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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.)

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Abstract

Capsicum annuum, 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 linkage 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 Biotechnology 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 chromosomes 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, screening 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 cultivars of this important field crop in the future.

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Acknowledgments

This work was supported by the National Key Technology R&D Program of the Ministry of Science and Technology (2012BAD50G00, 2012BAD02B02), Beijing Municipal Natural Science Foundation (6152010), and National Natural Science Foundation of China (31201624).

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Authors and Affiliations

  1. College of Horticulture, China Agricultural University, Beijing, 100193, People’s Republic of China

    Xiao-fen Zhang & Qian Wang

  2. Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, 100097, People’s Republic of China

    Xiao-fen Zhang, Hong-he Sun, Yong Xu, Bin Chen, Shuan-cang Yu & San-sheng Geng

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  1. Xiao-fen Zhang
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  2. Hong-he Sun
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  6. San-sheng Geng
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Correspondence to San-sheng Geng or Qian Wang.

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Fig. S1

Photographs of parental lines PM702 (A) and FS871 (B). (PNG 4998 kb)

Fig. S2

Graphical genotypes of RILs for all chromosomes. Individual codes are listed on the left side, and all chromosome numbers are listed above. The chromosomes are presented in columns with red parts and blue parts representing FS871 and PM702, bice parts and brown parts representing FS871 and PM702 too, which mean loci are single dominant, and green parts indicate the data absent, and light blue parts represent heterozygosity. (JPEG 3331 kb)

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Zhang, Xf., Sun, Hh., Xu, Y. et al. 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.). Mol Breeding 36, 92 (2016). https://doi.org/10.1007/s11032-016-0517-4

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