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Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.)

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Abstract

Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di—(26.1 %), tetra—(11.5 %), penta—(9.7 %), and hexanucleotide (3.9 %). One hundred EST–SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST–SSR markers. Based on the 29 EST–SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST–SSR markers was also found for relative species.

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Acknowledgments

This research was funded by a Grant from National Key Technology R&D Program (2011BAD17B01) of People’s Republic of China and the Fundamental Scientific Research Fund from Chinese Academy of Agricultural Sciences of People’s Republic of China (2011cj-15).

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Authors and Affiliations

  1. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People’s Republic of China

    Zan Wang, Hongwei Yan, Xinnian Fu & Hongwen Gao

  2. Forage Improvement Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA

    Xuehui Li

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  1. Zan Wang
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  2. Hongwei Yan
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  3. Xinnian Fu
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  4. Xuehui Li
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Correspondence to Hongwen Gao.

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Wang, Z., Yan, H., Fu, X. et al. Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.). Mol Biol Rep 40, 3291–3298 (2013). https://doi.org/10.1007/s11033-012-2404-3

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  • DOI: https://doi.org/10.1007/s11033-012-2404-3

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