Annotation of Cultivar Variations at the Multigeneic Rhg1/Rfs2 Locus:

Abstract

Soybean (Glycine max (L.) Merr.) suffers yield loss due to root infection from soil infestation by Heterodera glycine I. (soybean cyst nematode SCN) and Fusarium virguliforme (Aoki; sudden death syndrome (SDS)). The major locus for SCN and SDS resistance has previously been identified as Rhg1/Rfs2 (chr18; LG G) (site reference). The objective of this experiment was to compare the Sanger DNA sequence of a resistant cultivar ('Forrest') and two susceptible cultivars ('Williams 82' and 'Asgrow A3244'). Sequences were downloaded from GenBank for Williams 82, Phytzome for A3244 and a newly sequenced BAC-B73P06 (82,157 bp) encompassing the Rfs2/Rhg1 locus. Using the resistant cultivars, 800 single nucleotide polymorphisms (SNPs) and 57 indels were identified. In contrast, the susceptible cultivars had just 12 SNPs and no indels between them. Polymorphisms were clustered within 59 kbp, divided into three sections. There were 5 predicted recombination breakpoints. The third and fourth breakpoints were located before gene 3 and after gene 5 (Glyma18g02680; the RLK at Rhg1/Rfs2) which were therefore inferred to be derived from Peking, within the Rhg1/Rfs2 region. Comparisons of SNPs identified in Illumina sequences from 31 semi-domesticated genomes showed 80% of the total SNPs in Forrest were found among the genomes. Annotation and gene prediction showed the BAC gene prediction encoded 9-10 genes. There were 31 SNPs within exons and 137 among introns. Just 11 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.SNPs caused amino acid changes. There were 5 SNPs in cis regulatory elements (CREs) and 14 in promoters. Polymorphisms indicated the regions that were introgressed from Peking had defined limits. Proteins across the region were highly conserved compared to non-coding regions, suggesting purifying selection occurred.