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http://dx.doi.org/10.7235/hort.2013.13004

Development of a Genetic Map of Chili Pepper Using Single Nucleotide Polymorphism Markers Generated from Next Generation Resequencing of Parents  

Lee, Jundae (Research and Development Unit, Pepper and Breeding Institute)
Park, Seok Jin (Research and Development Unit, Pepper and Breeding Institute)
Do, Jae Wahng (Research and Development Unit, Pepper and Breeding Institute)
Han, Jung-Heon (Research and Development Unit, Pepper and Breeding Institute)
Choi, Doil (Department of Plant Science, Seoul National University)
Yoon, Jae Bok (Research and Development Unit, Pepper and Breeding Institute)
Publication Information
Horticultural Science & Technology / v.31, no.4, 2013 , pp. 473-482 More about this Journal
Abstract
Molecular markers, as an efficient selection tool, have been and is being used for practical breeding program in chili pepper (Capsicum annuum L.). Recently, a lot of researches on inheritance and genetic analysis for quantitative traits including capsaicinoids, carotenoids, and sugar content in pepper are being performed worldwide. It has been also reported that QTL mapping is a necessary tool to develop molecular markers associated with the quantitative traits. In this study, we suggested a new method to construct a pepper genetic map using SNP (HRM) markers generated from NGS resequencing of female and male parents. Plant materials were C. annuum 'NB1' (female parent), C. chinense 'Jolokia' (male parent), and their $F_2$ population consisting of 94 progenies. Sequences of 4.6 Gbp and 6.2 Gbp were obtained from NGS resequencing of 'NB1' and 'Jolokia', respectively. Totally, 4.29 million SNPs between 'NB1' and 'Jolokia' were detected and the 1.76 million SNPs were clearly identified. Among them, total 145 SNP (HRM) primer pairs covering pepper genetic map were selected, and the 116 SNP (HRM) markers of them were located on this map. Total distance of the map, which consisted of 12 linkage groups and matched with basic chromosome numbers of pepper, was 1,167.9 cM. According to the mapping result, we concluded that our mapping method was suitable to construct a pepper genetic map fast and accurately. In addition, the genetic map could be directly used for QTL analysis of traits different between both parents.
Keywords
Capsicum annuum; Capsicum chinense; HRM; Jolokia; resequencing;
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