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CELL BIOLOGY & MOLECULAR GENETICS

Incorporation of Sequenced cDNA and Genomic Markers into the Soybean Genetic Map

^a Climate Stress Laboratory, USDA-ARS, Beltsville, MD 20705
^b Cheju National Univ., Dep. of Horticulture, Cheju, Korea
^c Life Technologies, Inc., Gaithersburg, MD 20877

Corresponding author (matthewb{at}ba.ars.usda.gov)

The soybean [Glycine max (L.) Merr.] expressed sequence tagged (EST) database is growing rapidly and promises to be a valuable resource for discovering agronomically important genes. Genetic maps featuring cDNA clones of known sequence and function are important because association of genes with phenotypes will increase understanding of the molecular mechanisms affecting valuable agronomic traits. Our objective is to place sequenced cDNA (EST) and genomic clones on an anchored soybean genetic map. The genetic mapping of these markers was conducted by standard restriction fragment length polymorphism (RFLP) techniques with an F₂ population of 149 individuals derived from a cross between two publicly available soybean genotypes cv. Noir 1 (PI 290136) and BARC-2 (Rj₄) (PI 547895). DNA sequences of mapped EST and genomic clones were compared with accessions in GenBank, and significant sequence similarities are reported. The ESTs were more likely than the genomic clones to have a significant similarity to a GenBank accession. Because the objective was to map ESTs and sequenced genomic clones, only the 24 linkage groups (1200 cM) containing the 39 mapped EST and sequenced genomic clone markers plus the four phenotypic traits root fluorescence (Fr₂), seed coat color (I), flower color (W₁) and nodulation response (Rj₄) were presented. Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were added to increase marker density. Simple sequence repeat (SSR) markers were included to align this map with other soybean maps. The population has been further advanced to develop a F_8:9 recombinant inbred line population available to researchers interested in associating the mapped cDNAs with quantitatively inherited traits.

Abbreviations: AFLP, amplified fragment length polymorphism • bp, base pairs • cM, centimorgan • Da, dalton • EST, expressed sequence tagged • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • RFLP, Restriction fragment length polymorphism • SSR, simple sequence repeat

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