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Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence

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Abstract

Like many widely cultivated crops, soybean [Glycine max (L.) Merr.] has a relatively narrow genetic base, while its perennial distant relatives in the subgenus Glycine Willd. are more genetically diverse and display desirable traits not present in cultivated soybean. To identify single-nucleotide polymorphisms (SNPs) between a pair of G. latifolia accessions that were resistant or susceptible to Sclerotinia sclerotiorum (Lib.) de Bary, reduced-representations of DNAs from each accession were sequenced. Approximately 30 % of the 36 million 100-nt reads produced from each of the two G. latifolia accessions aligned primarily to gene-rich euchromatic regions on the distal arms of G. max chromosomes. Because a genome sequence was not available for G. latifolia, the G. max genome sequence was used as a reference to identify 9,303 G. latifolia SNPs that aligned to unique positions in the G. max genome with at least 98 % identity and no insertions and deletions. To validate a subset of the SNPs, nine TaqMan and 384 GoldenGate allele-specific G. latifolia SNP assays were designed and analyzed in F2 G. latifolia populations derived from G. latifolia plant introductions (PI) 559298 and 559300. All nine TaqMan markers and 91 % of the 291 polymorphic GoldenGate markers segregated in a 1:2:1 ratio. Genetic linkage maps were assembled for G. latifolia, nine of which were uninterrupted and nearly collinear with the homoeologous G. max chromosomes. These results made use of a heterologous reference genome sequence to identify more than 9,000 informative high-quality SNPs for G. latifolia, a subset of which was used to generate the first genetic maps for any perennial Glycine species.

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Abbreviations

ITS:

Internal transcribed spacer

PCR:

Polymerase chain reaction

PI:

Plant introduction

QTL:

Quantitative trait loci

SNP:

Single-nucleotide polymorphism

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Acknowledgments

This study was supported by funding from the National Sclerotinia Initiative and the United States Department of Agriculture-Agricultural Research Service. Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the USDA or the University of Illinois and does not imply its approval to the exclusion of other products or vendors that may also be suitable.

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Authors and Affiliations

  1. Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA

    Sungyul Chang, Glen L. Hartman, Kris N. Lambert, Houston A. Hobbs & Leslie L. Domier

  2. United States Department of Agriculture, Agricultural Research Service, Urbana, IL, 61801, USA

    Glen L. Hartman, Ram J. Singh & Leslie L. Domier

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  1. Sungyul Chang
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  2. Glen L. Hartman
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Correspondence to Leslie L. Domier.

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Communicated by J. Ray.

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Chang, S., Hartman, G.L., Singh, R.J. et al. Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence. Theor Appl Genet 126, 1627–1638 (2013). https://doi.org/10.1007/s00122-013-2079-8

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