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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #347122

Research Project: Development and Characterization of Soybean Germplasm, Curation of Stored Accessions, and Regional Evaluations of New Genotypes

Location: Crop Genetics Research

Title: Development of SSR markers for genetic diversity and phylogenetic studies of Phomopsis longicolla causing Phomopsis seed decay in soybean

Author
item Li, Shuxian
item Song, Qijian

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/17/2017
Publication Date: 1/13/2018
Citation: Li, S., Song, Q. 2018. Development of SSR markers for genetic diversity and phylogenetic studies of Phomopsis longicolla causing Phomopsis seed decay in soybean. Annual International Plant & Animal Genome Conference. Available: http://intlpag.org/2018/images/pdf/PAGXXVI-abstracts-posters.pdf. Paper No. P0786.

Interpretive Summary:

Technical Abstract: Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. The genome of P. longicolla type strain TWH P74 represents one of the important fungal pathogens in the Diaporthe-Phomopsis complex. In this study, the draft genome sequence of P. longicolla type strain TWH P74 was de novo assembled. The P. longicolla genome sequence provides molecular resources for developing genetic markers for P. longicolla. The draft genome size was approximately 64 Mb. We examined the simple sequence repeat (SSR) in the genome, and identified 12,624 SSRs with di-, tri-, and tetranucleotide repeats of five or more in the TWH P74 whole genome sequence, which included 1,972 SSRs consisting of repeat units of di- (>,= 9) (919), tri- (>,= 8) (369), and tetranucleotide (>,= 7) (684). Among the 1,972 SSRs, (AT)n, (ATT)n and (AAAT)n were the most abundant motifs among di-, tri-, and tetranucleotide SSRs, respectively. The SSR markers developed from whole genome sequence will be used to analyze the genetic diversity among P. longicolla isolates collected from different geographical origins, as well as their phylogenetic relationships.