Lore4^LS
QTL Variant Detail

Summary

• QTL variant: Lore4^LS
• Name: loss of righting induced by ethanol 4; LS
• MGI ID: MGI:2389051
• QTL: Lore4 Location: Chr11:79156009-107616472 bp Genetic Position: Chr11, Syntenic

Variant origin

• Strain of Specimen: LS

Variant description

• Allele Type: QTL
• Mutation: Undefined
• Mutation details: This allele confers increased loss of righting response (LORR) following alcohol challenge compared to SS. (J:76104)
• Inheritance: Other (see notes)

Notes

Lore4 exhibits an additive mode of inheritance.

Candidate Genes

J:80012

Analysis of 5 Lore4 interval specific congenic strains (ISCS) excluded Ppard and Gfap as candidate genes for Lore4.

J:93175

Potential candidate genes mapping near Lore4 on mouse Chromosome 11 are Gabarap, Slc6a4 (42 cM), Pparbp, Cnp1 (61 cM), Hcrt (61.2 cM), and Gfap (62 cM). Pparbp, Cnp1, and Gfap have been sequenced and are polymorphic between inbred strains LS and IS.

J:105312

Candidate genes for ethanol sensitivity QTL Lore1 (loss of righting induced by ethanol 1), Lore2, Lore4, and Lore5 were identified using Affymetrix gene microarray analysis. RNA from the cerebella of male animals from inbred strains LS and SS were hybridized to 2 different sets of Affymetrix gene chips and analyzed for gene expression differences. The inbred strain LS exhibits increased alcohol sensitivity compared to SS. A total of 15 candidate genes were identified, 4 of which have polymorphisms between LS and SS.

Xrcc5 (42 cM) was identified as candidate gene for Lore1 (54 cM) on mouse Chromosome 1. Xrcc5 exhibits 2.5-fold increased expression in the SS inbred strain compared to the LS inbred strain. In addition the human ortholog XRCC5 is also associated with ethanol-induced loss of righting response.

Pcsk2 (81.4 cM), Slc22a4 (28 cM), and Rassf2 were identified as candidate genes for Lore2 (85 cM) on mouse Chromosome 2. Pcsk2 and Slc22a4 exhibit 2.9-fold and 2.4-fold increased expression in LS compared to SS, respectively, whereas Rassf2 exhibits 2.4-fold increased expression in SS compared to LS. Two polymorphisms were detected in the promoter region of Slc22a4, one of which disrupts a putative SP-1 transcription factor binding site in the SS sequence. In addition, the human ortholog SLC22A4 is associated with ethanol-induced loss of righting response in humans. Six polymorphisms were detected in the Rassf2 promoter, two of which disrupt putative SP-1 transcription factor binding sites in the SS sequence.

Myo1d (46 cM), BG075643 (a cDNA clone), Ebf1 (20 cM), Stx8, Tax1bp3, and Tnfaip1 (45 cM) were identified as candidate genes for Lore4 (49 cM) on mouse Chromosome 11. Myo1d and BG075643 are expressed 6.2-fold higher in LS compared to SS strains.Ebf1 is expressed 2.1-fold higher, Stx8 is expressed 2-fold higher, Tax1bp3 is expressed 2.2-fold higher, and Tnfaip1 is expressed 2-fold higher in SS compared to LS strains. The Stx8 promoter sequence has 2 polymorphisms between LS and SS, and the Tax1bp3 promoter sequence has 4 polymorphisms, one of which results in disruption of a putative NF-kB transcription factor binding site in the LS strain.

Cthrc1, Krt2-8 (58.9 cM), Lgals2, Scrt1, and Atf1 were identified as candidate genes for Lore5 (46 cM) onmouse Chromosome 15. Atf1 is expressed 2-fold higher in SS compared to LS strains. Cthrc1 (3.2-fold), Krt2-8 (2.3-fold), Lga1s2 (2-fold), and Scrt1 (2.4-fold) are expressed higher in LS compared to SS strains.

Mapping and Phenotype information for this QTL, its variants and associated markers

J:38534

A large (LSxSS)F2 intercross was used to confirm QTLs involved in ethanol-induced sleep time and identify new QTLs. The LS (long sleep) inbred strain sleeps an average of 2 hours when administered an intraperitoneal ethanol injection. In contrast, the SS(short sleep) inbred strain sleeps an average of 10 minutes when administered an intraperitoneal ethanol injection. Lore1, previously identified in 27 LSxSS RI (recombinant inbred) strains (Bennett, J:40119), was confirmed in this study on mouse chromosome 1 spanning 43 cM - 59 cM (peak LOD = 5.4 at 54 cM). Possible candidate genes in this region are Chrnd (Acrd-acetylcholine receptor subunit delta) and Chrng (Acrg-acetylcholine receptor subunit gamma) at 52.3 cM. Lore2 on chromosome 2 spanning 78 cM - 95 cM (peak LOD = 6.6 at 85 cM) was also confirmed. A possible candidate gene for Lore2 is Ntsr at 107 cM on chromosome 2. New QTLs Lore3 (chromosome 8 spanning 44 cM - 71 cM, peak LOD = 3.4 at 59 cM), Lore4 (chromosome 11 spanning 44 cM - 56 cM, peak LOD = 6.5 at 49 cM), and Lore5 (chromosome 15 spanning 32 cM - 55 cM, peak LOD = 4.0 at 46 cM) were mapped. Suggestive QTLs Lore6 mapped to chromosome 18 (spanning 24 cM - tel, peak LOD = 1.8 at 41 cM) and Lore7 mapped to chromosome 7 (spanning 25 cM - 61 cM,peak LOD = 1.7 at 50 cM). Lore1 - Lore7 are inherited in an additive fashion. Lore1, Lore2, Lore4, and Lore5 map near QTLs associated with NT (neurotensin) receptor density. No evidence of epistasis between Lore1 - Lore7 was detected. Loci associated with blood ethanol concentration (BEC) were also analyzed in the (LSxSS)F2 population. SS mice wake with higher BEC than LS mice. 6 putative BEC QTLs (LOD = 2.0 - 3.0) were identified on chromosomes 2, 8, 9, 22, 14, and 15, and will be further analyzed for confirmation.

J:52088

Authors construct several lines of speed congenics using the QMACS (QTL-Marker-Assisted Counter Selection) strategy to confirm previously mapped QTLs associated with hypnotic sensitivity to ethanol (Markel, J:38534). Each Lore QTL was separately backcrossed onto either the inbred short sleep (ISS) background or the inbred long sleep background (ILS) for 6-8 generations. Lore1, Lore2, Lore4, and Lore5 were confirmed using this strategy. Lore3, a suggestive QTL, appears to have been lost. Significance scores for each congenic line Lore QTL are as follows: Lore1 on mouse chromosome 1 at 54 cM, P = 0.01; Lore2 on mouse chromosome 2 at 85 cM, P = 0.006; Lore4 on mouse chromosome 11 at 49 cM, P = 0.0008; and Lore5 on mouse chromosome 15 at 46 cM, P = 0.003.

J:114558

Analysis of 75 LXS (L= LS long sleep inbred strain; S=SS short sleep inbred strain) recombinant inbred strains replicated and confirmed previously identified QTLs associated with ethanol-induced loss or righting reflex Lore1, Lore3, Lore4, Lore5, and Lore6. Animals were tested for loss of righting reflex (n=952) and blood ethanol concentration after i.p. injection (n=814) between 55-65 days of age. Over 4000 polymorphic SNPs were used for genotype analysis. Three different methods of QTL mapping were employed: R/qtl, QTL Cartographer, and WebQTL. No sex-specific loci were identified.

Lore1 at 54 cM on mouse Chromosome 1 was replicated, however there is evidence for a second linked locus more distal between 103 Mb - 173 Mb (LOD=2.8). This new locus isdesignated Lore9 (loss of righting induced by ethanol 9). Lore9 appears to have a stronger effect in females compared to males.

A suggestive locus on mouse Chromosome 3 from a previous study was replicated in the present study at approximately 62 cM or133 Mb - 151.7 Mb (LOD=3.28). This locus is named Lore10 (loss of righting induced by ethanol 10) and maps near D3Mit127 (70.3 cM) and D3Mit86 (76.2 cM). Lore10 appears to have a stronger effect in males compared to females.

Lore3 at 59 cM on mouse Chromosome 8 was replicated in this study and the QTL interval was narrowed to 102 Mb - 128.3 Mb using SNP analysis. Slc6a2 (formerly NET; 45 cM) is a strong candidate gene for Lore3 as exons 4 and 11 are polymorphic between parental strains LS and SS.

Haplotype analysis excluded Slc6a4 (42 cM) as a potential candidate gene for Lore4 (49 cM) on mouse Chromosome 11.

Linkage to loss of righting reflex mapped to 71 Mb - 97.7 Mb on mouse Chromosome 14 in the current study (LOD=2.77). This locus is designated Lore11 (loss of righting induced by ethanol 11). Lore11 is associated with DNA markers D14Mit228 (46 cM) and D14Mit97 (58 cM).

Lore6 on mouse Chromosome 18 was replicated in this study and the QTL interval was narrowed to 77 Mb - 89.2 Mb using SNP analysis.

J:151159

A multistage mapping strategy involving Long sleep (LS) and short-sleep (SS) mice was employed to refine the QTL mapping of Lore1, Lore2, Lore4 and Lore5. ( see Table 1 of text)

Using 39 progeny from ISCS (Interval-specific congenic strains) lines 11, 4and 13 the mapping of Lore1 was refined to a region of mouse Chromosome 1 bounded by D1Mit180 and D1Mit192.

Using 79 progeny from ISCS (Interval-specific congenic strains) lines 10, 14, 2 and 5 the mapping of Lore2 was refined to a region of mouse Chromosome 2 bounded by D2Mit403 and D2Mit457.

Using 24 progeny from ISCS (Interval-specific congenic strains) lines 9 and 1 the mapping of Lore4 was refined to a region of mouse Chromosome 11 bounded by D11Mit40 and D11Mit258.

Using 38 progeny from ISCS (Interval-specific congenic strains) lines 2 and 11 the mapping of Lore5 was refined to a region of mouse Chromosome 15 bounded by D15Mit84 and D15Mit121.

The evidence for these mappings are shown figuratively in figs 2-5 of the text.

References

• Original: J:76104 Bennett B, et al., Reciprocal congenics defining individual quantitative trait Loci for sedative/hypnotic sensitivity to ethanol. Alcohol Clin Exp Res. 2002 Feb;26(2):149-57
• All: 2 reference(s)