Zea mays. Zea mays

We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (Maize GeneChip). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.] Overall design: protocol: mRNA - genotype: B73 maize inbred(3-replications) protocol: mRNA - genotype: Mo17 maize inbred(3-replications) protocol: mRNA - genotype: CML69 maize inbred(3-replications) protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications) protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications) protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications) protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications) protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications) protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications) protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications) protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications) protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)