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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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Abstract

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 (http://www.soybeangenome.siu.edu; 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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References

  • Ansari HA, Ellison NW, Griffiths AG, Williams WM (2004) A lineage-specific centromeric satellite sequence in the genus Trifolium. Chromosome Res 12:357–367

    Article  PubMed  CAS  Google Scholar 

  • Areshchenkova T, Ganal MW (1999) Long tomato microsatellites are predominantly associated with centromeric regions. Genome 42:536–544

    Article  PubMed  CAS  Google Scholar 

  • Cregan PB, Mudge J, Fickus EW, Danesh D, Denny R, Young ND (1999a) Two simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1 locus. Theor Appl Genet 99:811–818

    Article  CAS  Google Scholar 

  • Cregan PB. Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler AL, Kaya N, VanToai TT, Lohnes DG, Chung J (1999b) An integrated genetic linkage map of the soybean genome. Crop Sci 39:1464–1490

    Article  Google Scholar 

  • Demirbas A, Rector BG, Lohnes DG, Fioritto RJ, Graef GL, Cregan PB, Shoemaker RC, Specht JE (2001) Simple sequence repeat markers linked to the soybean Rps genes for phytophthora resistance. Crop Sci 41:1220–1227

    Article  CAS  Google Scholar 

  • Gore MA, Hayes AJ, Jeong SC, Yue YG, Buss GR, Maroof S (2002) Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 45:592–599

    Article  PubMed  CAS  Google Scholar 

  • Guo B, Sleper DA, Arelli PR, Shannon JG, Nguyen HT (2005) Identification of QTLs associated with resistance to soybean cyst nematode races 2, 3 and 5 in soybean PI 90763. Theor Appl Genet. 111:965–971

    Article  PubMed  CAS  Google Scholar 

  • Iqbal MJ, Meksem K, Njiti VN, Kassem M, Lightfoot DA (2001) Microsatellite markers identify three additional quantitative trait loci for resistance to soybean sudden death syndrome (SDS) in Essex x Forrest RILs. Theor Appl Genet 102:187–192

    Article  CAS  Google Scholar 

  • Kassem MA, Shultz J, Meksem K, Wood AJ, Iqbal MJ, Lightfoot DA (2006) An Updated ‘Essex’ by ‘Forrest’ Linkage Map and First Composite Interval Map of QTL Underlying Six Soybean Traits. Theor Appl Genet 113:1015–1026

    Article  PubMed  CAS  Google Scholar 

  • Kazi S (2005) Minimum tile derived microsatellite markers improve the physical map of the soybean genome and the Flyer by Hartwig Genetic map. MS. MBMB, SIUC. Pp208

  • Kazi S, Shultz JL, Bashir R, Afzal J, Njiti VN, Lightfoot DA (2006) Identification of loci underlying resistance to soybean sudden death syndrome in ‘Hartwig’ by ‘Flyer’. Theoret Appl Genet (in review)

  • Lightfoot DA, Njiti VN, Gibson PT, Kassem MA, Iqbal JM, Meksem K (2005) Registration of the Essex by Forrest recombinant inbred line mapping population. Crop Sci 45:1678–1681

    Article  Google Scholar 

  • Lark KG, Weisemann JM, Mathews BF, Palmer R, Chase K, Macalma T (1993) A genetic map of soybean (Glycine max L.) using an intraspecific cross of two cultivars: ‘Minsoy’ (sic) and ‘Noir 1’. Theor Appl Genet 86:901–906

    Article  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom RJ, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  PubMed  CAS  Google Scholar 

  • Meksem K, Zobrist K, Ruben E, Hyten D, Quanzhou T, Zhang HB, Lightfoot DA (2000) Two large-insert soybean genomic libraries constructed in a binary vector: applications in chromosome walking and genome wide physical mapping. Theor Appl Genet 101:747–755

    Article  CAS  Google Scholar 

  • Meksem K, Pantazopoulos P, Njiti VN, Hyten DL, Arelli PR, Lightfoot DA (2001a) ‘Forrest’ resistance to the soybean cyst nematode is bigenic: saturation mapping of the Rhg1 and Rhg4 loci. Theor Appl Genet 103:710–718

    Article  CAS  Google Scholar 

  • Meksem K, Njiti VN, Banz WJ, Iqbal MJ, Kassem MA, Hyten DL, Yuang J, Winters TA, Lightfoot DA (2001b) Genomic regions that underlie soybean seed isoflavone content. J Biomed Biotechnol 1:38–44

    Article  CAS  Google Scholar 

  • Njiti VN, Meksem K, Iqbal MJ, Johnson JE, Kassem MA, Zobrist KF, Kilo VY, Lightfoot DA (2002) Common loci underlie field resistance to soybean sudden death syndrome in Forrest, Pyramid, Essex, and Douglas. Theor Appl Genet 104: 294–300

    Article  PubMed  CAS  Google Scholar 

  • Paniego N, Echaide M, Munoz M, Fernandez L, Torales S, Faccio P, Fuxan I, Carrera M, Zandomeni R, Suarez EY, Hopp HE (2002) Microsatellite isolation and characterization in sunflower (Helianthus annuus L.). Genome 45:34–43

    Article  PubMed  CAS  Google Scholar 

  • Rota ML, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23–32

    Article  PubMed  CAS  Google Scholar 

  • Ruben E, Jamai A, Afzal J, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Arelli PR, Town CD, Meksem K, Lightfoot DA (2006) Genomic analysis of the ‘Peking’ rhg1 locus: Candidate genes that underlie soybean resistance to the cyst nematode. Mol Gen Genome 276:320–330. doi: s00438-006-0150-8

    Google Scholar 

  • Shultz JL, Meksem K, Lightfoot DA (2003a) Evaluating physical maps by clone location comparison. Genome Lett 2:99–107

    Article  CAS  Google Scholar 

  • Shultz JL, Meksem K, Shetty J, Town CD, Koo H, Potter J, Wakefield K, Zhang HB, Wu C, Lightfoot DA (2003b) End sequencing of BACs comprising a provisional tiling path from a fingerprint physical map of soybean (Glycine max) cultivar Forrest. Genbank. CG812653 to CG826126 (13,473 sequences)

  • Shultz JL, Kurunam DJ, Shopinski KL, Iqbal MJ, Kazi S, Zobrist K, Bashir R, Yaegashi S, Lavu N, Afzal A, Yesudas CR, Kassem MA, Wu C, Zhang HB, Town CD, Meksem K, Lightfoot DA (2006) The soybean genome database (SoyGD): a browser for display of duplicated, polyploid regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max. Nucleic Acids Res 34:D758–D765

    Article  PubMed  CAS  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  PubMed  CAS  Google Scholar 

  • Temnykh SG, DeClerck A, Lukashova L, Lipovich S, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • Triwitayakorn K, Njiti VN, Iqbal MJ , Yaegashi S, Town CD, Lightfoot DA (2005) Genomic analysis of a region encompassing QRfs1 and QRfs2: genes that underlie soybean resistance to sudden death syndrome. Genome Génome 48:125–138

    Article  CAS  Google Scholar 

  • Walling JG, Shoemaker RC, Young ND, Mudge J, Jackson SA (2006) Chromosome level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps. Genetics 172: 1893–1900

    Article  PubMed  CAS  Google Scholar 

  • Wu CS, Sun P, Nimmakayala P, Santos FA, Meksem K, Springman R, Ding K, Lightfoot DA, Zhang HB (2004) A BAC- and BIBAC-based physical map of the soybean genome. Genome Res 14:319–26

    Article  PubMed  CAS  Google Scholar 

  • Yuan J, Njiti VN, Meksem K, Iqbal MJ, Triwitayakorn K, Kassem MA, Davis GT, Schmidt ME, Lightfoot DA (2002) Quantitative trait loci in two soybean recombinant inbred line populations segregating for yield and disease resistance. Crop Sci 42:271–277

    Article  PubMed  CAS  Google Scholar 

  • Yamanaka N, Ninomiya S, Hoshi M, Tsubokura Y, Yano M, Nagamura Y, Sasaki T, Harada K (2001) An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion. DNA Res 8:61–72

    Article  PubMed  CAS  Google Scholar 

  • Zhang WK, Wang YJ, Luo GZ, Zhang JS, He CY, Wu XL, Gai JY, Chen SY (2004). QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor Appl Genet 108:1131–9

    Article  PubMed  CAS  Google Scholar 

  • Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–34

    PubMed  CAS  Google Scholar 

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Acknowledgments

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). https://doi.org/10.1007/s00122-007-0501-9

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