Algorithms for a location database

Morton, N. E.; Collins, Amanda; Lawrence, Steve; Shields, Denis C.

doi:10.1111/j.1469-1809.1992.tb01147.x

Cited by 55 publications

(34 citation statements)

References 15 publications

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“…With this Markers are listed in their relative genetic order, and the distance in centiMorgans is from the top of the short arm of chromosome 20. Sex-averaged recombination distances were derived from an integrated genetic and physical map available from the Genome Location Data Base (66). All phenotypes were adjusted for age and sex.…”

Section: Resultsmentioning

confidence: 99%

Identification of an obesity quantitative trait locus on mouse chromosome 2 and evidence of linkage to body fat and insulin on the human homologous region 20q.

Lembertas¹,

Pérusse²,

Chagnon³

et al. 1997

J. Clin. Invest.

212

118

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Section: Resultsmentioning

confidence: 99%

Identification of an obesity quantitative trait locus on mouse chromosome 2 and evidence of linkage to body fat and insulin on the human homologous region 20q.

Lembertas¹,

Pérusse²,

Chagnon³

et al. 1997

J. Clin. Invest.

212

118

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“…Since the genetic distance between close markers may not be precise, hence as an alternative, the distances were also calculated from the bovine Location DataBase (bLDB) (http://medvet.angis.org.au/ldb/; [32]) with distance expressed in kb. The bLDB is an integrated map constructed from all the major public-domain physical and genetic maps of cattle, using the LDB software of Morton et al [30], which had previously been used for construction of an integrated human map before completion of the human annotated sequence. Genotyping was carried out using a LI-COR 4200 sequencer (LI-COR, Lincoln, USA) with fluorescent dye-labeled primers.…”

Section: Markers and Genotypingmentioning

confidence: 99%

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Khatkar¹,

Thomson²,

Tammen³

et al. 2006

Genet. Sel. Evol.

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-We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D . Estimates of D from the two approaches were in close agreement (r = 0.91). The mean estimates of D for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (∼37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.linkage disequilibrium / dairy cattle / markers / chromosome 6

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“…The bovine map was a customized version of the integrated bovine map known as the bovine Location DataBase (bLDB) (http:/ / medvet.angis.org.au/ldb/; Nicholas 2005). The bLDB, in which distance between markers is expressed in kilobases, is an integrated map constructed from all the major public-domain physical and genetic maps of cattle using the LDB software of Morton et al (1992). This approach has previously been used for construction of an integrated human map before the completion of the human annotated sequence Tapper et al 2001) and was found to be reliable in both location and marker order compared with the full genome sequence ).…”

Section: Methodsmentioning

confidence: 99%

A First-Generation Metric Linkage Disequilibrium Map of Bovine Chromosome 6

et al. 2006

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We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein-Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.

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Algorithms for a location database

Cited by 55 publications

References 15 publications

Identification of an obesity quantitative trait locus on mouse chromosome 2 and evidence of linkage to body fat and insulin on the human homologous region 20q.

Identification of an obesity quantitative trait locus on mouse chromosome 2 and evidence of linkage to body fat and insulin on the human homologous region 20q.

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

A First-Generation Metric Linkage Disequilibrium Map of Bovine Chromosome 6

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