Fine mapping of the SCN resistance QTL cqSCN-006 and cqSCN-007 from Glycine soja PI 468916

The majority of soybean cyst nematode (Heterodera glycines Ichinohe, SCN) resistant cultivars available to growers in the northern USA have resistance originating from PI 88788, which is losing its effectiveness to shifting SCN populations. The novel resistance quantitative trait loci (QTL) cqSCN-006 and cqSCN-007 were mapped from Glycine soja Sieb. and Zucc. plant introduction 468916. The objective of this study was to further narrow down these QTL intervals to improve the effectiveness of marker-assisted selection for resistance and to provide resources for cloning these genes. The fine mapping was initiated by screening recombinant plants using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers that flank these QTL. Selected recombinant plants were tested with additional genetic markers saturating the QTL intervals and progeny from the recombinant plants were then tested for resistance in a SCN bioassay. These efforts resulted in the fine mapping of cqSCN-006 into a 212.1 kb interval and cqSCN-007 to a 103.2 kb interval on the Williams 82 reference genome (Glyma.Wm82.a2), which reduced the interval size compared to previous fine mapping by 74 and 30%. One gene located in the cqSCN-006 region was predicted to encode a γ-soluble N-ethylmaleimide–sensitive factor attachment protein, which is involved in the same process as α-SNAP, one of the required components in Rhg1 mediated SCN resistance. The identified SSR and SNP markers close to these novel SCN resistance QTL and the candidate gene information presented in this study will be significant resources for MAS and gene cloning research.