From: A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes
Breed | Chr | Start | End | State | N | Gene | QTL_Terms: Trait Names |
---|---|---|---|---|---|---|---|
AZE | 1 | 186,836,088 | 187,487,608 | complex | 14 | PDE9A | Bovine respiratory disease, Milk fat yield susceptibility, Milk protein yield, Milk yield |
SLC37A1 | Milk phosphorus content | ||||||
1 | 20,942,758 | 21,126,649 | loss | 16 | PRAG1 | Bovine tuberculosis susceptibility | |
2 | 57,805,999 | 58,006,839 | gain | 18 | BIN1 | Residual feed intake | |
8 | 26,033,634 | 26,136,325 | complex | 13 | SNX13 | Milk protein percentage | |
10 | 72,266,178 | 72,898,604 | complex | 16 | FAM184A | Subcutaneous fat | |
12 | 15,024,107 | 15,144,657 | loss | 13 | TTC27 | Milk fat yield | |
15 | 78,109,455 | 78,335,826 | loss | 12 | COL22A1 | Milk fat percentage, Milk protein percentage, Milk fat yield, Milk yield, Milk protein yield | |
15 | 8,242,728 | 8,744,577 | loss | 13 | DECR1 | Fat thickness at the 12th rib | |
15 | 16,595,357 | 16,770,941 | gain | 14 | STK3 | Milk fat yield, Milk protein percentage, Milk protein yield | |
16 | 21,588,533 | 21,771,264 | gain | 18 | WT1 | Carcass weight, Milk fat percentage | |
KHU | 2 | 70,740,089 | 70,803,405 | gain | 5 | TTN | Udder cleft |
2 | 159,382,105 | 159,476,051 | loss | 5 | SLC11A1 | Bovine tuberculosis susceptibility, M. paratuberculosis susceptibility | |
3 | 38,990,851 | 39,088,431 | gain | 5 | ITGAE | Milk conjugated linoleic acid content | |
5 | 36,870,251 | 37,136,533 | gain | 7 | SPSB1 | Milk protein yield, Somatic cell score | |
5 | 98,013,455 | 98,218,453 | loss | 6 | ANO5 | Milk C14 index, Curd firming rate, Meat texture | |
6 | 26,325,308 | 26,500,901 | gain | 8 | CD2 | Calving to conception interval, Inseminations per conception, Milk fat percentage, Net merit, Somatic cell score | |
7 | 31,368,913 | 31,752,823 | loss | 5 | RUFY3 | Milk protein percentage, Milk protein yield, Milk yield, Residual feed intake, Somatic cell score | |
8 | 116,160,601 | 116,290,580 | gain | 6 | DPP6 | Average daily gain, Body weight (birth), Body weight (weaning), Bovine respiratory disease susceptibility | |
9 | 62,716,777 | 62,830,823 | loss | 5 | SPOCK1 | Body depth, Calving ease (maternal), Calving ease, Conception rate, Daughter pregnancy rate, Feet and leg conformation, Foot angle, Length of productive life, Milk fat percentage, Milk fat yield, Milk protein percentage, Milk protein yield, Milk yield, Net merit, PTA type, Rear leg placement - rear view, Rump width, Somatic cell score, Stillbirth, Udder attachment, Udder depth | |
10 | 90,708,913 | 91,158,966 | gain | 5 | CD109 | First service conception, Inseminations per conception | |
15 | 51,487,540 | 51,850,347 | complex | 5 | CRH | Average daily gain, Carcass weight, Conformation score, Connective tissue amount, Longissimus muscle area, Marbling score, Muscle pH, Subcutaneous fat | |
TRIM55 | Carcass weight | ||||||
16 | 10,532,220 | 10,757,353 | loss | 5 | ACCS | Serotonin level | |
ACCSL | Conception rate, Serotonin level | ||||||
ALKBH3 | Stayability | ||||||
17 | 17,338,207 | 17,457,683 | gain | 6 | CIT | First service conception QTL, Inseminations per conception | |
17 | 21,924,791 | 22,056,117 | complex | 6 | SCARB1 | Bovine respiratory disease susceptibility, Milk beta-carotene content, Milk fat percentage, Milk protein percentage | |
18 | 39,524,271 | 39,714,171 | loss | 6 | HYDIN | Marbling score | |
18 | 64,081,682 | 64,220,127 | complex | 5 | PEG3 | Body depth, Fat cover, Rump width, Stature, Stillbirth | |
Angularity, Body depth, Stature, Stillbirth | |||||||
19 | 41,270,588 | 41,632,848 | gain | 6 | PDZD2 | Somatic cell score | |
20 | 61,571,126 | 61,672,190 | gain | 8 | IGF1R | Age at puberty, Body size, Body weight (birth), Body weight (weaning), Milk protein yield, Milk yield, Milk protein percentage, Milk fat yield, Milk fat percentage, Inseminations per conception, Bovine respiratory disease susceptibility, Body weight (yearling) | |
22 | 4,920,880 | 5,171,378 | gain | 5 | NEDD4L | Abomasum displacement | |
MAZ | 3 | 133,069,378 | 133,117,242 | gain | 2 | LOXL2 | Milk fat yield |
6 | 96,104,850 | 96,210,725 | loss | 3 | AGBL4 | Milk protein yield, Milk yield | |
6 | 81,057,321 | 81,285,031 | loss | 2 | ROR1 | Body depth, Calving ease (maternal), Calving ease, Daughter pregnancy rate, Length of productive life, Milk protein percentage, Net merit, PTA type, Rump width, Somatic cell score, Stature, Stillbirth (maternal), Stillbirth, Strength, Udder attachment, Udder depth, Udder height | |
9 | 15,430,969 | 15,568,337 | gain | 2 | ELL2 | Milk fat yield, Milk protein yield, Milk yield, Somatic cell score | |
12 | 44,167,548 | 44,199,735 | loss | 2 | SH3RF3 | Teat placement | |
18 | 49,428,499 | 49,811,006 | gain | 2 | NUMBL | Shear force | |
Conception rate, Daughter pregnancy rate | |||||||
AZE KHU | 1 | 139,476,110 | 139,719,306 | loss | 26 | FNDC3B | Calving ease (maternal), Daughter pregnancy rate, Length of productive life, Milk protein yield, Rear leg placement - side view, Somatic cell score, Teat length, Dairy form, Dry matter intake, Milk protein percentage, Net merit, Residual feed intake, Stillbirth, Udder cleft, Calving ease |
GHSR | Average daily gain, Body weight (slaughter), Body weight (test end), Carcass weight | ||||||
TNFS10 | Interval from first to last insemination, Milk fat percentage, Milk fat yield, Milk protein yield | ||||||
3 | 7,562,702 | 7,799,466 | gain | 22 | ACOX1 | Marbling score, Subcutaneous fat, Subcutaneous fat | |
3 | 67,310,421 | 67,462,093 | complex | 18 | GALNTL6 | Bovine tuberculosis susceptibility | |
3 | 68,223,946 | 68,369,724 | gain | 23 | GALNTL6 | Bovine tuberculosis susceptibility | |
4 | 91,862,787 | 92,034,556 | gain | 68 | GALNT6 | Milk linoleic acid content, Udder cleft, Udder texture | |
11 | 12,884,241 | 13,195,697 | complex | 20 | NRXN3 | Milk protein yield | |
14 | 10,786,055 | 10,971,651 | complex | 28 | HNF4A | Body length, Body weight (24 months), Chest girth, Height (24 months) | |
16 | 30,256,354 | 30,582,499 | complex | 46 | ARRB1 | Bovine respiratory disease susceptibility, Milk fat percentage, Milk fat yield, Milk yield | |
NEU3 | Conception rate, Daughter pregnancy rate, Net merit, Length of productive life | ||||||
16 | 75,669,845 | 75,781,021 | complex | 42 | CNTN5 | Body depth, Calving ease (maternal), Calving ease, Feet and leg conformation, Foot angle, Milk fat percentage, Milk fat yield, Milk protein percentage, Milk protein yield, Net merit, PTA type, Rear leg placement - rear view, Residual feed intake, Rump width, Somatic cell score, Stature, Stillbirth, Strength, Udder attachment, Udder depth, Udder height | |
18 | 12,571,250 | 12,842,177 | complex | 37 | ZCCHC14 | Inseminations per conception | |
20 | 40,344,161 | 40,510,307 | gain | 69 | PCSK6 | Metabolic body weight, Residual feed intake, Dry matter intake | |
23 | 16,558,338 | 16,817,683 | complex | 26 | PDLIM1 | Rump angle | |
23 | 18,714,144 | 18,844,893 | complex | 30 | CRTAC1 | Milk C14 index, Milk fat yield, Milk myristoleic acid content | |
AZE MAZ | 8 | 70,758,890 | 71,075,937 | complex | 14 | OSBPL3 | Fat thickness at the 12th rib |
9 | 94,954,953 | 95,685,910 | loss | 17 | ANGPTL8 | Body length | |
ARHGEF18 | Fat area to ribeye area ratio |