PARC Alcohol QTLs by Phenotype

This is a list that was developed primarily for internal use by PARC investigators. Presently it consists largely, but not solely, of QTLs discovered by PARC researchers using C57BL/6J x DBA/2J mouse cross mapping populations. It does not include QTLs for responses to other drugs. For more about “QTL Code,” see the end of this introduction.

It is arranged by phenotype, broadly defined. We have updated the peak position and range, and statistical status to date (reference is to genome wide "significance" at p < .01 or "suggestive" at p < .05, corrected for multiple comparisons).

Clicking on an individual QTL leads to more detailed information, including name, alias(es), the drug (“Alcohol” = ethanol), the broad phenotype designation, and a somewhat more detailed description of how that phenotype was assessed (“Assay”). LOD scores are typically based on df = 2 (i.e., two degrees of freedom). “Strains Tested” gives mapping populations for which data have been cumulated to test significance, which often includes selectively bred lines and/or congenic lines or strains. The sex specificity is given if known, the increaser allele identified as D2 (DBA/2J) or B6 (C57BL/6J), and dominance given if known. Where results are published, the references are given. Where unpublished, the PI's laboratory is stated. The time of the last update of the tabled information is indicated. QTL information for loss of righting reflex was obtained from Beth Bennett and Tom Johnson at the Institute for Behavior Genetics in Boulder.

QTL Code - Names and Aliases
There is now terminological confusion for many traits. We at PARC adopted early on (and have maintained) the practice of not "naming" our QTLs in the literature unless they reached Lander & Kruglyak "significant" levels. These lists also report our "suggestive" QTLs by that standard. Mouse Genome Informatics has of their own initiative named several of our published QTLs. They also assigned names to some QTLs regardless of statistical significance. They made assumptions about the phenotypes in several instances. For instance, they treated Actre QTLs mapped in the Hitzemann lab as representing the same trait as Etact QTLs mapped in the Phillips lab. Both groups assessed Alcohol Stimulated Activity, but they used different doses of ethanol and different time periods after injections. To our way of very conservative thinking, these are not the same trait. So, we list a number of aliases in our table to try to indicate what is going on. The “QTL Code” name is our new local name, and sometimes combines two earlier names. For example, the Chronic Alcohol Withdrawal QTL on chromosome 14 we originally named Caws5 was renamed by MGI as Alcw7. We now also name all suggestive QTLs using the suffix "prov" for provisional, which allows us to keep them with the same basic name, and to upgrade them later if additional data render them significant.

For additional information, contact Mark Rutledge-Gorman (rutledgm@ohsu.edu). For specific information about the traits and their assessment, and the further mapping progress, contact the individual PIs indicated.



Acute Alcohol Withdrawal

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Alcw1 1 96 cM 66-ter 172.3 - 174.0, 174.0 - 176.5 Significant
Alcw4 2 38 cM 28-53 Suggestive
Alcwprov1 2 60 cM ND Suggestive
Alcw2 4 38 cM 38-38.7 80.3 - 82.1 Significant
Alcw3 11 20 cM 16-28 34.7 - 55.9 Significant

Chronic Alcohol Withdrawal

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Alcdpprov2 1 20 cM 12-35 Suggestive
Calw1/Alcdp1 1 96 cM 89-106.3 172.3 - 191.3 Significant
Caws1/Alcw5 1 28-47 Significant
Alcdpprov3 4 37 cM 30-44 Suggestive
Caws2 4 33-51 Significant
Caws3/Alcw6 8 16-43 Significant
Caws4/Alcw3 11 15-36 Significant
Alcdpprov1 13 37 cM 16-59 Suggestive
Caws5/Alcw7 14 24-48 Significant
Calw2/Alcdp2 19 47 cM 36.5-ter 10.4 - 55.2 Significant

Alcohol Preference Drinking

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Ap1q 1 76 cM 45-95   Significant
Alcp1 2 28 cM 19-35   Significant
Etp1/Etohc1 2 28 cM   20.2 - 153.3 Significant
Etp2/Etohc2 2 49 cM     Significant
Ap2q 2 40 cM 30-50   Suggestive
Etp3 3 75 cM     Significant
Ap6q 3 45 cM 38-60   Suggestive
Etohcprov1 4 59 cM     Suggestive
Ap3q 4 75 cM 65-ter   Significant
Ap5q 9 25 cM 10-35   Significant
Etp5/Etohc3 9 29 cM   0 - 124 Significant
Ap4q 10 28 cM 18-57   Suggestive
Etohcprov2 15 43 cM     Suggestive

Alcohol Acceptance

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Aaq1/Etacc 15 30 cM 15-48   Significant

Alcohol Stimulated Activity

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Actre1/Actre1q 1 90 cM     Significant
Etact3 1 62.6 Mb     Significant
Actre7 1 113 cM     Significant
Etact1 2 51 cM 41-61 20.2 - 153.3 Significant
Actre3/Actre3q 2 60 cM     Significant
Actre2 2 56 cM     Significant
Actre4 2 65 cM     Significant
Etactprov1 2   73 - 93 cM   Suggestive
Etactprov2 3 19 cM 9-29   Suggestive
Etactprov3 3 18.8 Mb     Suggestive
Actre5 3 56 cM     Significant
Actre8 4 8 cM     Significant
Etactprov4 5 124.2 Mb     Suggestive
Etactprov5 6 36.5 Mb     Suggestive
Actre9 6 17 cM     Significant
Actre10 7 34 cM     Significant
Actre11 7 61 cM     Significant
Etactprov6 7 91.1 Mb     Suggestive
Actre12 8 48 cM     Significant
Etact2 9 113.5 Mb 51-71 cM 0 - 124 Significant
Actre6 9 52 cM     Significant
Actre13 10 51 cM     Significant
Etactprov7 10 93.3 Mb     Suggestive
Actre14 11 37 cM     Significant
Etactprov8 13 85.5 Mb     Suggestive
Actre15 14 37 cM     Significant
Actre16 15 67 cM     Significant
Etactprov9 16 6.1 Mb     Suggestive
Etactprov10 18 25 Mb     Suggestive
Actre17 19 24 cM     Significant
Actre18 X 33 cM     Significant
Actre19 X 50 cM     Significant

Alcohol Metabolism

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Et3metprov1 1 102 cM     Suggestive
Et2metprov1 3 49 cM     Suggestive
Et3becprov1 12 52 cM     Suggestive
Et3becprov2 15 39 cM     Suggestive
Et2met1/Etmr 17 6.27 cM     Significant
Et3met1/Etmr 17 6.27 cM     Significant
Et2becprov1 17 6.27 cM     Suggestive
Et3becprov3 17 6.27 cM     Suggestive

Loss of Righting Reflex

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Lore1 1   36.9-41   Significant
Lore2 2   75.6-81.7   Significant
Lore3 8   44-71   Suggestive
Lore4 11   36-42   Significant
Lore5 15   18.8-61.7   Significant

Alcohol Response Conditioning

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Etcta1/Etohcta1 1 73 cM     Significant
Etcta2/Etohcta2 4 82 cM     Significant
Etohctaprov1 6 57 cM     Suggestive
Etohctaprov2 7 36 cM     Suggestive
Etohcppprov1 7 51 cM     Suggestive
Etcpp2 8 43 cM     Provisional

Hypothermia

QTL Code Chr Peak Pos. Range (cM) Max Range (Mb) Status
Ethypprov1 5 59 cM     Suggestive