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An updated ‘Essex’ by ‘Forrest’ linkage map and first composite interval map of QTL underlying six soybean traits

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Abstract

DNA marker maps based on single populations are the basis for gene, loci and genomic analyses. Individual maps can be integrated to produce composite maps with higher marker densities if shared marker orders are consistent. However, estimates of marker order in composite maps must include sets of markers that were not polymorphic in multiple populations. Often some of the pooled markers were not codominant, or were not correctly scored. The soybean composite map was composed of data from five separate populations based on northern US germplasm but does not yet include ‘Essex’ by ‘Forrest’ recombinant inbred line (RIL) population (E × F) or any southern US soybean cultivars. The objectives were, to update the E × F map with codominant markers, to compare marker orders among this map, the Forrest physical map and the composite soybean map and to compare QTL identified by composite interval maps to the earlier interval maps. Two hundred and thirty seven markers were used to construct the core of the E × F map. The majority of marker orders were consistent between the maps. However, 19 putative marker inversions were detected on 12 of 20 linkage groups (LG). Eleven marker distance compressions were also found. The number of inverted markers ranged from 1 to 2 per LG. Thus, marker order inversions may be common in southern compared to northern US germplasm. A total of 61 QTL among 37 measures of six traits were detected by composite interval maps, interval maps and single point analysis. Seventeen of the QTL found in composite intervals had previously been detected among the 29 QTL found in simple interval maps. The genomic locations of the known QTL were more closely delimited. A genome sequencing project to compare Southern and Northern US soybean cultivars would catalog and delimit inverted regions and the associated QTL. Gene introgression in cultivar development programs would be accelerated.

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Acknowledgments

This research was funded over the past 11 years in part by grants from the NSF 9872635, ISA 95-122-04; 98-122-02 and 02-127-03 and USB 2228-6228. The integrated genetic and 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 MJI and DAL is appreciated. The authors thank Drs. P. Gibson, O. Myers Jr. and M. Schmidt for assistance with germplasm development and maintenance from 1991 to 2000.

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  1. J. Shultz

    Present address: Crop Genetics and Production Research Unit, USDA, Stoneville, MS, USA

  2. M. J. Iqbal

    Present address: Institute of Advance Learning, Blacksburg, VA, USA

Authors and Affiliations

  1. Plant Biotechnology and Genomics Core-Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA

    M. A. Kassem, J. Shultz, M. J. Iqbal & D. A. Lightfoot

  2. Plants and Microbes Genomics and Genetics Lab, Department of Plant Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901-4415, USA

    K. Meksem

  3. Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901-6509, USA

    A. J. Wood & D. A. Lightfoot

  4. Center for Excellence in Soybean Research, Teaching and Outreach, Southern Illinois University, Carbondale, IL, 62901, USA

    K. Meksem, Y. Cho, A. J. Wood & D. A. Lightfoot

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  1. M. A. Kassem
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Kassem, M.A., Shultz, J., Meksem, K. et al. An updated ‘Essex’ by ‘Forrest’ linkage map and first composite interval map of QTL underlying six soybean traits. Theor Appl Genet 113, 1015–1026 (2006). https://doi.org/10.1007/s00122-006-0361-8

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