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Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum

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Abstract

To facilitate marker-assisted breeding and genetic analyses of pepper (Capsicum annuum), we developed non-redundant 2- or 3-base simple sequence repeat (SSR) markers from enriched C. annuum genomic libraries and from C. annuum cDNA sequences in public databases. The SSR-enriched libraries were constructed using combinations of three restriction enzymes (AluI, HaeIII, and RsaI) and two biotinylated oligonucleotides [b(GA)15 and b(CA)15]. Ultimately, we obtained 1,736 genomic SSR markers and 1,344 cDNA-derived SSR markers from 6,528 clones and 13,003 sequences, respectively. We mapped 597 markers, including 265 of the newly developed SSR markers, onto a linkage map by using doubled-haploid (DH) lines derived from an intraspecific cross of two pure lines of C. annuum (K9-11 × MZC-180). The map, designated as the KL-DH map, consisted of 12 linkage groups. The map covered a genetic distance of 2,028 cM, and the average distance between markers was less than 4 cM. The frame structure of the KL-DH map was compared with the published standard conserved ortholog set II (COSII) map, which was derived from an interspecific F2 population (C. frutescens × C. annuum), by using tomato (Solanum lycopersicum) chromosomal sequences to bridge the two maps. The intraspecific KL-DH map constructed in this study and the interspecific COSII map were similar in map length and marker distribution, suggesting that the KL-DH map covers nearly the whole genome of C. annuum.

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Acknowledgments

We thank N. Fukushima and Y. Kitamura of NIVTS for their technical assistance. This work was supported by grants from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Research and Development Projects for Application in Promoting New Policy of Agriculture, Forestry and Fisheries, grants 18047 and 22064).

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Author notes

  1. Yukari Semi

    Present address: Miyazaki Prefectural Higashiusuki Agricultural Community Development Bureau, 2-15 Atago, Nobeoka, Miyazaki, 882-0872, Japan

  2. Hiromasa Sawada

    Present address: Kochi Agricultural College, 234 Hakawa, Ino, Agawa, Kochi, 781-2128, Japan

  3. Yumi Utoyama

    Present address: Miyazaki Prefectural Nishiusuki Branch Office, 22 Mitai, Takachiho, Miyazaki, 882-1101, Japan

Authors and Affiliations

  1. Miyazaki Agricultural Research Institute, 5805 Shimonaka, Sadowara, Miyazaki, 880-0212, Japan

    Toru Sugita, Yukari Semi, Yumi Utoyama, Yuki Maehata & Ryutaro Nagata

  2. Kochi Prefectural Agriculture Research Center, 1100 Hataeda, Nankoku, Kochi, 783-0023, Japan

    Hiromasa Sawada, Yuko Hosomi & Eri Yoshimoto

  3. NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan

    Hiroyuki Fukuoka & Akio Ohyama

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  1. Toru Sugita
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  2. Yukari Semi
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  8. Hiroyuki Fukuoka
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  9. Ryutaro Nagata
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Correspondence to Akio Ohyama.

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Sugita, T., Semi, Y., Sawada, H. et al. Development of simple sequence repeat markers and construction of a high-density linkage map of Capsicum annuum . Mol Breeding 31, 909–920 (2013). https://doi.org/10.1007/s11032-013-9844-x

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