Table 3 Top five associated genes per chromosome for each trait: average daily gain (ADG), backfat thickness (BFT), meat to fat ratio (MFR), and carcass length (CRCL). Gene type in brackets. The variants overlapping or in the proximity of these genes were selected not to be in high LD (r² < 0.8) with the previously associated SNPs and small indels

ADG

1

ZFAND5 (protein coding), TMC1 (protein coding)

2

AP2A2 (protein coding), ENSSSCG00000012835 (pseudogene)

4

UBE2V2 (protein coding)

7

U6 (snRNA), ENSSSCG00000044971 (lncRNA), HMGCLL1 (protein coding), PRIM2 (protein coding), COL21A1 (protein coding)

16

ENSSSCG00000050375 (protein coding), CDH10 (protein coding)

BFT

1

ENSSSCG00000048964 (lncRNA), ENSSSCG00000043016 (lncRNA), ENSSSCG00000051116 (lncRNA), TXNL1 (protein coding), ENSSSCG00000043998 (protein coding)

2

SHANK2 (protein coding), STX3 (protein coding), TNNT3 (protein coding), CBLIF (protein coding), MRPL16 (protein coding)

4

PREX2 (protein coding), CHD7 (protein coding)

7

COL21A1 (protein coding), DST (protein coding), ENSSSCG00000001612 (protein coding), PRIM2 (protein coding), ENSSSCG00000041331 (processed pseudogene)

16

ENSSSCG00000050819 (lncRNA), ISL1 (protein coding)

MFR

1

PLPP7 (protein coding), PRRC2B (protein coding), RALGPS1 (protein coding), RABGAP1 (protein coding), ASTN2 (protein coding)

2

STX3 (protein coding), CBLIF (protein coding), MRPL16 (protein coding), SHANK2 (protein coding), TNNT3 (protein coding)

4

ENSSSCG00000051273 (lncRNA), LRP12 (protein coding), CHD7 (protein coding), RAB2A (protein coding), RGS20 (protein coding)

5

VDR (protein coding), RPAP3 (protein coding)

7

COL21A1 (protein coding), ENSSSCG00000002296 (protein coding), VTI1B (protein coding), KIF6 (protein coding), ENSSSCG00000031184 (protein coding)

14

BTRC (protein coding), XKR6 (protein coding), ENSSSCG00000045361 (lncRNA), ENSSSCG00000051786 (lncRNA), ENSSSCG00000051722 (protein coding)

15

IGFBP5 (protein coding), TNP1 (protein coding)

18

HERPUD2 (protein coding), ENSSSCG00000042613 (lncRNA), AOAH (protein coding), KIAA0895 (protein coding), SND1 (protein coding)

CRCL

4

UBE2V2 (protein coding)

7

COL21A1 (protein coding), HMGCLL1 (protein coding), DAAM2 (protein coding), ZNF451 (protein coding), ENSSSCG00000044971 (lncRNA)

8

NOCT (protein coding), ENSSSCG00000049816 (lncRNA)

9

PON2 (protein coding), ASB4 (protein coding), ENSSSCG00000049806 (lncRNA), NECTIN1 (protein coding), ENSSSCG00000044947 (lncRNA)

14

ANKRD13A (protein coding), SPPL3 (protein coding), WSCD2 (protein coding), SGSM1 (protein coding)

16

ENSSSCG00000050819 (lncRNA), ISL1 (protein coding)

17

ENSSSCG00000044805 (lncRNA), PLCB4 (protein coding), ENSSSCG00000043546 (protein coding), ENSSSCG00000047884 (lncRNA), PLCB1 (protein coding)