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Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]

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Abstract

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F2 population, i.e. “B100” of cultivated S. italica and “A10” of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces’ grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

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Acknowledgments

We thank Dr M. Gale of John Innes Center for providing seeds of the mapping population, Dr K. Devos of the University of Georgia at Athens for providing RFLP data and advice, and Prof. Ping Lu for providing seeds of foxtail millet accessions. We also thank two anonymous reviewers for valuable suggestions and careful corrections. This research was supported by the Basic Research Program (grant no. 2005CCA02500) and National Research Program for Public Will (grant no. 2005DIA4J019) of the Ministry of Science and Technology of China, and National Natural Science Foundation (grant no. 30571168).

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  1. Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), 100081, Beijing, People’s Republic of China

    Xiaoping Jia, Zhongbao Zhang, Yinghui Liu, Chengwei Zhang, Yunsu Shi, Yanchun Song, Tianyu Wang & Yu Li

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  1. Xiaoping Jia
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  2. Zhongbao Zhang
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Correspondence to Tianyu Wang or Yu Li.

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Communicated by A. Schulman.

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Jia, X., Zhang, Z., Liu, Y. et al. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theor Appl Genet 118, 821–829 (2009). https://doi.org/10.1007/s00122-008-0942-9

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