Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

Abstract

Background: To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.).

Results: Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity.

Conclusion: The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers.

Figure 1

Comparison of homoeologous linkage groups (LGs) of composite maps for white spruce (on the left) and black spruce (species complex Picea mariana × P. rubens) (on the right). For each taxon, the composite map was obtained by assembly of two parental datasets and use of JoinMap 3.0 and 4.0. [49,50]. Genetic distances are indicated on the left of the figure (Kosambi). Markers in bold are gene SNPs, markers in bold and underlined are ESTPs, markers in bold and italics are SSRs, markers in italic and underlined are RAPDs and all other markers are AFLPs. Markers with a grey background are common between both taxa. Orthologous and paralogous markers are connected by a solid line and dashed line, respectively. Markers not positioned onto homoeologous LGs are printed in white on a black background.

Figure 2

Comparison of homoeologous linkage groups (LGs) of composite maps for white spruce (on the left) and black spruce (species complex Picea mariana × P. rubens) (on the right). For each taxon, the composite map was obtained by assembly of two parental datasets and use of JoinMap 3.0 and 4.0. [49,50]. Genetic distances are indicated on the left of the figure (Kosambi). Markers in bold are gene SNPs, markers in bold and underlined are ESTPs, markers in bold and italics are SSRs, markers in italic and underlined are RAPDs and all other markers are AFLPs. Markers with a grey background are common between both taxa. Orthologous and paralogous markers are connected by a solid line and dashed line, respectively. Markers not positioned onto homoeologous LGs are printed in white on a black background.

Figure 3

Comparison of homoeologous linkage groups (LGs) of composite maps for white spruce (on the left) and black spruce (species complex Picea mariana × P. rubens) (on the right). For each taxon, the composite map was obtained by assembly of two parental datasets and use of JoinMap 3.0 and 4.0. [49,50]. Genetic distances are indicated on the left of the figure (Kosambi). Markers in bold are gene SNPs, markers in bold and underlined are ESTPs, markers in bold and italics are SSRs, markers in italic and underlined are RAPDs and all other markers are AFLPs. Markers with a grey background are common between both taxa. Orthologous and paralogous markers are connected by a solid line and dashed line, respectively. Markers not positioned onto homoeologous LGs are printed in white on a black background.

Figure 4

Comparison of homoeologous linkage groups (LGs) of composite maps for white spruce (on the left) and black spruce (species complex Picea mariana × P. rubens) (on the right). For each taxon, the composite map was obtained by assembly of two parental datasets and use of JoinMap 3.0 and 4.0. [49,50]. Genetic distances are indicated on the left of the figure (Kosambi). Markers in bold are gene SNPs, markers in bold and underlined are ESTPs, markers in bold and italics are SSRs, markers in italic and underlined are RAPDs and all other markers are AFLPs. Markers with a grey background are common between both taxa. Orthologous and paralogous markers are connected by a solid line and dashed line, respectively. Markers not positioned onto homoeologous LGs are printed in white on a black background.