Investigation of regions impacting inbreeding depression and their association with the additive genetic effect for United States and Australia Jersey dairy cattle

Table 1 Regions of the genome associated with a run of homozygosity of at least 4 Mb for milk and fertility traits across countries

Country^a	Trait	BTA (Region)^b	Location^c	Frequency	P-value*
Country^a	Trait	BTA (Region)^b	Location^c	Frequency	Single marker regression	Gradient boosted machine
US	Milk Yield	7 (96.2–96.7)	96,541,131	0.07	0.0005	0.07
		13 (19.3–19.9)	19,388,240	0.10	0.0001	0.02
		23 (32.7–33.3)	32,682,177	0.18	0.0001	0.0019
		25 (24.8–27.5)	25,450,477	0.05	0.00009	0.03
		25 (29.1–29.9)	29,113,430	0.06	0.0009	-
	Fat Yield	8 (82.5–83.4)	83,048,502	0.08	0.0003	0.19
		8 (106.6–107.1)	106,817,894	0.11	0.0002	0.07
		19 (12.7–15.5)	14,409,010	0.07	0.0002	0.005
		20 (34.7–36.3)	36,240,997	0.24	0.0003	0.04
		23 (32.7–33.3)	32,682,177	0.18	0.0003	0.04
	Protein Yield	7 (96.1–96.7)	96,192,503	0.07	0.0002	0.04
		13 (19.3 – 19.5)	19,388,240	0.10	0.0004	0.16
		23 (31.9–33.3)	32,682,177	0.18	0.00008	0.004
		25 (24.8–30.7)	29,113,430	0.06	0.00002	0.02
	Calving Interval	7 (82.1–83.0)	82,173,456	0.09	0.0004	0.003
AU	Milk Yield	17 (72.1–73.5)	73,055,503	0.04	0.00004	0.03
	Milk Yield	20 (28.4–29.5)	29,322,034	0.33	0.0001	0.04
	Fat Yield	2 (90.4–91.1)	91,117,564	0.16	0.0004	0.08
		3 (113.8–114.2)	113,930,518	0.06	0.0007	0.20
		7 (6.6–16.7)	8,860,921	0.17	0.00007	0.02
		17 (72.1–75.0)	73,257,794	0.04	0.00002	0.006
		18 (50.8–53.0)	52,024,379	0.15	0.00001	0.005
	Protein Yield	3 (113.4–114.6)	113,845,303	0.06	0.000006	0.02
		7 (8.8–12.8)	8,860,921	0.17	0.0003	0.05
		17 (68.9–75.0)	73,055,503	0.04	0.0000008	0.005
		18 (49.0–52.2)	49,446,631	0.13	0.0005	0.47

^aAU refers to Australia and US refers to United States
^bBTA refers to chromosome and the region and location are in Mb build UMD 3.1 (http://bovinegenome.org/cgi-bin/gbrowse/bovine_UMD31/)
^cReferrs to the location with regions with the highest significance based on Single Marker Regression Analysis
*P-values were generated based on a permutation test (Doerge and Churchill [23]) for each analysis

ISSN: 1471-2164