High-density genetic maps are valuable and effective tools for exploring complex quantitative traits, including mapping quantitative trait loci and developing linkage markers. Here, we developed 4797 single nucleotide polymorphic (SNP) markers using specific length amplified fragment sequencing. As a result, 4664 SNP markers, combined with 201 simple sequence repeat markers, were used to build a high-density linkage map ofthe F1 population ‘Red Clapp’s Favorite’(Pyrus communis L.) × ‘Mansoo’(Pyrus pyrifolia Nakai). The integrated map contained 17 linkage groups, spanning 2,703.61 cM, with an average distance of 0.56 cM between adjacent markers. Each linkage groups anchored from 6 to 18 SSR markers. Additionally, detailed information on the female and male maps was determined. We also identified the SNP markers’ physical map locations in the P. communis L. ‘Bartlett’ genome. The results will be useful for identifying candidate genes associated with economically important characteristics.
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