SOYBEAN UNIGENES – USING SNPS TO DETERMINE THEIR GENETIC MAP POSITION

Authors: CHOI, IK-YOUNG - KOREA; SONG, Q - UNIVERSITY OF MARYLAND; HYTEN, DAVID; REITER, R - MONSANTO CO.; LEE, M - GENAISSANCE PHARMAC.; HWANG, E - UNIVERSITY OF MARYLAND; COSTA, J - UNIVERSITY OF MARYLAND; SHOEMAKER, RANDY; CHASE, K - UNIVERSITY OF UTAH; LARK, K - UNIVERSITY OF UTAH; SPECHT, J - UNIVERSITY OF NEBRASKA; CREGAN, PERRY

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 5/30/2006
Publication Date: 5/30/2006
Citation: Choi, I., Song, Q.J., Hyten, D.L., Reiter, R., Lee, M.S., Hwang, E.Y., Costa, J.M., Shoemaker, R.C., Chase, K., Lark, K.G., Specht, J.E., Cregan, P.B. 2006. Soybean unigenes – using snps to determine their genetic map position [abstract]. Annual International Plant & Animal Genome Conference, January 13-17, 2006, San Diego, CA. p.189.

Interpretive Summary:

Technical Abstract: Single Nucleotide Polymorphisms (SNPs) were discovered in more than 1000 soybean unigenes via resequencing. Resequencing determined the presence of polymorphism in two of the five mapping populations used to develop the current simple sequence repeat-based soybean linkage map constructed using JoinMap analysis (http://bldg6.arsusda.gov/~pooley/soy/cregan/soymap.htm). SNPs were mapped in either the Univ. of Utah Minsoy x Noir 1 or Minsoy x Archer recombinant inbred line (RIL) mapping populations each consisting of 89 RILs. Assays were designed and genotypes were determined using the Sequenom Mass Array system. Analysis of the genotyping data indicated that the density of unigene-based SNPs mapped to each linkage group deviated from expectation in only two of the 20 linkage groups indicating a generally uniform distribution of unigenes, except for the greater than anticipated unigene density present on linkage groups D2 and J. A theoretical distribution of map distances between adjacent unigenes was estimated based on the assumption that the unigenes are randomly distributed over the total length of the linkage map. A total of 1000 permutations were used to provide a representative theoretical distribution of adjacent unigenes. The observed and theoretical distributions of map distances between adjacent unigenes were significantly different as determined by Fisher’s Exact Test. Thus, more unigenes than expected were closely linked (i.e., within less than 1 cM intervals). This result clearly indicates soybean unigenes are aggregated into clusters along linkage groups.