Table 1 Overview of fat gene transcription profiling in congenic strains of the GK rat
Replicated GK vs. BNReplicated eQTL
Congenic NameGene DensityTotal DEGsTranscriptional FootprintDEGs in Congenic Intervals, %N%N (%)Replicated cis-eQTL
BN.GK1b203 (128)12576.2012 (1.0)120 (3)9.5 (2.5)179 (14)6
BN.GK1d24 (11)123951.711 (0.1)76 (0)6.1 (0)171 (14)0
BN.GK1f394 (224)8742.2421 (2.3)77 (7)8.7 (9.1)148 (17)8
BN.GK1h994 (620)10391.0546 (4.4)92 (15)8.8 (16.3)176 (17)23
BN.GK1p1407 (812)13510.9658 (4.3)132 (20)9.7 (15.2)268 (20)155
BN.GK1q90 (45)94710.572 (0.2)54 (0)5.7 (0)148 (16)2
BN.GK1t9 (4)47152.560 (0)30 (0)6.3 (0)88 (19)0
BN.GK1u541 (363)13372.4819 (1.3)114 (9)8.5 (7.9)196 (15)11
BN.GK1v210 (49)9314.456 (0.6)55 (2)5.9 (3.6)122 (13)28
BN.GK2c1243 (627)1010.0827 (26.7)33 (16)32.7 (48.5)36 (36)28
BN.GK4b1578 (812)2320.1526 (11.1)45 (13)19.2 (28.9)49 (21)26
BN.GK5a511 (275)940.189 (9.6)18 (6)19.1 (33.3)17 (18)10
BN.GK5c259 (112)5572.1512 (2.2)44 (6)7.9 (13.6)67 (12)5
BN.GK7a576 (345)910.1613 (14.3)30 (8)33.0 (26.7)30 (33)14
BN.GK7d275 (151)730.274 (5.5)9 (2)12.3 (22.2)13 (18)5
BN.GK8b448 (259)3120.718 (2.5)36 (5)11.3 (13.9)25 (8)7
BN.GK10a1432 (870)2940.2138 (12.9)34 (12)11.6 (35.3)50 (17)25
GK.BN7a1014 (580)540.0511 (20.4)19 (6)35.2 (31.6)16 (30)12
GK.BN81149 (675)4860.4232 (6.6)74 (12)15.2 (16.2)71 (15)19
GK.BN10_7a2166 (1276)1400.0739 (27.7)49 (22)34.8 (44.9)54 (38)40
  • Gene density indicates the number of genes localized in the congenic interval and in parentheses those represented on the Illumina BeadChip. Transcriptome data were analyzed to identify differentially expressed genes (DEGs) (P < 0.05) in BN.GK and GK.BN congenic series when compared to BN and GK controls, respectively. The transcriptional regulatory footprint of each congenic region was calculated as the ratio of the total number of DEGs between congenics and control to the number of genes localized in the corresponding congenic interval. The number and percentage of DEGs localized in each congenic interval were determined. Replication of expression changes in parental strains and in congenics was evaluated by the number (N) and percentage of genes found consistently differentially expressed (same direction of expression change) between congenic and controls and between GK and BN, including those localized in congenic intervals (in parentheses). Replicated eQTL effects correspond to DEG between congenic and controls that are linked to eQTLs showing consistent direction of expression changes mediated by GK alleles in the F2 rats and in congenics. Cis eQTLs replicated in congenics are shown. Full details of individual DEG in inbred strains (GK, BN, and congenics) and eQTLs are given in Table S4