Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Table 1 Genetic effects of selective sweeps associated with 56-day body weight in the Virginia Advanced Intercross Line. Estimates are provided for one marker in each associated sweep. Genetic effects were estimated in generation F₁₅ of the AIL

GGA	Position^a (Mb)	Marker	Additive^b (a ± SE)	Sign^c	RMIP^d (FDR 5/20 %)	Sign^e
1	87	rs13899455	−22.7 ± 6.2	2.4 × 10⁻⁴	0.63/0.71	5 %
1	133	rs13942473	16.5 ± 8.0	3.9 × 10⁻²	0.38/0.59	20 %
1	142	rs15448487	16.5 ± 6.8	1.5 × 10⁻²	0.37/0.65	20 %
1	169	rs14916997	28.9 ± 6.3	6.0 × 10⁻⁶	0.93/0.98	5 %
2	61	GGaluGA149337	25.8 ± 7.9	1.2 × 10⁻³	0.75/0.85	5 %
2	112	rs15143460	23.8 ± 6.9	6.4 × 10⁻⁴	0.55/0.66	5 %
2	148	rs15158686	19.0 ± 6.3	2.8 × 10⁻³	0.76/0.86	5 %
3	34	rs15321683	24.6 ± 6.0	4.7 × 10⁻⁵	0.65/0.73	5 %
3	75	GGaluGA228961	15.5 ± 6.8	2.2 × 10⁻²	0.28/0.47	20 %
4	2	rs14417942	14.5 ± 6.7	3.0 × 10⁻²	0.31/0.48	20 %
4	12	GGaluGA246087	17.8 ± 6.6	7.3 × 10⁻³	0.37/0.51	20 %
4	45	rs15560796	14.5 ± 6.6	2.8 × 10⁻²	0.39/0.55	20 %
4	82	rs14498744	−31.3 ± 6.6	2.0 × 10⁻⁶	0.94/0.96	5 %
10	9	GGaluGA068581	11.3 ± 6.4	8.0 × 10⁻²	0.35/0.52	20 %
13	10	rs14059068	16.6 ± 6.3	8.6 × 10⁻³	0.42/0.61	20 %
23	5	rs15205573	18.5 ± 6.6	5.4 × 10⁻³	0.49/0.75	5 %

GGA: Gallus gallus autosome
^aNovember 2011 (galGal4) assembly
^bAdditive genetic effect ± Standard Error estimated in model (C) or (D)
^cSignificance for additive genetic effect in model including all loci significant at 20 % FDR
^dResample Model Inclusion Probability [15] using 5 % or 20 % FDR threshold [13]
^eSignificance thresholds 5/20 % FDR that the marker was selected at with RMIP >0.46 in after Bagging procedure [15] to correct for population structure

ISSN: 1474-760X