title: Identification of high-quality single-nucleotide polymorphisms in Glycine latifolia using a heterologous reference genome sequence.
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.
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA.
authors.forename: Sungyul
authors.initials: S
authors.lastname: Chang
authors.forename: Glen L
authors.initials: GL
authors.lastname: Hartman
authors.forename: Ram J
authors.initials: RJ
authors.lastname: Singh
authors.forename: Kris N
authors.initials: KN
authors.lastname: Lambert
authors.forename: Houston A
authors.initials: HA
authors.lastname: Hobbs
authors.forename: Leslie L
authors.initials: LL
authors.lastname: Domier
mesh_terms: D001203:Ascomycota; D001483:Base Sequence; D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000382:microbiology; D013045:Species Specificity