Polymorphisms at a Multi-Genic Multi-Pathogen Resistance Locus in Soybean

Soybean’s (Glycine max (L.) Merr.) major pathogens are Heterodera glycine I. (agent of soybean cyst nematode SCN or moonlight disease) and Fusarium virguliforme (Snyder, Haas, Aoki; agent of sudden death syndrome (SDS)). The major resistance locus to both pathogens was the Rhg1/Rfs2 locus located on chromosome 18. Analysis of Sanger DNA sequence of a bacterial artificial chromosome (BAC) clone, (B73P06) of 82,157 bp in insert size, that contained the Rfs2/Rhg1 locus identified 800 SNPs (1bp) and 57 indels (of 2-56 bp) between a resistant (‘Forrest’) and two susceptible cultivars (‘Williams 82’ and ‘Asgrow 3244’). The susceptible cultivars had just 12 SNPs and no indels between them. The 800 polymorphisms between the resistant and susceptible cultivars clustered within 59 kbp of the insert, in three sections that had probably resulted from 6 or more recombination events (743 SNPs in the 59 Kbp; from 1,500–60,500 bp). There were 5 predicted recombination breakpoints found at 733; 6,601; 15,035; 44,740 and 79,211 bp. The third and fourth breakpoints were located before gene 3 (Glyma18g02670) and after gene 5 (Glyma18g02680; the RLK at Rhg1/Rfs2) so genes 3,4 and 5 were inferred to be Peking derived DNA within Rhg1/Rfs2 region.  The highly polymorphic DNA was inferred to be from the resistance donor Peking. Comparisons of single nucleotide polymorphisms (SNPs) identified in Illumina sequences from 31 semi-domesticated and domesticated Glycine sp. genomes showed 80% of the total SNPs that were found in B73P06 and that Forrest had 79% of all SNPs found among the 31 genomes.