A general method for gene isolation in tagging approaches: amplification of insertion mutagenised sites (AIMS)

Frey, Monika; Stettner, Cornelia; Gierl, Alfons

doi:10.1046/j.1365-313x.1998.00091.x

Cited by 74 publications

(71 citation statements)

References 11 publications

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“…Additionally, a small population of 24 individuals segregating for the ig1-mum allele was used to test for a cosegregating Mu band using a modified amplification of insertion mutagenized sites protocol (Frey et al, 1998). One band that cosegregated with ig1-mum contained a Mu (Iwakawa et al, 2002;Shuai et al, 2002).…”

Section: Fine Mapping and Cloning Of Ig1mentioning

confidence: 99%

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Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

2007

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Angiosperm embryo sac development begins with a phase of free nuclear division followed by cellularization and differentiation of cell types. The indeterminate gametophyte1 (ig1) gene of maize (Zea mays) restricts the proliferative phase of female gametophyte development. ig1 mutant female gametophytes have a prolonged phase of free nuclear divisions leading to a variety of embryo sac abnormalities, including extra egg cells, extra polar nuclei, and extra synergids. Positional cloning of ig1 was performed based on the genome sequence of the orthologous region in rice. ig1 encodes a LATERAL ORGAN BOUNDARIES domain protein with high similarity to ASYMMETRIC LEAVES2 of Arabidopsis thaliana. A second mutant allele of ig1 was identified in a noncomplementation screen using active Mutator transposable element lines. Homozygous ig1 mutants have abnormal leaf morphology as well as abnormal embryo sac development. Affected leaves have disrupted abaxial-adaxial polarity and fail to repress the expression of meristem-specific knotted-like homeobox (knox) genes in leaf primordia, causing a proliferative, stem cell identity to persist in these cells. Despite the superficial similarity of ig1-O leaves and embryo sacs, ectopic knox gene expression cannot be detected in ig1-O embryo sacs.

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Section: Fine Mapping and Cloning Of Ig1mentioning

confidence: 99%

“…Amplification of insertionmutagenized sites was performed using a protocol modified from that of Frey et al (1998). Approximately 500 ng of DNA was digested per sample with 5 units of HinP1I (New England Biolabs), and then adaptors were ligated overnight using 1 unit of T4 DNA ligase (Fermentas).…”

Section: Cloning Of Ig1mentioning

confidence: 99%

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

2007

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“…Six tightly linked and cosegregating low-copy amplification of insertion mutagenized sites (AIMS) fragments (Frey et al, 1998) were identified from three rf1-m families (Wise et al, 1996) and, along with sequences selected from the cosegregating 6140-1 cDNA (Wise et al, 1999), were used as probes against the first B73 library filters (ZMMBBa; Clemson University Genomics Institute). From each of the resulting short nonoverlapping contigs, overgo probes were designed off sequenced BAC ends.…”

Section: Analysis Of Multiple B73 Maize Bac Libraries Leads To Two Sementioning

confidence: 99%

“…Three maize (Zea mays) rf1-m allele families (rf1-m3207, rf1-m7323, and rf1-m7212; Wise et al, 1996) were analyzed by a modification of the AIMS method (Frey et al, 1998). DNA was extracted from each individual plant of a segregating population.…”

Section: Identification Of Bacs In the Rf1 Regionmentioning

confidence: 99%

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Kronmiller

Wise

2009

Plant Physiology

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The architecture of grass genomes varies on multiple levels. Large long terminal repeat retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are required to obtain completely finished genomes as well as to investigate gene and transposable element distributions. To characterize the organization and distribution of repeat clusters and gene islands across large grass genomes, we present 961-and 594-kb contiguous sequence contigs associated with the rf1 (for restorer of fertility1) locus in the near-centromeric region of maize (Zea mays) chromosome 3. We present two methods for computational finishing of highly repetitive bacterial artificial chromosome clones that have proved successful to close all sequence gaps caused by transposable element insertions. Sixteen repeat clusters were observed, ranging in length from 23 to 155 kb. These repeat clusters are almost exclusively long terminal repeat retrotransposons, of which the paleontology of insertion varies throughout the cluster. Gene islands contain from one to four predicted genes, resulting in a gene density of one gene per 16 kb in gene islands and one gene per 111 kb over the entire sequenced region. The two sequence contigs, when compared with the rice (Oryza sativa) and sorghum (Sorghum bicolor) genomes, retain gene colinearity of 50% and 71%, respectively, and 70% and 100%, respectively, for high-confidence gene models. Collinear genes on single gene islands show that while most expansion of the maize genome has occurred in the repeat clusters, gene islands are not immune and have experienced growth in both intragene and intergene locations.

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“…The sxd1 gene is expressed in bundle sheath cells and is upregulated in maturing leaf blades. Mezitt cloned the sxd1 allele using a protocol for differential display of Mu transposons by amplification of insertion-mutagenized sites (Frey et al, 1998). Mu transposontagging is a popular strategy of mutagenesis in maize, and the continued development of new Mu-cloning procedures promises to augment the existing protocols for gene discovery.…”

Section: Transposon Tagging and Gene Identificationmentioning

confidence: 99%

Cytokinesis: The Art of Partitioning

Jürgens

2000

Plant Cell

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A general method for gene isolation in tagging approaches: amplification of insertion mutagenised sites (AIMS)

Cited by 74 publications

References 11 publications

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

Theindeterminate gametophyte1Gene of Maize Encodes a LOB Domain Protein Required for Embryo Sac and Leaf Development

Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-Associated Region of Maize

Cytokinesis: The Art of Partitioning

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