Table 3.
QTL regions identified for clinical mastitis incidence traits and their overlap with the previously reported QTLs for mastitis and other traits
| BTA | QTL start (bp) | QTL end (bp) | QTL length | No. of SNPs | −log10 (p value) for significant SNP | No. of genes | Genes | Traits for which QTLs reported | Reported QTL ID | Reported QTL position (bp) |
|---|---|---|---|---|---|---|---|---|---|---|
| Clinical mastitis incidence in first lactation | ||||||||||
| 4 | 4,090,824 | 4,668,574 | 577,750 | 5 | 4.35 | 1 | COBL |
Udder swelling score Milk yield |
106,571 106,683 |
3,827,792–6,359,338 2,845,004–4,898,788 |
| 7 | 56,140,368 | 56,464,491 | 324,123 | 9 | 4.18 | 2 |
ARHGAP26 NR3C1 |
Milk yield Milk beta-casein percentage |
10,291 21,539 |
25,254,399–64,995,512 20,669–56,958,148 |
| 13 | 32,725,444 | 33,601,894 | 876,450 | 8 | 3.78 | 4 |
SLC39A12 CACNB2 NSUN6 EPC1 |
Teat length SCS |
1386 4983 |
8,230,392–76,386,569 33,021,666–53,561,417 |
| 28 | 26,638 | 583,883 | 557,245 | 7 | 3.44 | 3 |
RAB4A ACTA1 NUP133 |
None | ||
| 17 | 18,528,356 | 18,686,517 | 158,161 | 2 | 3.43 | 2 |
RAB33B NAA15 |
Udder height | 1612 | 17,139,346–25,083,645 |
| 19 | 56,499,004 | 57,152,368 | 653,364 | 3 | 3.39 | 26 |
ITGB4 SAP30BP RECQL5 SMIM6 SMIM5 LLGL2 TSEN54 CASKIN2 GRB2 SLC25A19 MIF4GD MRPS7 GGA3 NUP85 SUMO2 JPT1 NT5C ARMC7 ATP5PD MRPL58 CDR2L HID1 OTOP3 OTOP2 USH1G FADS6 |
Clinical mastitis SCS |
57,308 10,446 |
57,101,615–57,198,154 677,484–58,947,524 |
| 4 | 59,020,173 | 60,733,009 | 1,712,836 | 13 | 3.28 | 5 |
ATRAID RNF167 DNAJB9 THAP5 ELMO1 |
SCS | 13,230 | 58,983,223–59,192,073 |
| Clinical mastitis incidence in second lactation | ||||||||||
| 18 | 15,946,472 | 16,073,485 | 127,013 | 3 | 3.71 | 0 | None |
SCS SCS |
3554 18,469 |
4,992,421–18,045,667 11,438,802–46,178,647 |
| 28 | 20,124,697 | 21,117,323 | 992,626 | 4 | 3.63 | 0 | None |
Udder height Udder composite index Milk yield |
1661 1663 2691 |
14,153,160–25,145,146 14,153,160–25,145,146 14,153,160–25,145,146 |
| 6 | 46,481,458 | 47,954,669 | 1,473,211 | 7 | 3.58 | 7 |
ANAPC4 SLC34A2 SEL1L3 SMIM20 RBPJ CCKAR TBC1D19 |
SCS Udder height Clinical mastitis Clinical mastitis Milk yield Milk yield Milk yield Milk yield Milk yield |
10,439 28,171 19,009 19,010 174,420 25,429 25,430 156,710 2512 |
4,380,012–65,653,453 46,834,289–46,834,365 46,178,647–52,998,234 46,178,647–52,998,234 23,227,144–76,844,549 46,834,289–46,834,365 46,834,289–46,834,365 47,132,494–47,132,534 39,094,762–50,534,735 |
| 3 | 96,827,079 | 97,854,341 | 1,027,262 | 8 | 3.58 | 0 | None | Milk yield | 175,933 | 97,690,467–97,690,507 |
| 3 | 81,094,906 | 82,106,296 | 1,011,390 | 5 | 3.39 | 1 | UBE2U |
SCS Somatic cell count |
2764 4619 |
81,616,554–81,817,752 81,616,554–81,817,752 |
| 6 | 30,988,645 | 30,990,436 | 1791 | 2 | 3.39 | 0 | None |
Clinical mastitis Udder swelling score SCS |
2493 106,577 10,439 |
9,283,340–33,227,425 30,805,204–31,600,938 4,380,012–65,653,453 |
| 25 | 29,227,859 | 29,855,993 | 628,134 | 7 | 3.35 | 2 |
CALN1 GALNT17 |
Milk yield Milk yield Milk yield Immunoglobulin G level Immunoglobulin G level |
161,652 1538 2591 66,230 66,234 |
29,715,968–29,716,008 27,460,729–39,618,958 27,460,729–35,322,340 21,632,493–30,033,432 21,632,493–30,033,432 |
| Clinical mastitis incidence in third lactation | ||||||||||
| 16 | 22,774,111 | 23,127,031 | 352,920 | 6 | 3.79 | 0 | None |
Milk yield Milk yield Teat length SCS |
177,953 177,856 1608 10,185 |
22,637,210–24,244,162 22,778,918–24,293,750 12,209,667–26,166,559 22,717,984–22,875,548 |
| 16 | 24,271,694 | 24,996,912 | 725,218 | 7 | 3.55 | 6 |
BPNT1 IARS2 RAB3GAP2 MARK1 C16H1orf115 MTARC2 |
Milk yield Teat length SCS SCS |
177,856 1608 48,237 6221 |
22,778,918–24,293,750 12,209,667–26,166,559 24,848,848–24,848,888 24,512,141–24,669,705 |