A multi-population consensus genetic map reveals inconsistent marker order among maps likely attributed to structural variations in the apple genome

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.

Figure 1. Genotyping plots of three SNPs showing segregation in Co-op 16 and Co-op 17 mapping population.

Plots were generated by BeadStudio package (Illumina, San Diego, CA, USA) using normalized intensities of cy3 and cy5 flourescent dyes. The genotypes with intensities shown in red represents homozygous “aa”, purple represents heterozygous “ab”, blue stands for homozygous “bb” and yellow represents the genotypes for both parents. A) For “MdSNPui08437”, both parents are heterozygous “ab” and progeny plants are either homozygous “aa” or homozygous “bb” or heterozygous “ab” B) For “MdSNPui08414”, one parent is heterozygous “ab” while other is homozygous “bb” and progeny plants are either heterozygous “ab” or homozygous “bb” C) For “MdSNPui11529”, one parent is heterozygous “ab” while other is homozygous “aa” and progeny plants are either heterozygous “ab” or homozygous “aa”.

Figure 2. Genetic linkage map of apple showing 17 linkage groups, developed for F1 cross between ‘Co-op 16’ and ‘Co-op 17’.

Markers in green font are genic SNPs from Khan et al. , markers in red font are genomic SNPs from Han et al. and markers in black font are those genotyped by .