Integrated genetic linkage maps for Korean pears (Pyrus hybrid) using GBS-based SNPs and SSRs

• Published in: Horticulture, environment and biotechnology Vol. 60; no. 5; pp. 779 - 786
• Main Authors: Han, Hyeondae, Oh, Youngjae, Kim, Keumsun, Oh, Sewon, Cho, Sunheum, Kim, Yoon-Kyeong, Kim, Daeil
• Format: Journal Article
• Language: English
• Published: Singapore Springer Singapore 01-10-2019; Springer Nature B.V; 한국원예학회
• Subjects: Agriculture; Annotations; Biomedical and Life Sciences; Chromosomes; Gene mapping; Genetic distance; Genomes; Genotyping; Interspecific; Life Sciences; Linearity; Mapping; Markers; Nucleotide sequence; Nucleotides; Pathogens; Pears; Plant Breeding/Biotechnology; Plant Ecology; Plant Physiology; Polymorphism; Pyrus bretschneideri; Quantitative trait loci; Research Report; Simple sequence repeats; Single-nucleotide polymorphism; 농학; Reference map; Minibae; Genotyping-by-sequencing; Synteny; Maleae; Whangkeumbae
• ISSN: 2211-3452; 2211-3460
• DOI: 10.1007/s13580-019-00171-3

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.