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United States Department of Agriculture

Agricultural Research Service


Location: Corn Insects and Crop Genetics Research

Title: Sequencing crop genomes: approaches and applications

item Jackson, Scott
item Lee, Suk-ha
item Schmutz, Jeremy
item Shoemaker, Randy

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/21/2011
Publication Date: 6/28/2011
Citation: Jackson, S.A., Lee, S., Schmutz, J., Shoemaker, R.C. 2011. Sequencing crop genomes: approaches and applications. New Phytologist. 191:915-925.

Interpretive Summary: Many challenges face plant scientists, in particular those working on crop production, such as a projected increase in population, decrease in water and arable land, changes in weather patterns and predictability. Advances in genenetic technologies for decoding the plant hereditary material can and should play a role in our response to meeting these challenges. In this article the authors review and discuss the several barriers that prevent rapid and effective deployment of these tools to a wide variety of crops. They point out that collecting rapid and accurate phenotypes in crop plants is a hinderance to integrating genomics with crop improvement and advances in informatics are needed to put these tools in the hands of the scientists on the ground. This information is important to students and scientists developing strategies for crop improvement using state of the art genetic technologies.

Technical Abstract: Plant genome sequencing methodology parrallels the sequencing of the human genome. The first projects were slow and very expensive. BAC by BAC approaches were utilized first and whole-genome shotgun sequencing rapidly replaced that approach. So called 'next generation' technologies such as short read pyro-sequencing have greatly increased the speed and output of data generation. The complexity of crop genomes makes de novo sequencing with next generation sequencing technologies fraught with difficulties that then create roadblocks to utilization of genome sequences for crop improvement. Two contributing factors to this complexity is polyploidy and large amounts of repetitive DNA. New and novel computer algorithms are being generated to overcome these difficulties. The burgeoning amount of genome sequence is making it possible to identify a seemingly endless number of molecular markers that are being adapted to marker assisted crop improvement. New alleles and genes underlying quantitative traits are being discovered daily. Next generation sequencing technologies are being adapted to sequence entire transcriptomes of plants, thus making it simpler to correlate agronomic traits with genomic sequence. This so called 'genetical genomics' is causing researchers to understand the limitations of 'reductionist' research and causing them to take on a systems approach to crop improvement.

Last Modified: 07/20/2017
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