The Development of a Highly Informative Mouse Simple Sequence Length Polymorphism (SSLP) Marker Set and Construction of a Mouse Family Tree Using Parsimony Analysis

Witmer, P. Dane; Doheny, Kimberly F.; Adams, Marcia K.; Boehm, Corinne D.; Dizon, Jane S.; Goldstein, Janet L.; Templeton, Tira M.; Wheaton, Ariana M.; Dong, Penny; Pugh, Elizabeth; Nussbaum, Robert L.; Hunter, Kent W.; Kelmenson, Jennifer A.; Rowe, Lucy B.; Brownstein, Michael J.

doi:10.1101/gr.717903

Cited by 62 publications

(56 citation statements)

References 15 publications

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“…Group 5 is anchored by the 129 strain, the final sequenced strain, and consists of Castle mice derivatives, including the 129 group and related strains LP/J and SB/LeJ. Groups 4 and 5 seem to be parts of a larger and probably related branch, as previously noted (Witmer et al 2003). Group 6 is anchored by DBA/2J and consists of C.C.…”

Section: Family Tree Of the Mouse Strainsmentioning

confidence: 84%

“…The genealogy of inbred mouse strains is well documented (Simpson et al 1997;Beck et al 2000): some share a common origin, some were either deliberately or accidentally crossed with pre-existing strains, and others are of entirely independent origin. Several genotypically based mouse family trees involving different sets of strains have been constructed using classical genotypes or SSLP markers (Atchley and Fitch 1993;Schalkwyk et al 1999;Witmer et al 2003). To further explore these relationships, we sought to reconstruct the phylogenetic relationships among the 102 inbred and wild-derived inbred strains tested in this study by using our SNP marker set (Fig.…”

Section: Family Tree Of the Mouse Strainsmentioning

confidence: 99%

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An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships

Petkov¹,

Ding²,

Cassell³

et al. 2004

Genome Res.

317

318

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A set of 1638 informative SNP markers easily assayed by the Amplifluor genotyping system were tested in 102 mouse strains, including the majority of the common and wild-derived inbred strains available from The Jackson Laboratory. Selected from publicly available databases, the markers are on average ∼1.5 Mb apart and, whenever possible, represent the rare allele in at least two strains. Amplifluor assays were developed for each marker and performed on two independent DNA samples from each strain. The mean number of polymorphisms between strains was 608±136 SD. Several tests indicate that the markers provide an effective system for performing genome scans and quantitative trait loci analyses in all but the most closely related strains. Additionally, the markers revealed several subtle differences between closely related mouse strains, including the groups of several 129, BALB, C3H, C57, and DBA strains, and a group of wild-derived inbred strains representing several Mus musculus subspecies. Applying a neighbor-joining method to the data, we constructed a mouse strain family tree, which in most cases confirmed existing genealogies.

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Section: Family Tree Of the Mouse Strainsmentioning

confidence: 84%

Section: Family Tree Of the Mouse Strainsmentioning

confidence: 99%

An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships

Petkov¹,

Ding²,

Cassell³

et al. 2004

Genome Res.

317

318

View full text Add to dashboard Cite

show abstract

“…Usually the PCR product size of SSLP markers ranges from 80 to 250 bp. A dense genetic map of the mouse with numerous SSLPs that distinguish different inbred strains has been established [35][36][37] which is freely accessible through various websites (Supplementary Table S5; please see http://lan. sagepub.com/content/suppl/2013/05/28/0023677212473 918.DC1/LAN473918_Supplementaryd_data.pdf) so that every molecular biology laboratory can easily establish its customized panel of SSLPs.…”

Section: Other Genotyping Methodsmentioning

confidence: 99%

FELASA guidelines for the refinement of methods for genotyping genetically-modified rodents

et al. 2013

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The use of genetically-modified (GM) animals as research models continues to grow. The completion of the mouse genome sequence, together with the high-throughput international effort to introduce mutations across the mouse genome in the embryonic stem (ES) cells (www.knockoutmouse.org) facilitates an efficient way to obtain mutated mouse strains as research models. The increasing number of available mutated mouse strains and their combinations, together with the increasing complexity in the targeting approaches used, reinforces the need for guidelines that will provide information about the mouse strains and the robust and reliable methods used for their genotyping. This information, however, should be obtained with a method causing minimal discomfort to the experimental animals. We have, therefore, compiled the present document which summarizes the currently available methods for obtaining genotype information. It provides updated guidelines concerning animal identification, DNA sampling and genotyping, and the information to be kept and distributed for any mutated rodent strain. As a starting point, we have decided to collect information on the genotyping practices applied in various European countries, in order to identify common problems and pitfalls faced and to better direct our recommendations. For this purpose, we have conducted a survey focused on genotyping-related procedures used. We have collected 158 responses from 25 countries (see Supplementary information http://lan.sagepub.com/ content/suppl/2013/05/28/0023677212473918.DC1/ LAN473918_Supplementaryd_data.pdf), which will be acknowledged in this report when appropriate. Only three replies were received with regard to rats, which seems to show that this species is still infrequently used for genetically-modified (GM) models. From the responses to this survey, we could conclude that the procedures are not harmonized among countries or even among different institutes within one country, and that the common practice is not always in accordance with the latest scientific findings.

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“…A genome scan was conducted in two steps with the end result being that the average distance between markers was approximately 10 cM, with no gap greater than 30 cM (Table 1). First, simple sequence repeat markers known to be polymorphic between the parental strains were selected to evenly cover all 19 autosomes (Witmer et al 2003). These fluorescently labeled microsatellite primers were amplified by PCR and the PCR products were scanned by an ABI 3100 capillary sequencer (Applied Biosystems, Forest City, CA).…”

Section: Dna Extraction and Genotypingmentioning

confidence: 99%

Genetic loci affecting body weight and fatness in a C57BL/6J × PWK/PhJ mouse intercross

2007

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To determine the genetic variation that contributes to body composition in the mouse, we interbred a wild-derived strain (PWK/PhJ; PWK) with a common laboratory strain (C57BL/6J; B6). The parental, F 1 , and F 2 mice were phenotyped at 18 weeks old for body weight and composition using dual-energy X-ray absorptiometry (DEXA). A total of 479 (244 male and 235 female) F 2 mice were genotyped for 117 polymorphic markers spanning the autosomes. Twenty-eight suggestive or significant linkages for four traits (body weight, adjusted lean and fat weight, and percent fat) were detected. Of these, three QTLs were novel: one on the proximal portion of Chr 5 for body weight (Bwq8; LOD = 4.7), one on Chr 3 for lean weight (Bwtq13; LOD = 3.6), and one on Chr 11 for percent fat (Adip19; LOD = 5.8). The remaining QTLs overlapped previously identified linkages, e.g., Adip5 on Chr 9. One QTL was sex-specific (present in males only) and seven were sex-biased (more prominent in one sex than the other). Most alleles that increased body weight were contributed by the B6 strain, and most alleles that increased percent fat were contributed by the PWK strain. Eight pairs of interacting loci were identified, none of which exactly overlapped the main-effect QTLs. Many of the QTLs found in the B6 × PWK cross map to the location of previously reported linkages, suggesting that some QTLs are common to many strains (consensus QTLs), but three new QTLs appear to be particular to the PWK strain. The location and type of QTLs detected in this new cross will assist in future efforts to identify the genetic variation that determines the ratio of lean to fat weight as well as body size in mice.

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The Development of a Highly Informative Mouse Simple Sequence Length Polymorphism (SSLP) Marker Set and Construction of a Mouse Family Tree Using Parsimony Analysis

Cited by 62 publications

References 15 publications

An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships

An Efficient SNP System for Mouse Genome Scanning and Elucidating Strain Relationships

FELASA guidelines for the refinement of methods for genotyping genetically-modified rodents

Genetic loci affecting body weight and fatness in a C57BL/6J × PWK/PhJ mouse intercross

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