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Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps

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Abstract

Despite the intensive soybean [Glycine max (L.) Merrill] genome studies, the high chromosome number (20) of the soybean plant relative to many other major crops has hindered the development of a high-resolution genomewide genetic map derived from a single population. Here, we report such a map, which was constructed in an F15 population derived from a cross between G. max and G. soja lines using indel polymorphisms detected via a G. soja genome resequencing. By targeting novel indel markers to marker-poor regions, all marker intervals were reduced to under 6 cM on a genome scale. Comparison of the Williams 82 soybean reference genome sequence and our genetic map indicated that marker orders of 26 regions were discrepant with each other. In addition, our comparison showed seven misplaced and two absent markers in the current Williams 82 assembly and six markers placed on the scaffolds that were not incorporated into the pseudomolecules. Then, we showed that, by determining the missing sequences located at the presumed beginning points of the five major discordant segments, these observed discordant regions are mostly errors in the Williams 82 assembly. Distributions of the recombination rates along the chromosomes were similar to those of other organisms. Genotyping of indel markers and genome resequencing of the two parental lines suggested that some marker-poor chromosomal regions may represent introgression regions, which appear to be prevalent in soybean. Given the even and dense distribution of markers, our genetic map can serve as a bridge between genomics research and breeding programs.

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Acknowledgements

This work was supported mainly by a grant from the Next-Generation BioGreen 21 Program (No. PJ008124), Rural Development Administration, and partly by the Korea Research Institute of Bioscience and Biotechnology Research Initiative Program. We are grateful to Dr. Perry Cregan for his critical comments on an early version of this paper and Dr. Scott Jackson for discussions.

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Authors and Affiliations

  1. Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk, 363-883, Republic of Korea

    Woo Kyu Lee, Namhee Jeong & Soon-Chun Jeong

  2. Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Republic of Korea

    Namshin Kim, Jiwoong Kim, Sang Cheol Kim & Won-Hyong Chung

  3. National Institute of Crop Science, Rural Development Administration, Suwon, 441-857, Republic of Korea

    Jung-Kyung Moon

  4. National Instrumentation Center for Environmental Management, Seoul National University, Seoul, 151-921, Republic of Korea

    Ik-Young Choi

  5. Department of Crop Science, Chungbuk National University, Cheongju, 361-763, Republic of Korea

    Hong Sig Kim

  6. Department of Plant Science, Research Institute for Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Republic of Korea

    Suk-Ha Lee

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  1. Woo Kyu Lee
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  2. Namshin Kim
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  3. Jiwoong Kim
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  9. Hong Sig Kim
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  10. Suk-Ha Lee
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Correspondence to Soon-Chun Jeong.

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Communicated by R. Snowdon.

W. K. Lee and N. Kim made equal contributions.

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Lee, W.K., Kim, N., Kim, J. et al. Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps. Theor Appl Genet 126, 1103–1119 (2013). https://doi.org/10.1007/s00122-012-2039-8

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