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

Association of markers and phenotypes through genetic linkage has focused primarily on two goals: marker The soybean [Glycine max (L.) Merr.] expressed sequence tagged assisted selection and map-based cloning. Marker as(EST) database is growing rapidly and promises to be a valuable resource for discovering agronomically important genes. Genetic sisted selection increases the efficiency of tracking traits maps featuring cDNA clones of known sequence and function are such as disease and pest resistance in cultivar developimportant because association of genes with phenotypes will increase ment programs by significantly reducing the amount of understanding of the molecular mechanisms affecting valuable agroscreening with pathogens and pests. Map-based cloning nomic traits. Our objective is to place sequenced cDNA (EST) and utilizes genetic linkages between molecular markers and genomic clones on an anchored soybean genetic map. The genetic important traits to establish physical linkages and evenmapping of these markers was conducted by standard restriction fragtually to isolate genes controlling economically imporment length polymorphism (RFLP) techniques with an F2 population tant phenotypes, such as resistance to nematodes (Cai of 149 individuals derived from a cross between two publicly available et al., 1997; Ganal et al., 1995) and bacterial diseases soybean genotypes cv. Noir 1 (PI 290136) and BARC-2 (Rj4) (PI (Mindrinos et al., 1994). Genetic maps containing EST 547895). DNA sequences of mapped EST and genomic clones were compared with accessions in GenBank, and significant sequence simiand sequenced genomic clone markers are especially larities are reported. The ESTs were more likely than the genomic useful toward this end. clones to have a significant similarity to a GenBank accession. Because Soybean genetic linkage maps have been developed the objective was to map ESTs and sequenced genomic clones, only with several different kinds of markers. These include the 24 linkage groups (1200 cM) containing the 39 mapped EST and RFLP, RAPD, AFLP, and SSR markers (Cregan et al., sequenced genomic clone markers plus the four phenotypic traits 1999; Keim et al., 1992; Lark et al., 1993; Shoemaker root fluorescence (Fr2), seed coat color (I ), flower color (W1) and and Olson, 1993; Shoemaker and Specht, 1995). Both nodulation response (Rj4) were presented. Amplified fragment length RFLP and SSR markers have been used reliably to align polymorphism (AFLP) and random amplified polymorphic DNA maps from different populations. SSR markers have (RAPD) markers were added to increase marker density. Simple been especially valuable because they are highly polysequence repeat (SSR) markers were included to align this map with other soybean maps. The population has been further advanced to morphic and utilize the ease and efficiency of the polydevelop a F8:9 recombinant inbred line population available to remerase chain reaction (PCR) (Akkaya et al., 1992; searchers interested in associating the mapped cDNAs with quantitaCregan et al., 1999). tively inherited traits. EST and sequenced genomic clone markers also can be converted to PCR based markers by designing primers from their sequences. When primers derived from T soybean expressed sequenced tag clone datathe sequences reveal useful polymorphisms with PCR base is growing rapidly and promises to be a valuassays, the loci they define are referred to as sequenced able resource for discovering genes of agronomic intertagged sites (STS). Primers designed to detect single est. ESTs are cDNA clones that have been partially or nucleotide differences between genotypes are called sincompletely sequenced. Sequence similarity to known gle nucleotide polymorphisms (SNPs). STS and SNP genes suggests gene function. These cDNA clones can assays are designed to be conserved with regard to gebe mapped by RFLP techniques just as cloned genomic nome location and to be highly polymorphic. Therefore, fragments have been mapped. Mapping of cDNA clones ESTs, sequenced genomic clone markers, and their places genes, some of known function and expression PCR-based derivatives are valuable tools for tracking pattern, in regions of the genome that can be correlated and isolating genes controlling economically important with phenotypes. Therefore, association of cDNA clone phenotypic traits. Our objective is to place EST and markers with phenotypes can increase our understandsequenced genomic clone markers on an anchored soying of biochemical pathways and mechanisms affecting bean genetic map. Several of these markers represent agronomically important traits. fully sequenced and characterized cDNA clones of known identity, and others have high sequence similarB.F. Matthews, J.M. Weisemann, H.S. Beard, K.S. Lewers, M.H. Macity with genes of known function. The map includes Donald, R. Maiti, and P.B. Cregan, Soybean and Alfalfa Research SSR and phenotypic markers, so it can be compared Laboratory, T.E. Devine, Weed Science Laboratory, M.J. Pedroni and J.A. Saunders, Climate Stress Laboratory, USDA-ARS, Beltsville, MD 20705; Y.-B. Park, Cheju National Univ., Dep. of HorticulAbbreviations: AFLP, amplified fragment length polymorphism; bp, ture, Cheju, Korea; J.-J. Lin and J. Kuo, Life Technologies, Inc., base pairs; cM, centimorgan; Da, dalton; EST, expressed sequence Gaithersburg, MD 20877. Received 22 March 2000. *Corresponding tagged; PCR, polymerase chain reaction; RAPD, random amplified author ([email protected]). polymorphic DNA; RFLP, Restriction fragment length polymorphism; SSR, simple sequence repeat. Published in Crop Sci. 41:516–521 (2001).