Journal
MOLECULAR BREEDING
Volume 34, Issue 3, Pages 963-975Publisher
SPRINGER
DOI: 10.1007/s11032-014-0089-0
Keywords
Capsicum; SNP; FISH; HRM; Linkage map
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Funding
- Golden Seed Project [213002-04-1-CG910]
- Ministry of Agriculture, Food and Rural Affairs (MAFRA)
- Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center) [PJ00906501]
- Rural Development Administration
- Basic Science Research Program through the National Research Foundation of Korea (NRF) - Ministry of Education, Science and Technology, Republic of Korea
- Ministry of Oceans and Fisheries (MOF), Rural Development Administration (RDA)
- Korea Forest Service (KFS)
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To facilitate marker-assisted breeding and analysis of the structure and/or organization of Capsicum (pepper) genomes, this study utilized expressed sequence tags (ESTs) to develop single-nucleotide polymorphism (SNP) markers. Three different types of PCR-based markers derived from pepper ESTs were developed: intron-based polymorphic markers (IBPs), conserved ortholog sets (COSIIs), and eSNPs (EST-SNPs). For scanning and detection of SNPs, high-resolution melting analysis was performed and the resultant markers were used for linkage analysis. A total of 512 markers, comprising 214 IBP, 143 COSII, 48 eSNP, and 107 previously reported markers, were mapped on 12 linkage groups (LGs) of the AC99 F2 population. This newly constructed interspecific map (AC2) covered 2,335.6 cM with an average marker interval distance of 4.5 cM and was aligned directly with another interspecific map (AF) for validation. Most LGs showed collinear relationships, except for the alignment of chromosomes 1 and 8 of the AC2 map to LG P1 of the AF map. Using our newly developed SNP markers, we generated chromosome-specific markers, and the previously predicted reciprocal translocation event between chromosomes 1 and 8 was revealed between wild and cultivated Capsicum by fluorescent in situ hybridization analysis. The results from this study will promote subsequent evolutionary studies of Capsicum species.
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