Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

Van Goor, Angelica; Bolek, Kevin J.; Ashwell, Chris M.; Persia, Mike E.; Rothschild, Max F.; Schmidt, Carl J.; Lamont, Susan J.

doi:10.1186/s12711-015-0176-7

Genetics Selection Evolution

Table 2 Identified windows that explain a significant percentage (≥0.5 %) of the genetic variance

From: Identification of quantitative trait loci for body temperature, body weight, breast yield, and digestibility in an advanced intercross line of chickens under heat stress

Windows explaining ≥0.5 % of genetic variance						SNP with highest model freq within window
Trait^a	Chr	Pos (Mb)	% of genetic variance explained	Nb of SNPs	Freq of iterations with (P > 0)^b	SNP name^c	SNP pos (bp)^d	Model freq^e	Allele freq^f
BT20	1	70	0.66	154	0.37	AX-75508759	70481838	0.0037	0.684
BT20	1	77	0.57	147	0.34	AX-75522132	77489841	0.0035	0.128
BT20	14	3	0.68	444	0.67	AX-75795199	3948035	0.0034	0.624
BT20	14	4	1.02	387	0.63	AX-75797528	4705324	0.0044	0.254
BT22	15	8	0.72	232	0.44	AX-75845885	8214511	0.0038	0.489
BT28	15	8	1.01	232	0.55	AX-80869149	8162150	0.0044	0.513
BT28	15	9	0.94	250	0.54	AX-80984099	9043951	0.0035	0.492
BT28	26	1	0.62	345	0.58	AX-76333878	1820964	0.0068	0.719
BT28-20	14	3	0.51	444	0.63	AX-75792785	3211698	0.0036	0.383
BT28-20	27	2	0.58	650	0.76	AX-76359339	2735538	0.0032	0.477
BW21	1	130	0.66	186	0.50	AX-75254200	130612102	0.0428	0.459
BW21	2	45	0.77	198	0.47	AX-76097146	45668714	0.0091	0.391
BW21	2	46	2.37	173	0.61	AX-76098569	46452516	0.0146	0.408
BW21	2	47	0.65	203	0.46	AX-76099514	47012242	0.0084	0.407
BW21	4	29	0.75	126	0.42	AX-76640215	29660145	0.0083	0.569
BW21	6	17	0.58	191	0.48	AX-76911192	17573301	0.0041	0.37
BW21	6	18	0.57	216	0.53	AX-76914599	18873299	0.0053	0.381
BW21	6	19	0.55	184	0.45	AX-76916544	19707190	0.0052	0.438
BW21	6	20	1.27	319	0.69	AX-76918160	20296520	0.0048	0.619
BW21	7	25	0.62	220	0.51	AX-77014466	25790174	0.0054	0.543
BW21	8	19	0.53	224	0.52	AX-77082473	19967735	0.0061	0.475
BW21	8	20	0.59	324	0.55	AX-77082837	20103726	0.0081	0.567
BW21	14	2	0.5	245	0.55	AX-75789727	2184924	0.0039	0.752
BW28	1	129	0.69	216	0.56	AX-75251743	129532260	0.0070	0.497
BW28	1	130	0.5	186	0.47	AX-80745974	130704373	0.0052	0.542
BW28	1	175	0.51	218	0.53	AX-75350071	175304877	0.0040	0.501
BW28	2	46	0.57	173	0.48	AX-76098569	46452516	0.0096	0.408
BW28	3	7	0.56	269	0.55	AX-76560040	7975734	0.0102	0.472
BW28	4	35	0.8	278	0.59	AX-80752029	35879320	0.0057	0.207
BW28	4	36	1.05	292	0.63	AX-80949517	36028465	0.0060	0.790
BW28	5	2	0.65	154	0.39	AX-76800406	2270651	0.0051	0.479
BW28	5	4	0.7	234	0.54	AX-76843401	4221327	0.0049	0.539
BW28	6	17	1.1	191	0.52	AX-80910640	17891764	0.0050	0.377
BW28	6	18	1.67	216	0.59	AX-76914769	18937498	0.0075	0.371
BW28	6	19	2.48	184	0.59	AX-76915818	19346379	0.0081	0.624
BW28	6	20	2.11	319	0.72	AX-76918815	20548526	0.0053	0.404
BW28	6	21	0.77	173	0.44	AX-76921099	21508397	0.0053	0.405
BW28	26	3	0.54	616	0.78	AX-76340801	3344288	0.0045	0.404
BW28-21	1	2	1	185	0.47	AX-75406964	2188529	0.0047	0.394
BW28-21	4	35	1.2	278	0.57	AX-76651146	35184184	0.0052	0.335
BW28-21	4	36	1.36	292	0.62	AX-80788958	36098921	0.0050	0.715
BW28-21	6	17	0.62	191	0.43	AX-76911330	17642627	0.0038	0.622
BW28-21	6	18	0.86	216	0.49	AX-80836439	18927710	0.0040	0.368
BW28-21	6	19	1.31	184	0.47	AX-76915818	19346379	0.0056	0.624
BW28-21	6	20	1.29	319	0.63	AX-76919341	20762964	0.0037	0.595
BW28-21	6	21	0.55	173	0.40	AX-76921368	21613870	0.0038	0.598
BW28-21	10	4	0.56	548	0.77	AX-75184920	4022205	0.0038	0.258
BW28-21	21	1	0.53	658	0.78	AX-80870523	1549522	0.0034	0.338
BW28-21	21	5	0.64	656	0.76	AX-76253089	5768734	0.0034	0.298
Digestibility	19	9	0.63	207	0.41	AX-75948077	9760405	0.0035	0.510
Digestibility	20	13	0.62	367	0.61	AX-76206206	13442859	0.0034	0.446
Digestibility	21	5	0.53	656	0.79	AX-76253122	5775142	0.0032	0.327
% Breast weight	1	42	0.58	107	0.27	AX-75450269	42731066	0.0035	0.350
% Breast weight	1	43	0.97	116	0.30	AX-75452817	43915634	0.0046	0.629
% Breast weight	1	44	15.35	158	0.74	AX-75454603	44752476	0.0220	0.428
% Breast weight	1	45	5.73	177	0.50	AX-75455154	45032476	0.0133	0.429
% Breast weight	1	46	1.85	176	0.46	AX-75457992	46437656	0.0056	0.401
% Breast weight	15	10	0.56	400	0.67	AX-75815669	10006485	0.0040	0.833
% Breast weight	22	3	1.11	573	0.79	AX-76267275	3079947	0.0052	0.542

^aBody temperature (BT) measured on days 20, 22, 28, and the differential 28-20; body weight (BW) measured on days 21, 28, and the differential 28-21; digestibility, measured from ileal content, on day 28; percent of breast weight, calculated from percent of total body weight, and measured on day 28
^bFrequency with which the window was included in the MCMC iterations (post-burn-in)
^cSNP within the specified window which was most frequently included in the MCMC iterations (post-burn-in), and is therefore predicted to have an effect on the phenotype
^dPosition of SNPs in base pairs on Gallus gallus (version 4.0) chromosomes
^eFrequency with which the SNP was included in the MCMC iterations (post-burn-in)
^fAllele frequency of the SNP within the genotyped population (N = 458)

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