The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution

Höglund, Andrey; Strempfl, Katharina; Fogelholm, Jesper; Wright, Dominic; Henriksen, Rie

doi:10.1186/s12864-020-06908-0

Table 2 Cerebrum eQTL CI overlapping with phenotypic QTL CI

From: The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution

Gene Name	Gene location	Trait	P-value	NEO
Gene Name	Gene location	Trait	P-value	Threshold	Edge	leo.nb.oca	leo.nb.cpa	Model	Overlap
PCBD2	chr13:16352132–16368162	Body mass	0.005	Distal	probeset - > trait	0.421	0.947	0.138	chr4@269–286 \| chr6@195–214
603848039F1	EST	Body mass	0.04	Distal	probeset - > trait	0.756	0.706	0.0254	chr4@265–332 \| chr24@6–18
MTF2 ^a	chr8:12939656–12962759	Absolute cerebrum size	0.018	Local	probeset - > trait	0.331	0.366	0.00000278	chr8@79–123 \| chr8@42–89
603231821F1	EST	Body mass	0.001***	NS	probeset - > trait	0.216	0.593	1.18E-09	chr12@43–65 \| chr12@45–79
603231821F1	EST	Body mass	0.004***	NS	probeset - > trait	−1.84	0.149	1.32E-09	chr4@270–285 \| chr4@254–274
GIP	chr27:6090482–6098133	Body mass	0.005***	NS	probeset - > trait	−1.62	−1.62	0.0175	chr27@60–86 \| chr27@56–80
ENSGALG00000034065	chr4:83916252–83928157	Body mass	0.005***	NS	probeset - > trait	0.00701	0.0012	8.4E-42	chr1@480–534 \| chr1@507–516
SCFD2	chr4:65762016–65941747	Body mass	0.011***	NS	trait - > probeset	−3.27	−0.0137	1.09E-12	chr4@250–290 \| chr4@254–274
EPAS1	chr3:26671415–26746226	Relative optic tectum size	0.014	NS	trait - > probeset	−2.86	−0.0183	0.0000187	chr4@219–252 \| chr4@201–223
NDUFAF2	chrZ:18970571–19017369	Body mass	0.015	NS	probeset - > trait	−2.37	0.287	1.44E-22	chr4@245–274 \| chr4@254–274
PNPLA8	chr1:28651041–28685420	Relative cerebrum size	0.017	NS	probeset - > trait	0.673	0.11	1.04E-28	chr21@4–35 \| chr21@0–19
FAM161B	chr5:37899536–37906784	Body mass	0.022	NS	probeset - > trait	−0.7	−0.7	0.0899	chr4@251–274 \| chr4@254–274
HDAC11	chr12:6100521–6125075	Body mass	0.025	NS	probeset - > trait	0.368	0.269	8.15E-09	chr12@24–72 \| chr12@45–79
HMCES	chr12:9520459–9523459	Body mass	0.037	NS	probeset - > trait	0.01	0.16	0.371	chr12@77–181 \| chr12@45–79
C12orf43	chr15:9385682–9389695	Body mass	0.04	NS	probeset - > trait	−1.03	0.107	1.15E-10	chr4@265–284 \| chr4@254–274

^a Gene retired in galgal6. gene name and location found in galgal4 *** P-values significant after multiple testing correction. In the neo-threshold: distal - the loci of the phenotypic QTL are all tested against the single loci of the eQTL when at least one of the phenotypic QTL loci is overlapping with the eQTL

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ISSN: 1471-2164

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