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ARS Home » Research » Publications at this Location » Publication #128191
Title: SNP DETECTION AND MAPPING IN SOYBEAN AND RELATED GLYCINE SPECIES

Author
item CREGAN, PERRY
item ZHU, YOULIN - CHINA
item SONG, QIJIAN - CHINA

Submitted to: Plant and Animal Genome
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2002
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The frequency of sequence polymorphism within coding regions of cultivated soybean and its annual progenitor G. soja is perhaps an order of magnitude lower than that present in maize. Introns, 3' and 5' UTRs and associated genomic DNA exhibit higher levels of polymorphism and appear to be a good source of single nucleotide polymorphisms (SNPs) in soybean. SNP frequency is sufficient to create dense genetic maps for use in linkage analysis for the detection of major genes controlling traits of economic interest. The likelihood that SNPs will function in association analyses for discovery of genetic factors underlying complex traits is a a great extent a function of linkage disequilibrium (LD). A recent report in maize suggested that the low level of LD in that species would require marker densities of one SNP every 100 to 200 bp for genome-wide SNP scans (http://www.pnas.org/cgi/content/ full/98/16/9161). Our estimates of LD in soybean indicate much higher levels of LD suggesting the likelihood that lower SNP densities will permit successful allele mining of soybean germplasm. We have found that the use of single base extension assays analyzed using a Luminex flow cytometer provides inexpensive and high throughput SNP detection.