A Haplotype-based Mutation Analysis of Soybean Mutants Derived from a Gamma Radiation.

An allele combination at different loci on the same chromosome called as a haplotype is assumed to be informative for estimating a mutation frequency and type. Advantages of an SNP marker include its redundancy in a whole genome and relatively low mutation rate (10^-8) when compared to 10^-3 in an SSR (simple sequence polymorphism) marker, which allows a more reliable SNP application. The objective is to identify locus-specific SNP markers from a mutant pool of soybean and to estimate genetic variation created by the gamma mutagenesis. A total of 193 soybean accessions including thirteen originals and the derived mutants from a gamma radiation at 200 to 250 Gy doses were selected for a sequence comparison. A core set of 23 SNPs which were unigene-based and evenly spaced over the soybean genome was used to amplify the SNP-containing genomic fragments. The average size of the amplified regions was 750bp. A total of 30 SNP markers were detected, and these SNPs were located on 18 linkage groups. Types of SNPs were classified into 7 groups, encompassing A/-, A/G, A/T, C/G, C/T, G/T, and T/-. Results indicated that the identified SNPs were genotype-specific. A cluster analysis among the mutants based on the proportion of shared alleles on SNP loci confirmed the increased genetic diversity by 150% from the gamma radiation. A mutagenesis using a gamma radiation was proven to be useful to create new genetic resources which can be directly used for cultivar development and other genetic or genomic studies of soybean.