Abstract
Genetic maps serve as frameworks for determining the genetic architecture of quantitative traits, assessing structure of a genome, as well as aid in pursuing association mapping and comparative genetic studies. In this study, a dense genetic map was constructed using a high-throughput 1,536 EST-derived SNP GoldenGate genotyping platform and a global consensus map established by combining the new genetic map with four existing reliable genetic maps of apple. The consensus map identified markers with both major and minor conflicts in positioning across all five maps. These major inconsistencies among marker positions were attributed either to structural variations within the apple genome, or among mapping populations, or genotyping technical errors. These also highlighted problems in assembly and anchorage of the reference draft apple genome sequence in regions with known segmental duplications. Markers common across all five apple genetic maps resulted in successful positioning of 2875 markers, consisting of 2033 SNPs and 843 SSRs as well as other specific markers, on the global consensus map. These markers were distributed across all 17 linkage groups, with an average of 169±33 marker per linkage group and with an average distance of 0.70±0.14 cM between markers. The total length of the consensus map was 1991.38 cM with an average length of 117.14±24.43 cM per linkage group. A total of 569 SNPs were mapped onto the genetic map, consisting of 140 recombinant individuals, from our recently developed apple Oligonucleotide pool assays (OPA). The new functional SNPs, along with the dense consensus genetic map, will be useful for high resolution QTL mapping of important traits in apple and for pursuing comparative genetic studies in Rosaceae.
Highlights
Genetic maps are routinely constructed and exploited for identifying marker-trait associations through quantitative trait loci (QTL) mapping
The oligonucleotide pool assays (OPAs) for apple consisted of 1536 SNPs containing 1411 genic SNPs, developed by Khan et al [24], and 125 genomic SNPs, developed by Velasco et al [23]
Of 1536 SNPs, 583 SNPs segregated in the mapping population of ‘Coop 16’6‘Coop 17’ while the remaining SNPs were either derived from duplicated regions, as predicted by Khan et al [6], or were non-polymorphic, and failed to segregate
Summary
Genetic maps are routinely constructed and exploited for identifying marker-trait associations through quantitative trait loci (QTL) mapping. Availability of an accurate and high-resolution genetic map, densely populated with high-throughput co-dominant and reproducible molecular markers, enhances efficiency and likelihood of success of a QTL mapping effort. A saturated and accurate map with co-dominant, reproducible, and high-throughput markers properly localizes a QTL, but it can yield an accurate estimate of the power of the QTL [6] and contributes to enhanced map resolution, transferability across laboratories and mapping populations, and to efficient genotyping
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