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  • Development of a large number of SSR and InDel markers and construction of a high-density genetic map based on a RIL population of pepper (Capsicum annuum L.).

    Author(s) : Zhang XiaoFenSun HongHeXu YongChen BinYu ShuanCangGeng SanShengWang Qian

    Author Affiliation : College of Horticulture, China Agricultural University, Beijing 100193, China.

    Author Email : gengsansheng@nercv.orgwangqian@cau.edu.cn

    Journal article : Molecular Breeding 2016 Vol.36 No.7 pp.92 ref.39

    Abstract : Capsicum annuumcapsicum annuumSubject Category: Organism Names
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    , the most widely cultivated species of pepper, is used worldwide for its important nutritional and medicinal values. The construction of an intraspecific high-density genetic linkagelinkageSubject Category: Miscellaneous
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    map would be of practical value for pepper breeding. However, the numbers of PCR-based simple sequence repeat (SSR) and insertion/deletion (InDel) markers that are available are limited, and there is a need to develop a saturated, intraspecific linkage map. The non-redundant Capsicum species' expressed sequence tag (EST) database from the National Center for BiotechnologybiotechnologySubject Category: Disciplines, Occupations and Industries
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    Information was used in this study to develop a total of 902 usable EST-SSR markers. Additionally, 177,587 SSR loci were identified based on the pepper genomic information, including 9182 SSR loci 500 bp both upstream and downstream of coding regions. Another 4497 stable and reliable InDel loci were also developed. From 9182 SSR and 4497 InDel loci, 3356 pairs of genomic SSR primers and 1400 pairs of InDel primers that were evenly distributed in 12 chromosomeschromosomesSubject Category: Anatomical and Morphological Structures
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    were selected. A high-density intraspecific genetic map of C. annuum was constructed using the F10-generation recombinant inbred line of parents PM702 and FS871 as the mapping population, screeningscreeningSubject Category: Techniques, Methodologies and Equipment
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    the selected 3356 pairs of genomic SSR primers and 1400 pairs of InDel primers and the 902 EST-SSR markers developed earlier, and 524 published SSR markers and 299 orthologous markers (including 263 COSII markers and 36 tomato-derived markers) used previously to develop an interspecific genetic map (C. annuum × C. frutescens). Eventually, a high-density complete genetic intraspecific linkage map of C. annuum containing 12 linkage groups and 708 molecular markers with a length of 1260.00 cM and an average map distance of 1.78 cM was produced. This intraspecific, high-density, complete genetic linkage map of C. annuum contains the largest number of SSR and InDel markers and the highest amount of saturation so far, and it will be of considerable significance for the breeding of improved cultivarscultivarsSubject Category: Organism Groups
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    of this important field crop in the future.

    ISSN : 1380-3743

    DOI : 10.1007/s11032-016-0517-4

    Record Number : 20163308286

    Publisher : Springer

    Location of publication : Amsterdam

    Country of publication : Netherlands

    Language of text : English

    Indexing terms for this abstract:

    Organism descriptor(s) : CapsicumcapsicumSubject Category: Organism Names
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    , Capsicum annuumcapsicum annuumSubject Category: Organism Names
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    Descriptor(s) : biotechnologybiotechnologySubject Category: Disciplines, Occupations and Industries
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    , chromosomeschromosomesSubject Category: Anatomical and Morphological Structures
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    , cropscropsSubject Category: Commodities and Products
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    , cultivarscultivarsSubject Category: Organism Groups
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    , expressed sequence tagsexpressed sequence tagsSubject Category: Chemicals and Chemical Groups
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    , field cropsfield cropsSubject Category: Commodities and Products
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    , gene mappinggene mappingSubject Category: Techniques, Methodologies and Equipment
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    , genetic mappinggenetic mappingSubject Category: Techniques, Methodologies and Equipment
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    , genetic markersgenetic markersSubject Category: Miscellaneous
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    , geneticsgeneticsSubject Category: Disciplines, Occupations and Industries
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    , inbred linesinbred linesSubject Category: Organism Groups
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    , linkagelinkageSubject Category: Miscellaneous
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    , molecular geneticsmolecular geneticsSubject Category: Miscellaneous
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    , plant breedingplant breedingSubject Category: Techniques, Methodologies and Equipment
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    , polymerase chain reactionpolymerase chain reactionSubject Category: Techniques, Methodologies and Equipment
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    , screeningscreeningSubject Category: Techniques, Methodologies and Equipment
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    , simple sequence repeatssimple sequence repeatsSubject Category: Miscellaneous
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    Identifier(s) : biochemical genetics, cultivated varieties, PCR, pure lines, screening tests

    Broader term(s) : CapsicumcapsicumSubject Category: Organism Names
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    , SolanaceaesolanaceaeSubject Category: Organism Names
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    , SolanalessolanalesSubject Category: Organism Names
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    , eudicotseudicotsSubject Category: Organism Names
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    , angiospermsangiospermsSubject Category: Organism Names
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    , SpermatophytaspermatophytaSubject Category: Organism Names
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    , plantsplantsSubject Category: Organism Names
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    , eukaryoteseukaryotesSubject Category: Organism Names
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