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

Table 1 Genotyping success rates obtained with the 768 and 1,536 SNPs Arborea bead arrays for each of two white spruce QTL mapping populations using the GoldenGate assay.

Bead array (cross)	Number of SNPs (percent success rate)			Number of genes (percent success rate)
	SNPs assayed	SNPs with GenTrain score ≥ 0.25^a	Segregating SNPs with GenTrain score ≥ 0.25^a	Genes assayed	Genes with segregating SNPs
Arborea PgLM0 (for mapping cross P) ^b
Total	768	603 (79%)	516 (67%)	425	330 (78%)
Number of resequenced SNPs ^c	730	572 (78%)	505 (69%)
Number of in silico SNPs ^d	38	31 (82%)	11 (30%)
Arborea PgLM1 (for mapping cross D)
Total	1,536	1,261 (82%)	1,100 (72%)	822 ^e	672 ^f (82%)
Number of resequenced SNPs ^b	1,416	1,159 (82%)	1,051 (74%)
Number of resequenced indels ^g	30	21 (70%)	21 (70%)
Number of in silico SNPs ^c	90	77 (86%)	28 (31%)

^a For SNPs with a GenTrain score ≥ 0.25, valid GenCall scores were obtained for 99.5% of samples, on average.
^b As reported by Pavy et al. [13].
^c Percentage obtained by using the total of 768 SNPs assayed per cross or the total number of genes assayed as a reference.
^d in silico SNPs were detected in clusters of aligned EST sequences derived from white spruce cDNA libraries from various individuals but not implicating the mapping parents Pavy et al. [50], which explains the lower rates of segregating SNPs obtained.
^e including 330 genes shared with PgLM0.
^f including 250 genes shared with PgLM0.
^g Including 21 gene indels of 1 to 2 bp, 6 indels of 3 to 6 bp, and 3 indels of over 10 bp, from untranslated regions.

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