Integrated genetic linkage maps for Korean pears (Pyrus hybrid) using GBS-based SNPs and SSRs
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Integrated linkage maps are a valuable tool for comparative mapping between and within genus and species. Novel single-nucleotide polymorphism (SNP) linkage maps integrated with simple sequence repeats (SSRs) based on pseudo-chromosomes of the Chinese pear reference genome of ‘Dangshansuli’ (Pyrus bretschneideri) were constructed. In total, 4801 qualified SNP markers were obtained using a customized pipeline. The consensus map for ‘Whangkeumbae’ and ‘Minibae’ contained 321 SNP and 30 SSR markers spanning 1511.1 cM with an average genetic distance of 4.3 cM. A total of 30 SSR markers made it possible to compare our consensus map to other pear and apple maps. SSR markers originating from pear and apple maps showed high co-linearity. SNPs coordinated with pseudo-chromosomes, provide information on physical length coverage for 17 corresponding linkage groups, and enable easier genome annotation for genomic regions detected by quantitative trait loci analysis. Genotyping-by-sequencing-based SNP maps integrated with SSRs in the interspecific mapping population illustrate the genomic structure of Korean pear resources and will be used as our reference maps for tribe Maleae.
KeywordsGenotyping-by-sequencing Maleae ‘Minibae’ Reference map Synteny ‘Whangkeumbae’
This work was supported by a Grant from the Next-Generation BioGreen 21 Program (No. PJ01311501), Rural Development Administration, Republic of Korea.
HH performed the overall data analysis including SNP calling and compared the linkage map with published pear and apple maps. YO constructed the linkage map using SNP and SSR markers. HH and YO drafted the manuscript together. KK, SO, and SC contributed SSR marker analysis including sample preparation and marker detection. YK generated and maintained the plant materials. DK designed and managed whole experiments and finalized the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
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