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Transferability of rice SSR markers to Miscanthus sinensis, a potential biofuel crop

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Abstract

Miscanthus sinensis (M. sinensis) is a perennial C4 photosynthesis grass, with high yield, high efficiency of water usage, low fertilizer requirement, tolerance to extreme environments, and is one of the plant species with good biofuel potential. Simple sequence repeat (SSR) markers are highly informative and widely used in plant genetic studies. In this study, 88 SSR primer pairs derived from the rice genome, including 47 EST-SSRs (eSSRs) and 41 genomic SSRs (gSSRs), were evaluated for cross-species transferability to M. sinensis. Forty-one SSR primer pairs in total could successfully amplify DNA fragments in M. sinensis, showing an overall transferability rate of 46.6 % between rice and M. sinensis. The transferability rate of eSSR (51.1 %) was higher than that of gSSR (41.5 %). A total of 140 SSR loci and 340 alleles in the set of rice and M. sinensis germplasm collections were detected. Nei’s gene diversity varied from 0 to 0.72 and averaged 0.35. Shannon’s information index varied from 0 to 1.49 and averaged 0.56. The observed heterozygosity ranged from 0 to 0.95 and averaged 0.08. Thirty-nine loci (27.86 %) were shown heterozygosity out of 140 SSR loci. A dendrogram based on genetic distance showed a significant geographic differentiation. Our results indicated that 46.6% of the rice SSR markers are transferable to M. sinensis, and are useful for germplasm evaluation and genetic analysis in M. sinensis.

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Acknowledgments

This project was supported in part by the National Natural Science Foundation of China (NSFC) Grant Nos. 30870233 and 31030055, and the Chinese Academy of Sciences under the Important Directional Program of Knowledge Innovation Project Grant No. KSCX2-YW-Z-0722.

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Authors and Affiliations

  1. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China

    Jiangyan Yu, Hua Zhao, Liang Chen & Junhua Peng

  2. University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China

    Jiangyan Yu

  3. Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China

    Tingting Zhu

  4. Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80526-1170, USA

    Junhua Peng

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  1. Jiangyan Yu
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  2. Hua Zhao
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  3. Tingting Zhu
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  4. Liang Chen
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  5. Junhua Peng
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Correspondence to Junhua Peng.

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Yu, J., Zhao, H., Zhu, T. et al. Transferability of rice SSR markers to Miscanthus sinensis, a potential biofuel crop. Euphytica 191, 455–468 (2013). https://doi.org/10.1007/s10681-013-0915-1

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