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Sequencing, Assembly, and Annotation of the Soybean Genome

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The Soybean Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

Abstract

Genome sequencing yields an exceptional resource of genetic information. Knowledge of whole genome sequence information helps characterize individual genomes, transcriptional states and genetic variation in populations and provide genetic architecture associated with each trait. After the release of the first human genome assembly, other model organism assemblies became available; including the model plant Arabidopsis thaliana. The soybean community published the first reference genome of the variety Williams 82 in 2010. Soybean has important syntenic relationships with the other legume species and is a model plant for the legumes. In this chapter, we discuss about the soybean genome assemblies and annotations, and its fine-tuning in view of the next-generation sequencing technologies and bioinformatics tools. In addition, comparison of the structural variations between the cultivated reference genome with the available wild soybean genome information will be discussed. This is followed by the discussion on the opportunities of next-generation sequencing technologies and challenges that we anticipate on the development of more pangenomes and reference genomes for soybean. This will significantly affect the discovery of rare alleles associated with key agronomic and quality traits and shape up the next-generation breeding technologies and crop improvement.

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Acknowledgements

The authors are grateful to the United Soybean Board and the United States Department of Agriculture for project support.

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Authors and Affiliations

  1. Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA

    Babu Valliyodan & Henry T. Nguyen

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

    Suk-Ha Lee

Authors
  1. Babu Valliyodan
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  2. Suk-Ha Lee
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  3. Henry T. Nguyen
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Correspondence to Babu Valliyodan .

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Editors and Affiliations

  1. Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, USA

    Henry T. Nguyen

  2. Department of Agronomy, Iowa State University, Ames, Iowa, USA

    Madan Kumar Bhattacharyya

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Valliyodan, B., Lee, SH., Nguyen, H.T. (2017). Sequencing, Assembly, and Annotation of the Soybean Genome. In: Nguyen, H., Bhattacharyya, M. (eds) The Soybean Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-64198-0_5

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