Table 2.
Haplotype association analyses for six milk production traits in buffalo
| Blocks | Haplotype | Frequency | Haplotype combination (n) | Traits (LSM ± SE) | |||||
|---|---|---|---|---|---|---|---|---|---|
| PM270/Kg | MY270/Kg | FY270/Kg | FP270/% | PY270/Kg | PP270/% | ||||
| D1.1 | H1: TA | 38.16% | H1H1 (55) | 15.4 ± 0.26 | 3073.0 ± 50.6 | 258.0 ± 4.6 | 8.40 ± 0.09 | 144.0 ± 2.2 | 4.67 ± 0.03 |
| H2: TT | 31.23% | H1H2 (106) | 15.0 ± 0.19 | 3007.0 ± 37.7 | 243.0 ± 3.4 | 8.13 ± 0.07 | 139.0 ± 1.7 | 4.64 ± 0.02 | |
| H3: CA | 30.61% | H1H3 (100) | 15.2 ± 0.21 | 3073.0 ± 40.8 | 254.0 ± 3.7 | 8.31 ± 0.07 | 141.0 ± 1.8 | 4.60 ± 0.02 | |
| H2H2 (35) | 15.0 ± 0.34 | 2993.0 ± 67.0 | 247.0 ± 6.1 | 8.26 ± 0.12 | 140.0 ± 2.9 | 4.69 ± 0.03 | |||
| H2H3 (77) | 15.2 ± 0.22 | 3056.0 ± 43.3 | 251.0 ± 4.0 | 8.27 ± 0.08 | 141.0 ± 1.9 | 4.63 ± 0.02 | |||
| H3H3 (37) | 15.1 ± 0.35 | 3119.0 ± 69.8 | 263.0 ± 6.4 | 8.41 ± 0.13 | 145.0 ± 3.1 | 4.66 ± 0.04 | |||
| D1.2 | H1: AATGAC | 37.30% | H1H1 (56) | 14.9 ± 0.23 | 2976.0 ± 45.3 | 250.0 ± 4.1 | 8.43 ± 0.08a | 139.0 ± 2.0 | 4.69 ± 0.02a |
| H2: GATGGC | 25.73% | H2H1 (75) | 15.3 ± 0.19 | 3031.0 ± 37.5 | 248.0 ± 3.4 | 8.19 ± 0.07 | 141.0 ± 1.6 | 4.65 ± 0.02a | |
| H3: GACGAC | 21.65% | H2H2 (34) | 15.5 ± 0.27 | 3142.0 ± 53.1 | 251.0 ± 4.8 | 8.02 ± 0.10b | 141.0 ± 2.3 | 4.51 ± 0.03b | |
| H3H1 (67) | 14.8 ± 0.21 | 3013.0 ± 41.3 | 251.0 ± 3.8 | 8.39 ± 0.08a | 141.0 ± 1.8 | 4.68 ± 0.02a | |||
| H3H2 (40) | 15.3 ± 0.25 | 3080.0 ± 49.0 | 255.0 ± 4.5 | 8.29 ± 0.09 | 142.0 ± 2.2 | 4.62 ± 0.03 | |||
| H3H3 (16) | 15.2 ± 0.43 | 3079.0 ± 85.3 | 261.0 ± 7.8 | 8.47 ± 0.15 | 146.0 ± 3.7 | 4.74 ± 0.04a | |||
| D2.1 | H1: CGTT | 44.68% | H1H1 (84) | 14.7 ± 0.27 | 2935.0 ± 52.3a | 238.0 ± 4.8 | 8.15 ± 0.1 | 136.0 ± 2.3 | 8.15 ± 0.10a |
| H2: TATC | 42.60% | H2H1 (152) | 15.0 ± 0.23a | 2968.0 ± 44.0a | 244.0 ± 4.0 | 8.27 ± 0.08 | 137.0 ± 1.9 | 8.27 ± 0.08ac | |
| H3: TAGC | 9.95% | H2H2 (72) | 15.0 ± 0.25a | 2988.0 ± 48.0 | 245.0 ± 4.4 | 8.25 ± 0.09 | 139.0 ± 2.1a | 8.25 ± 0.09 | |
| H2H3 (34) | 13.8 ± 0.34b | 2705.0 ± 66.4b | 228.0 ± 6.1 | 8.46 ± 0.12 | 128.0 ± 2.9b | 8.46 ± 0.12b | |||
| H3H1 (37) | 14.4 ± 0.34 | 2811.0 ± 66.0 | 232.0 ± 6.1 | 8.30 ± 0.12 | 130.0 ± 2.9 | 8.30 ± 0.12 | |||
| H3H3 (8) | 15.0 ± 0.68 | 2903.0 ± 131.9 | 240.0 ± 12.1 | 8.30 ± 0.24 | 141.0 ± 5.8 | 8.30 ± 0.24b | |||
| D2.2 | H1: TATTCCT | 69.04% | H1H1 (189) | 14.9 ± 0.19 | 2969.0 ± 36.3 | 243.0 ± 3.3 | 8.19 ± 0.07 | 138.0 ± 1.6 | 8.19 ± 0.07 |
| H2: GGCCGTG | 21.20% | H1H2 (117) | 14.6 ± 0.17 | 2911.0 ± 33.5 | 243.0 ± 3.1 | 8.37 ± 0.06 | 137.0 ± 1.5 | 8.37 ± 0.06 | |
| H3: TATTGTT | 6.71% | H1H3 (44) | 14.4 ± 0.30 | 2819.0 ± 58.9 | 231.0 ± 5.4a | 8.23 ± 0.11 | 133.0 ± 2.6 | 8.23 ± 0.11 | |
| H2H2 (23) | 15.1 ± 0.35 | 3080.0 ± 68.3a | 256.0 ± 6.3b | 8.33 ± 0.12 | 144.0 ± 3.0a | 8.33 ± 0.12 | |||
| H3H2 (10) | 13.9 ± 0.59 | 2674.0 ± 114.3b | 227.0 ± 10.4 | 8.51 ± 0.21 | 126.0 ± 5.0b | 8.51 ± 0.21 | |||
| H3H3 (3) | 14.9 ± 0.90 | 2855.0 ± 175.4 | 228.0 ± 16.0 | 8.10 ± 0.32 | 134.0 ± 7.7 | 8.10 ± 0.32 | |||
| D3.1 | H1: ACG | 51.88% | H1H1 (116) | 15.1 ± 0.14a | 2973.0 ± 27.1 | 248.0 ± 2.5a | 8.34 ± 0.05a | 139.0 ± 1.2a | 4.67 ± 0.01a |
| H2: GTA | 24.53% | H1H2 (92) | 14.3 ± 0.17b | 2864.0 ± 31.9a | 236.0 ± 3.0b | 8.27 ± 0.06a | 134.0 ± 1.4ac | 4.69 ± 0.02a | |
| H3: GCG | 11.88% | H1H3 (42) | 15.3 ± 0.23a | 3071.0 ± 43.8b | 253.0 ± 4.1a | 8.28 ± 0.08a | 141.0 ± 2.0ab | 4.63 ± 0.02ab | |
| H2H2 (24) | 15.1 ± 0.30 | 3075.0 ± 58.6b | 250.0 ± 5.4ab | 8.15 ± 0.11a | 141.0 ± 2.6 | 4.61 ± 0.03 | |||
| H2H3 (25) | 15.2 ± 0.30 | 3090.0 ± 57.5b | 260.0 ± 5.3a | 8.41 ± 0.10a | 140.0 ± 2.6 | 4.56 ± 0.03b | |||
| H3H3 (6) | 16.6 ± 0.64b | 3248.0 ± 124.0b | 300.0 ± 11.5c | 9.25 ± 0.22b | 157.0 ± 5.5b | 4.84 ± 0.06c | |||
| D4.1 | H1: AG | 77.51% | H1H1 (243) | 15.3 ± 0.76 | 3138.0 ± 146.0a | 260.0 ± 13.2a | 8.3 ± 0.26 | 142.0 ± 6.5 | 4.53 ± 0.07a |
| H2:GT | 13.96% | H1H2 (89) | 15.3 ± 0.76 | 2988.0 ± 148.0b | 248.0 ± 13.4b | 8.31 ± 0.26 | 138.0 ± 6.5 | 4.64 ± 0.07b | |
| H3:GG | 8.06% | H1H3 (51) | 14.8 ± 0.78 | 2985.0 ± 152.0 | 243.0 ± 13.7b | 8.2 ± 0.27 | 134.0 ± 6.7 | 4.51 ± 0.08ac | |
| H2H2 (10) | 14.7 ± 0.99 | 3020.0 ± 191.0 | 246.0 ± 17.3 | 8.19 ± 0.34 | 144.0 ± 8.5 | 4.74 ± 0.10b | |||
| H3H2 (11) | 15.2 ± 0.97 | 2991.0 ± 187.0 | 242.0 ± 17.1 | 8.1 ± 0.34 | 138.0 ± 8.3 | 4.62 ± 0.09 | |||
| H3H3 (2) | 12.5 ± 2.07 | 2360.0 ± 400.0 | 180.0 ± 36.3 | 7.74 ± 0.71 | 103.0 ± 17.7 | 4.40 ± 0.20 | |||
| D4.2 | H1:TC | 74.50% | H1H1 (240) | 14.1 ± 0.50 | 2797.0 ± 96.7 | 220.0 ± 8.8a | 7.94 ± 0.17a | 128.0 ± 4.3a | 4.58 ± 0.05a |
| H2: CT | 25.24% | H1H2 (135) | 14.2 ± 0.50 | 2851.0 ± 96.2 | 235.0 ± 8.7b | 8.25 ± 0.17b | 133.0 ± 4.3b | 4.64 ± 0.05b | |
| H2H2 (31) | 14.9 ± 0.54 | 2901.0 ± 105 | 239.0 ± 9.5b | 8.23 ± 0.19 | 136.0 ± 4.6b | 4.68 ± 0.05b | |||
| D4.3 | H1: CGGTC | 51.44% | H1H1 (108) | 15.0 ± 0.77 | 2918.0 ± 148.0 | 242.0 ± 13.5 | 8.3 ± 0.27 | 135.0 ± 6.6 | 4.64 ± 0.07a |
| H2: TATCT | 37.75% | H1H2 (153) | 14.7 ± 0.76 | 2885.0 ± 148.0 | 235.0 ± 13.4 | 8.16 ± 0.26 | 134.0 ± 6.5 | 4.65 ± 0.07a | |
| H3: CGGCT | 8.43% | H1H3 (39) | 14.8 ± 0.80 | 2899.0 ± 155.0 | 239.0 ± 14.1 | 8.25 ± 0.28 | 132.0 ± 6.9 | 4.54 ± 0.08b | |
| H2H2 (63) | 14.7 ± 0.79 | 2886.0 ± 152.0 | 231.0 ± 13.8 | 8.04 ± 0.27 | 133.0 ± 6.7 | 4.62 ± 0.08 | |||
| H3H2 (25) | 14.6 ± 0.82 | 2946.0 ± 159.0 | 236.0 ± 14.4 | 8.06 ± 0.28 | 134.0 ± 7.0 | 4.56 ± 0.08 | |||
| H3H3 (2) | 13.9 ± 2.05 | 2949.0 ± 397.0 | 237.0 ± 35.9 | 8.02 ± 0.71 | 131.0 ± 17.5 | 4.42 ± 0.20 | |||
Frequency (%), the frequency of individuals with each haplotype among population; Haplotype combination (n), the number of individuals with each haplotype combination among population; LSM ± SE represent the least square means ± standard error; PM270, 270-day peak milk yield; MY270, 270-day total milk yield; FY270, 270-day fat yield; FP270, 270-day fat percentage; PY270, 270-day protein yield and PP270, 270-day protein percentage. For each haplotype block each trait, values with different superscripts differ significantly at Bonferroni corrected P < 0.05