A high-resolution linkage map for comparative genome analysis and QTL fine mapping in Asian seabass, Lates calcarifer

Table 2 Location of QTL and magnitude of QTL effects on growth traits in Asian seabass

Trait	QTL	LG	Position (cM)	CI (cM)	Flanking markers	Interval of flanking markers (cM)	Nearest marker and gene	Distance to the nearest marker (cM)	LOD	LOD threshold		PVE (%)	Phenotype means
										Experiment-wise	Linkage group-wise		m1f1	m1f2	m2f1	m2f2
Body weight	qBW2-a	LG2	20.3	20.3-22.3	Lca182-Lca287	6.0	Lca287	2	4.9**	3.6	3.5	30.2	26.8	23.6	39.5	26.9
	qBW2-b	LG2	26.4	24.4-30.5	Lca562-Lca524	6.1	Lca562	0	4.0**	3.6	3.5	5.3	29.3	25.8	32.9	28.1
	qBW2-c	LG2	32.5	32.5-33.9	Lca371-Lca480	1.4	Lca371 in cathepsin D	0	4.5**	3.6	3.5	7.0	25.4	29.0	28.9	34.0
	qBW2-d	LG2	35.2	35.2-36.4	LcaTe0359-LcaTe0138	0.6	LcaTe0359	0	4.5**	3.6	3.5	5.3	33.0	28.4	29.1	25.7
	qBW2-e	LG2	39.1	37.6-40.1	Lca250-Lca568	0.2	Lca568 in KCTD15; LcaTe0265 in csmd2	0	4.0**	3.6	3.5	4.7	28.6	32.8	25.9	29.0
	qBW3	LG3	0	0-0.1	Lca137-LcaB002	0.1	Lca137	0	5.3**	3.6	2.6	6.3	31.8	25.1	32.3	28.0
Total length	qTL2-a	LG2	22.3	20.3-20.5	Lca182-Lca287	6.0	Lca287	2	5.5**	5.5	5.5	53.1	120.1	105.0	138.0	130.5
	qTL2-c	LG2	32.5	32.5-32.7	Lca371-Lca480	1.4	Lca371 in catheps D	0	5.5**	5.5	5.5	8.6	116.5	123.3	123.0	131.0
	qTL2-d	LG2	35.2	35.2-35.4	LcaTe0359-LcaTe0138	0.6	LcaTe0359	0	5.5**	5.5	5.5	6.5	129.6	121.8	123.2	117.5
	qTL3	LG3	0	0-0.1	Lca137-LcaB002	0.1	Lca137	0	5.7**	5.5	2.3	6.7	127.2	116.9	128.2	121.6
Standard length	qSL2-a	LG2	22.3	20.3-20.5	Lca182-Lca287	6.0	Lca287	2	5.1	5.4	5.3	53.8	98.7	86.7	114.2	108.1
	qSL2-c	LG2	32.5	32.5-32.7	Lca371-Lca480	1.4	Lca371 in catheps D	0	5.0	5.4	5.3	7.9	96.6	101.8	101.5	108.1
	qSL2-d	LG2	35.2	35.2-35.4	LcaTe0359-LcaTe0138	0.6	LcaTe0359	0	5.3*	5.4	5.3	6.2	107.1	100.6	101.8	97.3
	qSL3	LG3	0	0-0.1	Lca137-LcaB002	0.1	Lca137	0	5.7**	5.4	2.5	6.7	105.2	96.5	106.0	100.4

For each QTL detected, the confidence interval (CI), linkage group maximum LOD score, and percentage of the phenotypic variance explained (PVE) are indicated. The experiment-wise LOD significance thresholds are 4.5 for body weight, and 6.1 for total length and body length. Mean phenotypic values of each trait were also calculated for those progeny with the alternate alleles at the most closely linked microsatellite markers, inherited from the male parent (m1 or m2), alleles from the female parent (f1 or f2). **: Experiment-wise significant QTL; * Linkage-group-wise significant QTL.

ISSN: 1471-2164