Genome position specific priors for genomic prediction

Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø; Bowman, Philip J; Goddard, Michael E; Hayes, Benjamin J

doi:10.1186/1471-2164-13-543

BMC Genomics

Table 3 Top 10 segments ranked by proportion of variance

From: Genome position specific priors for genomic prediction

Protein yield				Fat yield				Milk yield
Prop Var	CHR	Start	End	Prop Var	CHR	Start	End	Prop Var	CHR	Start	End
JER-AUS
2.51	14	1324152	2524432	2.63	14	1324152	2524432	9.23	14	1324152	2524432
0.94	8	53145498	53823453	0.53	6	32804873	33205790	1.03	23	33488986	34003600
0.49	29	32616370	33148216	0.5	16	34988324	35436695	0.88	20	17220850	17690967
0.46	13	63320438	64620664	0.26	9	47503904	48177473	0.75	16	35920	804371
0.38	23	36309465	36929103	0.21	27	35936818	36385854	0.45	23	39769575	40258674
0.34	3	89581663	89898693	0.2	1	127226200	127917611	0.33	10	30761581	31494927
0.31	17	69563223	70374082	0.18	22	60504152	60873210	0.24	8	73117701	73898467
0.31	29	33157623	33719571	0.17	12	34663468	35292842	0.22	5	93922247	94302255
0.3	29	34401183	34817726	0.15	13	27805120	28346480	0.2	20	28252035	28774228
0.25	9	48742490	49474068	0.15	5	120908187	121179132	0.17	20	34452105	35077755
HOL-AUS
10.38	14	1324152	2524432	17.97	14	1324152	2524432	16.05	14	1324152	2524432
1.27	6	88537190	88996262	2.71	5	93922247	94302255	0.7	6	88537190	88996262
0.58	7	82862759	83380203	0.34	5	93301390	93920010	0.66	20	31054019	31704692
0.52	18	58283983	59602905	0.31	2	107799001	108408740	0.63	5	93301390	93920010
0.48	3	117198648	117541474	0.28	26	20643699	21338653	0.46	18	33639529	33910770
0.44	6	89469872	90304531	0.25	4	106613116	107060437	0.42	7	82862759	83380203
0.31	28	18048845	18758510	0.18	25	8073067	8481205	0.37	14	69793328	70364164
0.3	11	38575857	38932630	0.16	11	102944335	103540503	0.33	20	34452105	35077755
0.2	1	136016808	136624372	0.12	20	36176136	36613401	0.31	25	14686647	15151658
0.2	18	57084113	57818432	0.11	16	56014214	56706854	0.28	11	46783081	47198727
HOL-NOR
4.85	14	1324152	2524432	24.35	14	1324152	2524432	13.49	14	1324152	2524432
0.39	19	26550090	27153052	2.65	5	93922247	94302255	2.37	20	29983162	31051302
0.31	7	23881292	24505374	0.76	19	20077363	20545023	0.9	5	92171816	92734379
0.31	5	20094983	20608440	0.64	5	20094983	20608440	0.89	5	92736297	93292054
0.28	6	86786552	87331055	0.5	15	44850860	45134081	0.63	5	20094983	20608440
0.25	11	102944335	103540503	0.26	20	63502967	63925075	0.46	5	93922247	94302255
0.23	22	42655109	43216893	0.25	19	26550090	27153052	0.38	15	52804974	53411913
0.18	23	11564383	12095383	0.23	2	127612583	128084951	0.33	24	59281770	59735242
0.16	24	59281770	59735242	0.21	26	20043160	20630551	0.33	6	88023038	88527916
0.16	20	69275055	69727331	0.19	13	10469479	11785572	0.23	11	101054186	101516564

Proportion of variance (Prop Var) explained for Jersey (JER-AUS), Australian Holstein (HOL-AUS) and Nordic Holstein (HOL-NOR) populations. Segment size is 100 SNPs. Start and end points of the segments are given as base positions of the first and last SNP in the segment. Segments that appear in more than one breed are highlighted in bold.

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ISSN: 1471-2164

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