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Table 2 QTL regions for meat tenderness detected using haplotype-based analysis on variable-sized sliding windows

From: Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle

BTA

Region

Position (bp)

Dist

LD

Additive genetic variance (kg2)

SNP

SW3

SW5

SW7

SW9

SW11

1

rs43761056 – rs137207255

6,317,864 – 6,324,488

6625

M

–

0.032

0.036

–

–

–

1

rs42493480 – rs42493494

125,981,534 – 126,011,455

29,922

M

–

–

0.031

0.034

0.038

–

3

rs109872503 – rs110244139

7,371,235 – 7,460,489

89,255

M

0.072

0.098

0.071

0.085

0.086

0.089

3

rs132795858 – rs134534136

29,474,206 – 29,610,884

136,679

S

–

0.038

0.049

0.051

0.051

0.050

3

rs132763845 – rs109427593

90,594,180 – 90,664,268

70,089

M

–

–

–

0.036

0.045

–

3

rs134111725 – rs133976586

93,949,186 – 94,067,553

118,368

S

–

–

–

–

–

0.040

4

rs43490295

1,008,553

–

N

0.028

–

–

–

–

–

4

rs137252969 – rs43385178

24,143,662 – 24,225,606

81,945

W

–

–

0.037

–

–

–

4

rs110513194 – rs135604613

27,834,564 – 27,894,006

59,443

S

–

–

–

–

0.042

–

5

rs136407209 – rs110430223

7,525,121 – 7,583,435

58,315

S

–

–

0.030

–

–

–

5

rs41587994 – rs109349300

18,434,417 – 18,465,179

30,763

S

–

0.036

0.034

–

–

–

8

rs133253155 – rs135484797

92,216,117 – 92,289,515

73,399

S

–

0.033

0.034

0.033

–

–

9

rs137367597

1,116,610

–

N

0.028

–

–

–

–

–

9

rs110938040 – rs135589084

12,339,368 – 12,406,450

67,083

M

–

–

–

–

0.048

0.053

9

rs136867942 – rs135252570

21,441,424 – 21,497,606

56,183

M

–

–

–

–

0.037

–

9

rs133390891 – rs43600182

61,168,282 – 61,197,874

29,593

S

–

–

0.037

–

–

–

9

rs110730224 – rs109847831

66,977,872 – 67,045,614

67,743

M

–

0.040

0.039

0.040

0.040

–

9

rs135160781 – rs110936646

100,716,451 – 100,721,452

5002

S

–

0.034

–

–

–

–

10

rs137812088 – rs133615734

20,448,593 – 20,541,764

93,172

M

0.063

0.040

0.041

0.038

0.044

0.052

10

rs134006987 – rs136312573

43,692,759 – 43,726,489

33,731

S

–

0.033

0.031

–

–

–

11

rs109122230 – rs41655045

5,751,331 – 5,768,629

17,318

M

–

0.033

–

–

–

–

11

rs43755797 – rs137032372

43,129,117 – 43,135,745

6629

M

–

0.032

–

–

–

–

11

rs136174419 – rs42731923

50,332,078 – 50,417,494

85,417

S

0.032

0.069

–

–

–

–

15

rs132639440 – rs136091960

72,439,829 – 72,470,564

30,736

M

–

–

0.036

0.040

0.051

–

17

rs110304377 – rs42926409

70,788,438 – 70,935,589

147,152

M

–

0.035

0.043

0.054

0.056

–

18

rs137081181 – rs134146295

14,849,540 – 14,991,573

142,034

S

–

0.039

0.041

0.043

0.043

0.045

24

rs135709192 – rs136715705

47,570,379 – 47,596,815

26,437

S

–

0.033

0.033

0.034

0.034

0.034

24

rs110779214 – rs109148899

48,585,933 – 48,632,298

46,366

S

–

0.038

0.038

–

–

–

24

rs136382747– rs135235176

55,868,854 – 55,975,740

106,887

M

–

–

–

0.040

–

–

25

rs110607501 – rs108984883

17,590,025 – 17,598,054

8030

S

–

0.033

0.034

0.034

–

–

26

rs133176306 – rs109605337

19,035,737 – 19,066,768

31,032

S

–

0.034

0.038

–

–

–

28

rs134774253 – rs42146826

26,876,269 – 26,885,074

8806

S

–

0.033

–

–

–

–

29

rs136755211 – rs42192064

43,980,089 – 44,042,363

62,275

S

–

–

0.032

0.032

–

–

  1. BTA Bos taurus autosome, Dist distance, LD linkage disequilibrium, SNP single nucleotide polymorphism, SW Sliding window haplotype, SW3 SW of three SNPs, SW5 SW of five SNPs, SW7 SW of seven SNPs, SW9 Haplotype SW of nine SNPs, SW11 SW of eleven SNPs, S strong LD (r2 > 0.6), M moderate LD (0.2 < r2 < 0.6), W weak LD (0.1 < r2 < 0.2), N not LD (r2 < 0.1)