Positional Cloning of a Gene for Nematode Resistance in Sugar Beet

Cai, Daguang; Kleine, Michael; Kifle, Sirak; Harloff, Hans-Joachim; Sandal, Niels; Marcker, Kjeld A.; Klein-Lankhorst, R. M.; Salentijn, E.M.J.; Lange, W.; Stiekema, Willem J.; Wyss, Urs; Grundler, Florian M. W.; Jung, Christian

doi:10.1126/science.275.5301.832

Cited by 427 publications

(202 citation statements)

References 25 publications

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“…Hs pr°-l, was cloned (Cai etal., 1997). This gene appears to encode a protein with a membrane anchor at its C terminus and a leucine-rich extra-cytoplasmic region.…”

Section: Introductionmentioning

confidence: 99%

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

et al. 1997

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“…Hs pr°-l, was cloned (Cai etal., 1997). This gene appears to encode a protein with a membrane anchor at its C terminus and a leucine-rich extra-cytoplasmic region.…”

Section: Introductionmentioning

confidence: 99%

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

et al. 1997

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“…Map-based cloning has proven to be a successful method for the isolation of, for example, resistance genes in several plant species such as tomato (Martin et al 1993;Dixon et al 1996), Arabidopsis (Bent et al 1994;Mindrinos et al 1994;Grant et al 1995), sugar beet (Cai et al 1997) and barley (Bu¨schges et al 1997). Most mapbased cloning projects start with a bulked segregant analysis (BSA) (Michelmore et al 1991) to find bulkspecific markers.…”

Section: Introductionmentioning

confidence: 99%

Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene

Brugmans¹,

Hutten²,

Rookmaker³

et al. 2005

Theor Appl Genet

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A marker-saturated linkage map of potato was used to genetically map a locus involved in the resistance against wart disease Synchytrium endobioticum race 1. The locus mapped on the long arm of chromosome 4 and is named Sen1-4 in contrast to a Sen1 locus on chromosome 11. The AFLP markers from the Sen1-4 interval enabled the isolation of BAC clones from an 11 genome equivalent BAC library. This was achieved via fingerprinting of BAC pools with the AFLP primer pairs that resemble the genetic marker loci. With non-selective AFLP primers, fingerprints of individual BAC clones were generated to analyse the overlap between BAC clones using FPC. This resulted in a complete contig and a minimal tiling path of 14 BAC clones enclosing the Sen1-4 locus. The BAC contig has a genetic length of $6 cM and a physical length of $1 Mb. Our results demonstrate that map-based cloning of Sen1-4 can be pursued on the basis of a strategy of marker saturation alone. Genetic resolution achieved by screening large numbers of offspring for recombination events may not be required. Together with the construction of the BAC contig, a physical map with the position of the markers is accomplished in one step. This provides proof of concept for the utility of the marker saturation that is offered by the ultra dense AFLP map of potato for gene cloning.

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Section: A N a Ly S I Smentioning

confidence: 99%

“…Mutant alleles of genes that are not present in the reference sequence cannot be identified within resequencing data alone. In particular, fast-evolving genes, such as those involved in disease resistance, might not always be represented in the reference sequence 16,17 .Alternative solutions for mapping-by-sequencing in species without reference sequences have been proposed, such as mappingby-sequencing based on reference sequences of related species or expressed sequence tag collections 11,18 . However, all of these methods greatly rely on low sequence divergence and high levels of synteny between the mutant genome and alignment target.…”

mentioning

confidence: 99%

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

et al. 2013

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Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F 2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M 3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.Forward genetic screens have been of fundamental importance in elucidating biological mechanisms in model species 1 . Their success, however, has relied on the feasibility of mutant gene isolation. Identification of causal mutations typically begins with genetic mapping, followed by candidate gene sequencing and complementation studies using transformation. Advances in DNA sequencing technologies have tremendously accelerated genetic mapping by combining bulk segregant analysis, that is, pooling recombinant genomes, with whole-genome sequencing, usually referred to as mapping by sequencing 2,3 . This approach is now becoming standard for mutation mapping and identification in many model species 3-12 and has even been applied to decipher quantitative traits with complex genetic architectures 13,14 . Recently, mutagen-induced changes have been used as novel markers, allowing mapping of mutations using isogenic mapping populations 10,15 . Nevertheless, all mapping-by-sequencing methods rely on resequencing, a method for whole-genome reconstruction based on aligning sequences to a reference sequence. Therefore, this requirement restricts the application of the technique to species for which such a reference genome sequence is available.Many reference-sequence assembly projects are currently in progress, including ones for most of the major crop species and breeding animals. However, even with an existing reference sequence, extending mapping-by-sequencing methods beyond the sequenced reference accessions has proved technically challenging. Mutant alleles of genes that are not present in the reference sequence cannot be identified within resequencing data alone. In particular, fast-evolving genes, such as those involved in disease resistance, might not always be represented in the reference sequence 16,17 .Alternative solutions for mapping-by-sequencing in species without reference sequences have been proposed, such ...

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Positional Cloning of a Gene for Nematode Resistance in Sugar Beet

Cited by 427 publications

References 25 publications

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

Map positions of 47 Arabidopsis sequences with sequence similarity to disease resistance genes

Exploitation of a marker dense linkage map of potato for positional cloning of a wart disease resistance gene

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers

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