QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

Table 3 Parameters used to assemble the individual and composite white spruce linkage maps.

Mapping parameters	Individual	maps			Composite map
	CrossP		CrossD
	♀80112	♂80109	♀77111	♂2388
Available markers ^a	600	671	521	508	1,578 ^b
Distorted markers ^c	10	12	15	19	33
Markers without segregation distortion	590	659	506	489	1545
Assigned markers	580	650	486	470	1,342
AFLP loci	256	289	-	-	470
SSR loci	9	10	-	-	12
Gene loci
ESTPs	22	23	20	20	33
SNPs	293	328	466	450	827 ^d
Total	315	351	486	470	860
Positioned marker loci (%)	549 (94.7)	570 (87.7)	471 (96.9)	454 (96.6)	1,301 (96.9)
AFLP loci	239	235	-	-	453
SSR loci	8	10	-	-	12
Gene loci
ESTPs	19	19	20	20	33
SNPs	283 ^e	306 ^f	451	434	803 ^g
Total	302	325	471	454	836
Major linkage groups (n > 10 markers)	12 (4 ^h)	12 (1 ^h)	12	12	12
Minor linkage groups (3 ≤ n ≤ 10 markers)	1	0	0	0	0
Unlinked markers	10	9	20	19	58
Map length G_F, cM (Kosambi)	2,163.6	2,276.1	2,055.6	1,700.1	2,086.8
Average map density, cM (Kosambi)	3.9	4.0	4.4	3.7	1.6
Average size for major linkage groups, cM (Kosambi)	143.3	162.6	171.3	141.7	173.9

^a For individual linkage maps, only markers segregating 1:1 or 1:1:1:1 were used.
^b 256 markers were shared between the two crosses.
^c Bonferroni correction: P ≤ 0.01/number of loci.
^d 373 gene loci from Arborea PgLM0 SNP array, 339 from Arborea PgLM1 array, and 115 from Treenomix array.
^e 215 gene loci from Arborea PgLM0 SNP array, and 68 from Treenomix array.
^f 239 gene loci from Arborea PgLM0 SNP array, and 67 from Treenomix array.
^g 370 gene loci from Arborea PgLM0 SNP array, 325 from Arborea PgLM1 array, and 108 from Treenomix array.
^h Number of linkage groups composed of 2 subgroups having more than 10 markers.

ISSN: 1471-2164