Table 3 Details of the 22 common_CNVRs identified in all three Buffalo breeds. Number of samples together with annotated genes and QTL_Terms (Trait Names) and IDs – traits are also reported. QTL are in concordance with Animal Genome Cattle QTL Database

chr1

26,703,602

26,982,884

gain

84

65

15

4

chr1

152,804,323

152,948,116

loss

28

21

5

2

LOC102407618

chr2

3,733,628

4,072,437

complex

29

19

7

3

LY86

chr2

101,529,318

101,684,916

complex

23

13

8

2

chr3

31,955,474

32,522,879

complex

84

53

29

2

ELAC2, ARHGAP44, MYOCD

chr3

114,751,926

114,833,959

loss

40

23

15

2

PCSK5

chr4

153,409,610

153,553,690

complex

38

27

8

3

chr5

56,890,564

57,111,573

loss

63

36

25

2

HLX, MARC1, MARC2

chr5

33,931,170

34,500,134

complex

35

24

9

2

RPL22, RNF207, ICMT, HES3, GPR153, ACOT7, HES2, ESPN, TNFRSF25, PLEKHG5, NOL9, TAS1R1, ZBTB48, KLHL21, PHF13, THAP3, DNAJC11, CAMTA1

ACOT7: Somatic cell score – QTL:157327; TAS1R1: Height (24 months) – QTL:20633, 20,630; Hip height – QTL:20629, 20,631.

chr6

10,583,089

11,004,788

loss

30

16

8

6

LOC102415566, LOC102415903, LOC102416230, LOC102416552, LOC102389114, LOC102389455, LOC102413384, SPTA1, LOC102414242, LOC112585453, LOC102391442, LOC102414573, LOC102391758

chr7

78,061,564

78,226,918

loss

55

35

18

2

chr7

102,880,560

103,212,455

complex

23

14

7

2

chr8

38,899,124

39,035,018

gain

157

91

52

14

chr11

78,128,432

80,062,848

complex

59

31

21

7

LOC102389658 (ADSL-like), LOC112587962

chr13

14,124,616

17,645,807

complex

209

150

50

9

CLDN10, ABCC4-like, OCIA-like

chr13

26,851,401

27,052,499

complex

39

29

8

2

chr14

52,975,663

53,315,557

complex

75

43

26

6

chr14

67,343,425

67,561,999

complex

55

38

15

2

LOC102389323, ECHDC3, USP6NL

chr16

49,791,674

50,216,803

complex

131

101

23

7

ABCC8, USH1C, MYOD1, OTOG, KCNC1, SERGEF

chr18

60,924,568

61,091,446

loss

69

44

18

7

cationic amino acid transporter 3-like

chr21

54,520,603

54,985,963

complex

36

15

19

2

SLC6A11, ATP2B2

chr24

37,455,258

37,684,596

complex

23

15

6

2

RBFOX1

RBFOX1: Dopamine level – QTL:194894, 194,895, 194,896; Sperm counts – QTL:62089.