Sequence-indexed mutations in maize using the UniformMu transposon-tagging population-4

<p><b>Copyright information:</b></p><p>Taken from "Sequence-indexed mutations in maize using the UniformMu transposon-tagging population"</p><p>http://www.biomedcentral.com/1471-2164/8/116</p><p>BMC Genomics 2007;8():116-116.</p><p>Published online 9 May 2007</p><p>PMCID:PMC1878487.</p><p></p> and sp. PCC 6803. Rice and proteins are identified by their locus numbers. The protein sequences used to generate the ClustalW alignment and tree were from the ORF of the locus and Genbank accessions: , , , , , , , , , ,

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population-1

<p><b>Copyright information:</b></p><p>Taken from "Sequence-indexed mutations in maize using the UniformMu transposon-tagging population"</p><p>http://www.biomedcentral.com/1471-2164/8/116</p><p>BMC Genomics 2007;8():116-116.</p><p>Published online 9 May 2007</p><p>PMCID:PMC1878487.</p><p></p>-specific primer. Each primer was tested on the initial template DNA used to develop the UniformMu FSTs (lane T) as well as DNA extracted from siblings (denoted by brackets). No DNA template controls were included in all assays (lane HO). W22 DNA was used to confirm that the insertion site did not amplify in the recurrent inbred parent of the UniformMu population

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population-0

<p><b>Copyright information:</b></p><p>Taken from "Sequence-indexed mutations in maize using the UniformMu transposon-tagging population"</p><p>http://www.biomedcentral.com/1471-2164/8/116</p><p>BMC Genomics 2007;8():116-116.</p><p>Published online 9 May 2007</p><p>PMCID:PMC1878487.</p><p></p>ics of the locus-specific primer design as constrained by available sequences. Left and right specific primers were designed when genomic sequence was available on either side of the insertion site. Right specific primers were designed when the insertion site defined novel maize genomic sequence. A presumptive right primer was designed for FSTs without a MuTIR sequence

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population-2

<p><b>Copyright information:</b></p><p>Taken from "Sequence-indexed mutations in maize using the UniformMu transposon-tagging population"</p><p>http://www.biomedcentral.com/1471-2164/8/116</p><p>BMC Genomics 2007;8():116-116.</p><p>Published online 9 May 2007</p><p>PMCID:PMC1878487.</p><p></p>Index EST contig, and the maize assembled genomic island, MAGI4_45584. The schematic shows the location of the MuTIR sequence (black arrow, not drawn to scale) and percent nucleotide identity is noted. The left and right primer sites are marked by gray arrows; primer sizes are not drawn to scale. () Co-segregation analysis with progeny from backcross generations 2 and 3 (BC2 and BC3) in a W22 introgression. Left/Right products amplify normal alleles. TIR8/Right products amplify the insertion site. () Co-segregation analysis with self progeny. PCR was completed with DNA extracted from homozygous normal (lanes 2–3) or mutants kernels (lanes 4–31)

Sequence-indexed mutations in maize using the UniformMu transposon-tagging population

<p>Abstract</p> <p>Background</p> <p>Gene knockouts are a critical resource for functional genomics. In Arabidopsis, comprehensive knockout collections were generated by amplifying and sequencing genomic DNA flanking insertion mutants. These Flanking Sequence Tags (FSTs) map each mutant to a specific locus within the genome. In maize, FSTs have been generated using DNA transposons. Transposable elements can generate unstable insertions that are difficult to analyze for simple knockout phenotypes. Transposons can also generate somatic insertions that fail to segregate in subsequent generations.</p> <p>Results</p> <p>Transposon insertion sites from 106 UniformMu FSTs were tested for inheritance by locus-specific PCR. We confirmed 89% of the FSTs to be germinal transposon insertions. We found no evidence for somatic insertions within the 11% of insertion sites that were not confirmed. Instead, this subset of insertion sites had errors in locus-specific primer design due to incomplete or low-quality genomic sequences. The locus-specific PCR assays identified a knockout of a 6-phosphogluconate dehydrogenase gene that co-segregates with a seed mutant phenotype. The mutant phenotype linked to this knockout generates novel hypotheses about the role for the plastid-localized oxidative pentose phosphate pathway during grain-fill.</p> <p>Conclusion</p> <p>We show that FSTs from the UniformMu population identify stable, germinal insertion sites in maize. Moreover, we show that these sequence-indexed mutations can be readily used for reverse genetic analysis. We conclude from these data that the current collection of 1,882 non-redundant insertion sites from UniformMu provide a genome-wide resource for reverse genetics.</p