Genome-wide association analysis and accuracy of genome-enabled breeding value predictions for resistance to infectious hematopoietic necrosis virus in a commercial rainbow trout breeding population

Table 2 Summary of QTL identified for IHNV survival DAYS

Omy	QTL^a	GWAS method^b	EGV (%)	Physical map (bp)		Window flanking SNP		SNPs per window
Omy	QTL^a	GWAS method^b	EGV (%)	Start	End	Start	End	SNPs per window
2	2.2	wssGBLUP	3.2	45,383,323	46,361,331	Affx-88954877	Affx-88928987	24
4	4.1	wssGBLUP	2.0	9,789,985	10,738,830	Affx-88917261	Affx-88929814	31
4	4.2	wssGBLUP	8.8	68,038,853	68,982,815	Affx-88923800	Affx-88922397	42
4	4.2	ssBMR	2.2	74,007,109	74,987,590	Affx-88939425	Affx-88928526	21
6	6.1	ssBMR	3.0	68,134,086	68,990,700	Affx-88929527	Affx-88939372	19
16	16.1	ssBMR	3.0	24,057,372	24,944,118	Affx-88954356	Affx-88951804	18
17	17.1	ssBMR	3.6	51,034,316	51,997,613	Affx-88955435	Affx-88944415	26
17	17.1	ssBMR	4.8	59,030,557	59,975,343	Affx-88934715	Affx-88947595	36
17	17.1	wssGBLUP	4.7	59,332,327	60,281,825	Affx-88919103	Affx-88944127	34
21	21.1	wssGBLUP	2.1	22,119,421	23,117,999	Affx-88932453	Affx-88916492	40
21	21.1	wssGBLUP	6.2	39,913,253	40,900,383	Affx-88932908	Affx-88907074	23
25	25.1	ssBMR	6.7	14,168,054	14,988,042	Affx-88923380	Affx-88924756	29
25	25.1	wssGBLUP	2.8	14,387,782	15,344,868	Affx-88930881	Affx-88908721	28
26	26.1	ssBMR	2.0	15,009,533	15,969,232	Affx-88931236	Affx-88925053	24
28	28.1	ssBMR	2.4	13,000,180	13,927,035	Affx-88912736	Affx-88929314	24

Offspring from year-class 2016 families from the nucleus breeding population of Clear Springs Foods, Inc.
^aSummary of QTL regions including only those 1-Mb genomic windows with an explained additive genetic variance (EGV) higher than 2%
^bGWAS was analyzed using weighted single-step GBLUP (wssGBLUP) and single-step Bayesian multiple regression (ssBMR); the ssBMR was performed using BayesB with the mixture parameter \(\pi\) = 0.999

ISSN: 1297-9686