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Development of a SCAR marker for early identification of S-cytoplasm based on mitochondrial SRAP analysis in pepper (Capsicum annuum L.)

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Abstract

Molecular markers, coxII SCAR, atp6-2 SCAR and accD-U, have been used for marker-assisted selection of cytoplasmic male sterility (CMS) in pepper. However, the presence of these markers at the sub-stoichiometric level in maintainer lines affects the reliable selection of male sterile (S-) cytoplasm. This study aimed to develop a new CMS-specific molecular marker, SCAR130, for reliable identification of S-cytoplasm in pepper, while the new and three previous molecular markers were used to determine the cytoplasm types of pepper lines. Based on mitochondrial genome sequence related amplified polymorphism (SRAP) analysis of the CMS lines and the maintainer lines, SCAR130 was developed from a 10-bp deletion at the SRAP primer binding site in the CMS line (130 bp) compared with that in the maintainer line (140 bp). S-cytoplasm could be unambiguously selected from the pepper lines by the different length of the marker bands. Application of the four molecular markers to various pepper lines revealed that SCAR130 is more reliable than the other three previous markers, orf507, ψatp6-2 and accD-U. Homology alignment with BLAST showed that the marker was located between trnE and trnS in the Nicotiana tabacum mitochondrial genome. Furthermore, expression of the marker-linked gene was significantly higher at the pollen abortive stage in the CMS line (HW203A) than in the maintainer line, which indicated that the marker was closely related to male sterility. Hence, factors other than orf507 and ψatp6-2 may exist for the regulation of male sterility in pepper.

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Acknowledgments

This research was supported by the National Natural Science Foundation of China (No. 31272163), “The Twelfth Five-Year” Plan of National Science and Technology in Rural Areas (No. 2011BAD12B03), the Shaanxi Provincial Science and Technology Coordinating Innovative Engineering Project (2012KTCL02-09) and the Northwest A&F University Cyrus Tang Seed Development Fund.

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Authors and Affiliations

  1. College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Jiao-Jiao Ji, Wei Huang, Yan-Xu Yin, Zheng Li & Zhen-Hui Gong

  2. State Key Laboratory for Stress Biology of Arid Region Crop, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Wei Huang, Zheng Li & Zhen-Hui Gong

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  1. Jiao-Jiao Ji
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  2. Wei Huang
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  3. Yan-Xu Yin
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  4. Zheng Li
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  5. Zhen-Hui Gong
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Correspondence to Zhen-Hui Gong.

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Jiao-Jiao Ji and Wei Huang have contributed equally to this work.

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Ji, JJ., Huang, W., Yin, YX. et al. Development of a SCAR marker for early identification of S-cytoplasm based on mitochondrial SRAP analysis in pepper (Capsicum annuum L.). Mol Breeding 33, 679–690 (2014). https://doi.org/10.1007/s11032-013-9984-z

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