Table 4 Candidate genes of surround runs of homozygosity island in Alpine and Mediterranean goats’ breeds

Alpine breeds:

 SAA

  6

86,056,773

86,076,276

51.11

-

  8

74,702,203

75,024,344

58.37

B4GALT1, U1, SPINK4, CHMP5, NFX1, AQP3, NOL6, UBE2R2

  11

78,348,517

78,577,786

54.56

SDC1, LAPTM4A, MATN3, WDR35

  12

50,102,227

50,675,369

53.2

ATP12A, RNF17, CENPJ, PARP4, MPHOSPH8, PSPC1, ZMYM5, ZMYM2, GJA3

  13

46,023,812

46,329,866

82.48

DIP2C, U6, SNORD31, ZMYND11

 CAM

  6

85,882,277

86,076,276

57.49

SULT1E1

  8

74,508,923

75,367,980

76.63

APTX, SMU1, B4GALT1, U1, SPINK4, CHMP5, NFX1, AQP3, NOL6, UBE2R2, UBAP2, SNORD121A, DCAF12, U6

  11

78,418,240

78,577,786

54.44

LAPTM4A, MATN3, WDR35

  12

50,221,647

50,675,369

53.53

RNF17, CENPJ, PARP4, MPHOSPH8, PSPC1, ZMYM5, ZMYM2, GJA3

  13

45,944,824

46,174,021

71.43

DIPC, U6

  13

52,782,768

53,376,104

53.73

GINS1, MYT1, NPBWR2, OPRL1, LKAAEAR1, RGS19, TCEA2, SOX18, PRPF6, U6, SAMD10, ZNF512B, UCKL1, TPD52L2, ABHD16B, ZBTB46, SLC2A4RG, ZGPAT, ARFRP1

  14

81,319,132

81,451,654

60.60

HSF1, DGAT1, SCRT1, TMEM249, FBXL6, SLC52A1, ADCK5, CPSF1, SLC39A4, VPS28, TONSL, ZFTRAF1

Mediterranean breeds:

 MUR

  6

86,011,549

86,081,135

58.47

-

  8

74,663,065

74,934,130

55.32

B4GALT1, U1, SPINK4, CHMP5, NFX1

  12

60,040,786

61,020,592

67.99

NBEA, MAB21L1

  13

45,868,691

46,454,224

80.16

LARP4B, DIP2C, U6, SNORD31, ZMYND11

  14

81,210,832

81,333,756

53.66

MAF1, HGH1, MROH1, BOP1, SCX, HSF1, DGAT1

  15

29,223,207

30,497,267

58.21

KCNE3, PGM2L1, P4HA3, PPME1, C2CD3, UCP3, UCP2, DNAJB13, PAAF1, COA4, MRPL48, RAB6A, PLEKHB1, FAM168A, U6, RELT, ARHGEF17, P2RY6, P2RY2, FCHSD2

  19

26,662,281

27,074,257

58.53

ASGR2, ASGR1, DLG4, ACADVL, MIR324, DVL2, PHF23, GABARAP, CTDNEP1, ELP5, CLDN7, SLC2A4, YBX2, GPS2, NEURL4, ACAP1, TMEM95, TNK1, PLSCR3, TMEM256, NLGN2, SPEM1, SPEM2, TMEM102, FGF11, CHRNB1, ZBTB4, POLR2A, TNFSF12, TNFSF13, SENP3, EIF4A1, SNORA48, SNORD10, CD68, MPDU1, SOX15, FXR2

 MAL

  6

36,585,519

36,982,281

58.23

HERC3, NAP1L5, PYURF, HERC5, HERC6, PPM1K

  6

83,526,335

84,218,404

51.27

CENPC, STAP1, UBA6, GNRHR

  12

50,554,041

51,186,124

54.36

ZMYM2, GJA3, GJB2, GJB6, CRYL1, IFT88, IL17D, EEF1AKMT1, XPO4, LATS2, SAP18, ZDHHC20

  13

45,944,824

46,196,889

85.62

DIP2C, U6

  14

81,297,625

81,478,514

61.36

BOP1, HSF1, DGAT1, SCRT1, TMEM249, FBXL6, SLC52A1, ADCK5, CPSF1, SLC39A4, VPS28, TONSL, ZFTRAF1, KIFC2, FOXH1

  19

26,662,281

26,986,682

58.31

ASGR2, ASGR1, DLG4, ACADVL, MIR324, DVL2, PHF23, GABARAP, CTDNEP1, ELP5, CLDN7, SLC2A4, YBX2, GPS2, NEURL4, ACAP1, TMEM95, TNK1, PLSCR3, TMEM256, NLGN2, SPEM1, SPEM2, TMEM102, FGF11, CHRNB1, ZBTB4, POLR2A|

  29

45,698,809

46,067,919

53.91

PNPLA2, RPLP2, SNORA52, PIDD1, SLC25A22, CEND1, GATD1, EPS8L2, TMEM80, DEAF1, DRD4, 5S_rRNA, CDHR5, IRF7, PHRF1, RASSF7, PGGHG, IFITM5, HRAS, RNH1, PTDSS2, ANO9, SIGIRR

 SAR

  6

86,013,561

86,080,969

56.72

-

  10

54,961,457

55,210,193

56.84

VPS13C, U6

  12

50,253,456

50,813,808

58.07

CENPJ, PARP4, MPHOSPH8, PSPC1, ZMYM5, ZMYM2, GJA3, GJB2, GJB6, CRYL1

  13

45,868,691

46,368,408

82.05

LARP4B, DIP2C, U6, SNORD31, ZMYND11

  14

16,887,785

17,689,652

50.05

OSR2, MIR599, SNORA70

  14

81,091,465

81,458,794

50.02

PARP10, GRINA, SPATC1, OPLAH, EXOSC4, GPAA1, CYC1, SHARPIN, MAF1, HGH1, MROH1, BOP1, SCX, HSF1, DGAT1, SCRT1, TMEM249, FBXL6, SLC52A1, ADCK5, CPSF1, SLC39A4, VPS28, TONSL, ZFTRAF1, KIFC2

  19

26,610,610

26,907,844

55.82

RNASEK, C17orf49, chi-mir-195, chi-mir-497, BCL6B, SLC16A13, SLC16A11, ASGR2, ASGR1, DLG4, ACADVL, MIR324, DVL2, PHF23, GABARAP, CTDNEP1, ELP5, CLDN7, SLC2A4, YBX2, GPS2, NEURL4, ACAP1, TMEM95, TNK1, PLSCR3, TMEM256, NLGN2