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The Hybrid Rat Diversity Panel

The Hybrid Rat Diversity Panel

The Hybrid Rat Diversity Panel (HRDP) is a panel of 96 inbred rat strains carefully chosen to maximize power to detect specific genetic loci associated with a complex trait and to maximize the genetic diversity among strains. The HRDP includes 33 genetically diverse inbred strains of rat and two panels of recombinant inbred rat strains, the FXLE/LEXF (33 strains) from Japan and the HXB/BXH (30 strains) from the Czech Republic. Recombinant inbred strains are panels of inbred strains derived from two inbred parental rat strains. The two parental strains are crossed to produce F1 pups. F1 pups are subsequently intercrossed to create an F2 generation. These genetically unique F2 generation rats are paired as founders and brother-sister mated for at least 20 generations to fix their genomes. The two RI panels used in the HRDP have been well characterized through studies focused on seizures, epilepsy, lymphoma and leukemia, blood pressure regulation, metabolic syndrome, and alcohol consumption.

The HXB/BXH recombinant inbred strains were derived from the Spontaneously Hypertensive Rat (SHR/Olalpcv) and the normotensive BN-Lx (BN-Lx/Cub), a Brown Norway congenic rat strain with polydactyly-luxate syndrome. The FXLE x LEXF recombinant inbred strains were derived from the Long Evans strain (LE/Stm) and the Fischer F344 strain (F344/Stm).

Notes:

  • In the tables below, an asterisk (*) designates that the tagged strain has been sequenced. The VCF files for these (48 strains in total) are available for download. These data have been mapped to both Rn6 and Rn7 and can be accessed here.
  • The double dagger icons () designate the strains that have been found by whole genome sequence comparison to be the most genetically similar to the Heterogeneous Stock (HS) Founder Strains. This data is courtesy of Dr. Abraham Palmer (University of California, San Diego) and Dr. Hao Chen (University of Tennessee Health Sciences Center). For more information about the HS Founders and the HRDP strains that are similar to them, click here.
  • The inbred Wistar WN/N strain is no longer available and no closely related substrains are included in the HRDP panel. However, DNA from a frozen tissue sample from the original NIH strain has been sequenced and that sequence compared to WGS from the HRDP strains. Of the strains currently available from the HRDP, the one found in this analysis to be most closely related to WN/N is WAG/RijCrl with a sequence similarity of approximately 76%.

 


The strains included in the HRDP panel are:

Divergent Classic Inbred Strains
Strain RGD ID Strain RGD ID Strain RGD ID
ACI/EurMcwi* ‡ 7364991 HTX/Kyo 1302600 PD/Cub 728161
BDIX/NemOda 2304285 LE/Stm* 629485 PVG/Seac* 1302722
BN/NHsdMcwi* ‡ 61498 LEW/Crl* 737932 RCS/LavRrrc 1358258
BN-Lx/Cub* 61117 LH/MavRrrc* 60990 SBH/Ygl 631572
BUF/Mna* ‡ 61118 LL/MavRrrc* 68077 SBN/Ygl 631573
COP/CrCrl 1358153 LN/MavRrrc* 61015 SHR/OlaIpcv* 631848
DA/OlaHsd* 734475 LOU/MNCr 9999143 SHRSP/A3NCrl* 2311051
F344/DuCrl* ‡ 734478 M520/N* ‡ 10024 SR/JrHsd* 1582184
F344/Stm* 1302686 MNS/N 2307319 SS/JrHsdMcwi* 61499
FHH/EurMcwi* 629509 MR/N* ‡ 70449 WAG/RijCrl* ‡ 2312498
GK/FarMcwi* 10395297 MWF/Hsd* 737906 WKY/NCrl* ‡ 1358112

 

 

SHR and BN-Lx derived RI strains Long Evans and F344 derived RI strains
Strain RGD ID Strain RGD ID Strain RGD ID Strain RGD ID
BXH/lpcv RI panel 61098 HXB/lpcv RI panel 61099 FXLE/Stm RI panel 7244374 LEXF/Stm RI panel 629500
BXH2/CubMcwi* 149735530 HXB1/Ipcv 2307094 FXLE12/Stm 1302602 LEXF1A/Stm* 1302641
BXH3/CubMcwi* 149735533 HXB-1-43/Ipcv 68049 FXLE13/Stm 1302665 LEXF1B/Stm 4140413
BXH5/Cub 2307115 HXB2/IpcvMcwi* 149735520 FXLE14/Stm 1302615 LEXF1C/Stm* 1302666
BXH6/Cub 2307136 HXB3/Ipcv 2307079 FXLE15/Stm 1302673 LEXF1D/Stm 4140412
BXH8/Cub 2307126 HXB4/IpcvMcwi* 149735518 FXLE16/Stm* 1302619 LEXF2A/Stm 1302605
BXH9/Cub 2307129 HXB5/Ipcv 2307099 FXLE17/Stm 1302708 LEXF2B/Stm* 1302710
BXH10/Cub 2307124 HXB7/Ipcv 2307086 FXLE18/Stm* 1302682 LEXF2C/Stm 1302646
BXH11/Cub 2307127 HXB10/IpcvMcwi* 38549351 FXLE19/Stm 1302690 LEXF2D/Stm 7349321
BXH12-1/Cub 2307139 HXB13/Ipcv 2307091 FXLE20/Stm 1302633 LEXF3/Stm* 1302707
BXH12-2/Cub 2307133 HXB14/Ipcv 2307092 FXLE21/Stm 1302607 LEXF4/Stm* 1302604
BXH13/Cub 2307123 HXB15/Ipcv 2307095 FXLE22/Stm 1302683 LEXF5/Stm 1302723
    HXB17/Ipcv 2307085 FXLE23/Stm 1302601 LEXF6A/Stm 4140405
    HXB18/Ipcv 2307082 FXLE24/Stm 1302611 LEXF6B/Stm 1302617
    HXB20/IpcvMcwi* 149735521 FXLE25/Stm 1302603 LEXF7A/Stm 1302652
    HXB21/Ipcv 2307097 FXLE26/Stm 1302598 LEXF7B/Stm 1302649
    HXB22/Ipcv 2307088     LEXF7C/Stm 1302597
    HXB23/Ipcv 2307093     LEXF8A/Stm 1302653
    HXB24/Ipcv 2307084     LEXF8B/Stm 7349322
    HXB25/Ipcv 2307098     LEXF8C/Stm 4140408
    HXB27/Ipcv 2307078     LEXF8D/Stm 1302699
    HXB29/Ipcv 2307089     LEXF9/Stm 1302618
    HXB31/IpcvMcwi* 149735519     LEXF10A/StmMcwi* 149735517
            LEXF10B/Stm 1302616
            LEXF10C/Stm 1302612
            LEXF11/Stm* 1302638


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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.