Skip to main content
ARS Home » Research » Publications at this Location » Publication #191365
Title: SATURATION OF THE RHG1 GENOMIC REGION WITH SNP MARKERS TO DETERMINE LINKAGE DRAG IN RESISTANT SOYBEAN CULTIVARS AND TO DEMONSTRATE ASSOCIATION ANALYSIS IN SOYBEAN

Author
item HYTEN, DAVID
item CREGAN, PERRY

Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 2/1/2006
Publication Date: 2/1/2006
Citation: Hyten, D.L., Cregan, P.B. 2006. Saturation of the rhg1 genomic region with snp markers to determine linkage drag in resistant soybean cultivars and to demonstrate association analysis in soybean. International Plant and Animal Genome IX Conference. January 13-17, 2006, San Diego, CA. p. 414.

Interpretive Summary:

Technical Abstract: The resistant gene rhg1, confers resistance to soybean cyst nematode (SCN), but can limit the gains produced from creating SCN resistant cultivars due to linkage drag. Since a candidate rhg1 gene has been identified, within a 336-kb sequenced region, the amount of linkage disequilibrium (LD) can determine if linkage drag is being eliminated, or if more targeted recombinant backcross breeding is needed. This region can also be used to demonstrate how well association analysis will work in soybean, since it is known that this region contributes to SCN resistance. We have previously discovered 291 single nucleotide polymorphisms (SNPs) throughout this 336-kb region. We genotyped, via resequencing, 135 of the 291 SNPs in 82 SCN resistant soybean cultivars and 50 SCN susceptible cultivars. The program Haploview was used to calculate linkage disequilibrium, determine haplotypes, and to perform a case/control association analysis for SCN. The entire region is under complete LD which contributes to 67 SNPs throughout the region being significantly associated with SCN. Specifically, the promoter region of the candidate SCN gene contained four SNPs which were highly associated with SCN. A few resistant cultivars had a recombination within the 336-kb region which eliminated sequence from the resistant parent thus reducing linkage drag. These cultivars with limited linkage drag should be used in future crosses to reduce the level of linkage drag upstream of the rhg1 gene. In addition, it seems likely that association analysis will be a successful method for mapping genes associated with traits in soybean.