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SNP Detection in O. sativa
The International Rice Functional Genomics Consortium (IRFGC) has been funded a project to investigate sequence variation within and between rice varieties and landraces on a genome-wide scale. Using high-density oligonucleotide microarrays 100 Mb of the unique fraction of the reference genome was interrogated for 20 diverse varieties. We analyzed the resequencing data using a machine learning method similar to the A. thaliana SNP project to identify SNPs in all varieties.
Further information on the OryzaSNP project can be found at the websites of our collaborators at Michigan State University and the Interational Rice Research Institute.
People specializing in this area
Alumnae and Alumni
Regina Bohnert, Ph.D.
Publications
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McNally, KL, Childs, KL, Bohnert, R, Davidson, RM, Zhao, K, Ulat, VJ, Zeller, G, Clark, RM, Hoen, DR, Bureau, TE, Stokowski, R, Ballinger, DG, Frazer, KA, Cox, DR, Padhukasahasram, B, Bustamante, CD, Weigel, D, Mackill, DJ, Bruskiewich, RM, Rätsch, G, Buell, CR, Leung, H, and Leach, JE (2009).
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
Proceedings of the National Academy of Sciences, 106(30):12273-8.
http://www.pnas.org/content/106/30/12273.full
Printable file
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Bohnert, R, Zeller, G, Clark, RM, Childs, KL, Ulat, V, Stokowski, R, Ballinger, D, Frazer, K, Cox, D, Bruskiewich, R, Buell, CR, Leach, J, Leung, H, McNally, KL, Weigel, D, and Rätsch, G (2008).
Revealing Sequence Variation Patterns in Rice with Machine Learning Methods
BMC Bioinformatics, 9(S10):O8.
http://www.biomedcentral.com/1471-2105/9/S10/O8
Printable file
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Bohnert, R (2007).
Polymorphism Detection in Rice
Diplom thesis, Friedrich Miescher Laboratory of the Max Planck Society and Eberhard Karls Universität Tübingen.
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