MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

Lander, Eric S.; Green, Philip; Abrahamson, Jeff; Barlow, Aaron; Daly, Mark J.; Lincoln, Stephen E.; Newburg, Lee

doi:10.1016/0888-7543(87)90010-3

Cited by 6,237 publications

(3,184 citation statements)

References 9 publications

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“…24 The order of markers onto chromosomes was identical to those in published maps. 55 As can be seen in Figure 1, the distribution of survival time was slightly skewed in the F2 data (skewness = 0.789).…”

Section: Resultsmentioning

confidence: 58%

“…Genome-wide multipoint linkage analysis was performed using Mapmaker/EXP version 3.0 and Mapmaker/QTL 1.1. 24 The results from this analysis are shown as multiple point LOD score traces ( Figure 4), and numerical data for individual intervals shown in Table 2. Statistically significant linkages were identified on two chromosomes, with a third chromosome showing suggestive evidence by genome-wide criteria.…”

Section: Resultsmentioning

confidence: 99%

“…Genomewide interval mapping analysis between the transformed quantitative trait phenotype and genetic markers for the identification of QTLs was performed using Mapmaker/EXP version 3.0 and Mapmaker/QTL 1.1. 24 LOD scores were calculated as 2 /2ln(10), with 2 values computed using the expectation/maximization algorithm in Mapmaker/QTL. Upon initial identification of linked regions, multi-locus models were fitted using Mapmaker/QTL to obtain estimates of the total phenotypic variance explained by the different chromosome regions.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Genetic control of susceptibility to infection with Mycobacterium tuberculosis in mice

Fortin

et al. 2000

Genes Immun

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Section: Resultsmentioning

confidence: 58%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Genetic control of susceptibility to infection with Mycobacterium tuberculosis in mice

Fortin

et al. 2000

Genes Immun

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“…The linkage map for the MDF2 mice was created with MapMaker3 (15). Linkage analysis was performed on each candidate chromosome with WinQTL Cartographer version 2.0 (16,17) based on the severity index and onset index as the indicators of phenotype.…”

Section: Methodsmentioning

confidence: 99%

Accelerating effect of an MRL gene locus on the severity and onset of arthropathy in DBA/1 mice

Oishi¹,

Miyazaki²,

Mizuki³

et al. 2005

Arthritis & Rheumatism

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Objective. To analyze the influence of the genetic background of an arthritis-prone strain of mice, MRL, on the spontaneous development of arthropathy in DBA/1 mice, which histopathologically resembles enthesopathy in humans, and to clarify the strain-specific gene loci and their interactions that confer susceptibility to arthropathy.Methods. MRL, DBA/1, (MRL ؋ DBA/1)F 1 , and (MRL ؋ DBA/1)F 2 intercross mice were prepared, and the severity and onset of arthropathy of the ankle joints in individual mice were quantified (0-3 and 0-5 scale, respectively). A genome-wide scan of 271 male F 2 intercross mice with polymorphic microsatellite markers was performed.Results. Only male DBA/1, (MRL ؋ DBA/1)F 1 , and (MRL ؋ DBA/1)F 2 mice developed arthropathy. The macroscopic and histopathologic findings of arthropathy in the F 2 mice were similar to those in the parental DBA/1 mice, but the onset was significantly earlier. In the quantitative trait locus analysis of male F 2 mice, 1 susceptibility locus for both the severity and early onset of the disease in the region of an MRL allele, Amd1, was located at marker D10Mit259 (map position 40.0 cM), which was common to 1 of the sialadenitis susceptibility loci in MRL mice, Asm1. Another susceptibility locus for the severity and early onset of arthropathy in the region of a DBA allele, Amd2, was located at D3Mit46 (29.5 cM). These loci manifested an additive effect on the development of arthropathy.Conclusion. Arthropathy in DBA/1 mice is under the control of an allelic combination of gene loci, one of which is common to the locus for sialadenitis in MRL/ MpJ-lpr/lpr mice.

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“…Linkage analysis was performed using Mapmaker/EXP 3.0 [21], whereas QTL analysis using QTL Cartographer 2.5 [22]. For composite interval mapping, the log-likelihood (LOD) thresholds (2.9 for root length with inoculation and 3.1 for root length with no inoculation and relative root length) were selected from 1,000 permutations tested at the 5% level.…”

Section: Methodsmentioning

confidence: 99%

Mapping of quantitative trait loci related to primary rice root growth as a response to inoculation with Azospirillum sp. strain B510

Masuda

Sasaki

Kazama

et al. 2018

Communicative & Integrative Biology

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Azospirillum sp. strain B510 has been known as the plant growth-promoting endophyte; however, the growth-promotion effect is dependent on the plant genotype. Here, we aimed to identify quantitative trait loci (QTL) related to primary root length in rice at the seedling stage as a response to inoculation with B510. The primary root length of “Nipponbare” was significantly reduced by inoculation with B510, whereas that of “Kasalath” was not affected. Thus, we examined 98 backcrossed inbred lines and four chromosome segment substitution lines (CSSL) derived from a cross between Nipponbare and Kasalath. The primary root length was measured as a response to inoculation with B510, and the relative root length (RRL) was calculated based on the response to non-inoculation. Three QTL alleles, qRLI-6 and qRLC-6 on Chromosome (Chr.) 6 and qRRL-7 on Chr. 7 derived from Kasalath increased primary root length with inoculation (RLI), without inoculation, (RLC) and RRL and explained 20.2%, 21.3%, and 11.9% of the phenotypic variation, respectively. CSSL33, in which substitution occurred in the vicinity region of qRRL-7, showed a completely different response to inoculation with B510 compared with Nipponbare. Therefore, we suggest that qRRL-7 might strongly control root growth in response to inoculation with Azospirillum sp. strain B510.

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MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations

Cited by 6,237 publications

References 9 publications

Genetic control of susceptibility to infection with Mycobacterium tuberculosis in mice

Genetic control of susceptibility to infection with Mycobacterium tuberculosis in mice

Accelerating effect of an MRL gene locus on the severity and onset of arthropathy in DBA/1 mice

Mapping of quantitative trait loci related to primary rice root growth as a response to inoculation with Azospirillum sp. strain B510

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