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Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.)

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Abstract

Simple sequence repeats (SSRs) are highly polymorphic and co-dominant markers, providing an important genomic resource for genetic research. Recently, large-scale transcriptome sequencing has become a reliable and efficient approach for the identification and development of new genic-SSR markers and has been successfully conducted in a few important plant species. However, SSR development based on transcriptome sequencing remains limited in radish (Raphanus sativus L.). In the present study, from a total of 73,084 unigenes and 150,455 contigs which were assembled from 71.95 million Illumina sequence reads of a radish taproot library, a collection of 11,928 genic-SSR loci were successfully identified in 11,311 unigene sequences. Trinucleotide repeats were the most abundant repeat units, as in many other plants, with a frequency of 52 %. Furthermore, a total of 5,503 genic-SSR primers were developed, from which 1,052 SSR primers were synthesized, and a subset of 823 (78.23 %) primers could generate stable bands. Moreover, 67 selected informative genic-SSR markers were used to determine the genetic diversity of 32 radish genotypes, in which the polymorphism information content values ranged from 0.49 to 0.89. For effective cultivar identification, a novel strategy called manual cultivar identification diagram was employed. Thirty-two radish accessions were clearly separated by six genic-SSR markers. Additionally, the cross-species/genera transferability of these SSRs was further validated in nine relatives in Brassicaceae. These results suggested that the novel genic-SSR markers, as a basis for future genetic linkage and gene tagging analysis, could be very valuable in facilitating genetic mapping, marker-assisted selection and comparative genome analysis.

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Acknowledgments

This work was in part supported by grants from the Program for the National Key Technologies R&D Program of China (2012BAD02B01), the NSFC (31171956, 31372064), Key Technology R&D Program of Jiangsu Province (BE2010328, BE2013429), JASTIF [CX (12)2006, CX(13)2007] and the PAPD. We thank Dr. X. Zhu at North Dakota State University for his critical review and helpful comments during the preparation of this manuscript.

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  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Lulu Zhai, Liang Xu, Yan Wang, Huan Cheng, Yiqin Gong & Liwang Liu

  2. School of Earth and Environment, The UWA’s Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia

    Yinglong Chen

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  1. Lulu Zhai
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  2. Liang Xu
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  3. Yan Wang
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  7. Liwang Liu
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Correspondence to Liwang Liu.

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Zhai, L., Xu, L., Wang, Y. et al. Novel and useful genic-SSR markers from de novo transcriptome sequencing of radish (Raphanus sativus L.). Mol Breeding 33, 611–624 (2014). https://doi.org/10.1007/s11032-013-9978-x

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