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Abstract Detail


Emerging Technologies

Ersoz, Elhan [1], Gore, Michael [2], Hurwitz, Bonnie [3], Narechania, Apurva [3], Wright, Mark [4], Grills, George [5], Ware, Doreen [6], Buckler, Edward [7].

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 Roché’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

Keywords:
SNP discovery
genome reduction
next-generation sequencing
HpaII
maize
Zea mays L..

Presentation Type: Plant Biology Abstract
Session: P
Location: Exhibit Hall (Northeast, Southwest & Southeast)/Hilton
Date: Sunday, July 8th, 2007
Time: 8:00 AM
Number: P44008
Abstract ID:425


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