Ersoz, Elhan , Gore, Michael , Hurwitz, Bonnie , Narechania, Apurva , Wright, Mark , Grills, George , Ware, Doreen , Buckler, Edward .
SNP Discovery with HpaII-Filtered Genomic Libraries of Maize using Next-Generation Sequencing Technologies.
Maize (Zea mays L.), possesses tremendous resources for mapping of quantitative traits down to the gene level through candidate-gene association mapping practices. However, in order to capture most of the LD structure in maize genome in a genome-wide association study, an estimated 1 million SNP markers are required. Until recently, the development costs of such high-density SNP markers were restraining the progress of such association projects in maize. Recent advancements in next generation sequencing technologies such as RochÃ©’s 454 and Illumina’s Solexa, present an enormous opportunity to bridge the gap between plant genomic studies and crop improvement practices via enabling the progression of genome-wide association mapping practices. In order to realize the objectives of (1) identification of 1 to 2 million SNP markers focused in the areas of active recombination, and (2) genotyping 27 diverse lines that are parents to a 5000 RIL nested-association-mapping population with these SNPs, we employed a library preparation method built on the differential cytosine methylation patterns of genes and retrotransposons, that are discriminated by the methylation-sensitive restriction enzyme HpaII. These gene-biased HpaII reduction-libraries, in conjunction with next-generation sequencing, is being used for high-throughput SNP discovery. Initial library that was prepared from DNA obtained from nuclei isolates of husk tissues of maize inbred line B73 displayed a superior enrichment for completely unique sequences compared to COT based and methylation-filtered libraries and contained only 20% repeat sequences. Progress to date will be presented.
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1 - Cornell University, Institute for Genomic Diversity, Room 175, Biotechnology Building, Ithaca, NY, 14853, USA
2 - Cornell University, Institute for Genomic Diversity
3 - Cold Spring Harbor Laboratory
4 - Cornell University, Genetics and Development
5 - Cornell University
6 - USDA-ARS, Cold Spring Harbor Laboratory
7 - USDA-ARS, Cornell University, Institute for Genomic Diversity
Zea mays L..
Presentation Type: Plant Biology Abstract
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM