong from the Australian Centre for Ancient DNA (ACAD).
ACAD Director Professor Alan Cooper says this finding suggests it may be possible to reconstruct the appearance of other extinct birds using feathers from fossil deposits.
“There are so many enigmatic extinct species that it would be great to see ‘clothed’," Professor Cooper says.
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