Table 7 CNVR genes of Nguni cattle subpopulations

A B C E

2

PCDH7 CHIC2

B C E

1

ATXN7L3B

A C E

1

NXNL2

A B C

4

TNFAIP8 CTNNA3 SI LOC780933

C E

2

KCND3 ATP5G3

B E

1

ARL6

A E

17

RAB40C KLHL1 CISD1 IPMK PWWP2B MRPL28 VPREB3 DECR2 TRNT1 PCDH10 ARL4C ZNF70 NME4 CHCHD10 IGLL1 TMEM8A OTOP1

A D

2

CLRN1 LRFN5

B C

2

HPS3 LOC514194

A C

8

BICD2 CENPP ATG2B CDH12 BDKRB1 BDKRB2 ZWINT MR1

A B

11

GABRG2 PDLIM1 LOC509513 DCTD NDST4 CDH2 C28H10orf35 COL13A1 PROM1 ADCY1 TMPRSS15

E

14

GRAP2 SERPINB8 CADPS2 HERC4 ENTHD1 KCND2 PPP1R14C FKBP5 MSX1 CTSD FARS2 HTATSF1 NUP210 SORBS2

D

2

ASPH FSTL5

C

44

NUP35 URB2 HCK INSL6 PDPN PLGRKT PECAM1 ZC3H7B GDA MMS22L C6H4orf32 RHAG CPS1 TM9SF4 POFUT1 GLYATL3 SERINC1 GBE1 TM4SF18 IL1R2 C23H6orf141 CYB5R1 WBSCR17 CDH10 PHYHIPL ATF2 CNTNAP3 ADCY8 ANKRD50 CRISP2 FAM204A MRPS31 CD274 SPAM1 CELF4 KCMF1 CRISP3 HMGXB4 CDC73 KIF3B CELF2 RAB21 LACTB2 RANGAP1

B

28

KATNBL1 MPPED2 C15H11orf70 FAM5C SH3BP4 HLTF C21H14orf49 TYW3 PAQR3 CHRM5 MIR1256 GJA1 RPL37A GPC5 CLN5 UBE2U OXR1 FAM98A COX7C SMAD4 ACSL1 LPHN2 TNNI3K CRYZ EMC7 PET112 DHX29 CADM1

A

149

TBC1D19 PTGER3 SEC62 LOC527441 NR3C2 CA8 PFKP DDT STUB1 GGT1 AMPH FBXL16 WDR24 C15H11orf96 PRKAR2B TMEM128 RPUSD1 FAF1 NPRL3 LARGE GRB10 AXIN1 LUC7L C11H2orf28 PDIA2 PROP1 MSLN PLEKHA3 NOL4 PDGFD LYAR SPECC1L RNF185 AMY2B SUSD2 QRFPR POLR3K RFC3 ARL4A ACSL6 WFIKKN1 CLN8 ACYP2 SLC22A18 GBA3 MIR2390 FUBP3 SLC5A1 SNRPD3 C25H16orf13 SELM FGGY OTX2 KCTD16 PTGS2 CARD11 C1QTNF7 ARHGDIG DDI1 HAGHL MIF NAP1L4 MTRR H2AFY2 ALX1 ERICH1 CHTF18 FGF9 WDR1 PLEKHA1 GNG13 SRSF6 RRAGC ADIG SEMA3A UPB1 FZD1 SORCS3 NARFL LUZP2 SMARCB1 C15H11orf58 HBA SELPLG BCHE ZNF703 TMEM119 HBQ1 RGS11 MGAT4C LIN7C ITFG3 LMF1 OSTN TMEM225 GSTT4 ASS1 NRG3 ALKBH3 STAB2 CTXN3 RHBDF1 PATZ1 C21H14orf2 SNRNP25 INO80D PRR5L DRG1 ZBTB49 C17H22orf13 SLC25A21 METRN FAM173A ZNF280A KCNJ3 RHOT2 ST6GAL2 PPAP2B INPP5J GSTT3 GSTT1 QTRTD1 GGT5 HTRA1 CARS SEMA3C LOC615200 SOX2 CFTR ZNF280B PHLDA2 LPHN3 LYPLAL1 HBM LSAMP NXPH2 KCNQ1 LIMK2 SLC2A11 FAM195A GRIN3A CDKN1C DRD1 AGPAT9 PIK3IP1 DERL3 SMTN LOC516108 XRCC2