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The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean

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The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the “Locus” class. Among the markers were 1,019 class I microsatellite markers with 2–3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2–5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map (; SoyGD). Identified were 1,053 1–6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20–24 bp oligomers that had Tm of 55 ± 1 C that would generate 100–500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.

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This research was funded in part by grants from the NSF 9872635, ISA 95–122–04; 98-122-02 and 02-127-03 and USB 2228-6228. The physical map was based upon work supported by the National Science Foundation under Grant No. 9872635. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. The continued support of SIUC, College of Agriculture and Office of the Vice Chancellor for Research to JA, SK and DAL is appreciated. The authors thank Dr. Q. Tao and Dr, H.B. Zhang for assistance with fingerprinting. We thank Dr. C. Town and Dr. C. Foo at TIGR for the BES.

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Correspondence to David A. Lightfoot.

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Communicated by F. J. Muehlbauer.

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Shultz, J.L., Kazi, S., Bashir, R. et al. The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114, 1081–1090 (2007).

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