Quantitative trait loci underlying resistance to the soybean cyst nematode in PI 507354

Due to the current prevalence and shift in virulence of Heterodera glycines, the soybean cyst nematode (SCN), there is a pressing need to find sustainable alternatives or complements to the commonly found Rhg1 and Rhg4 resistance loci. The objective of this study was to find novel quantitative trait loci (QTL) to expand the toolbox for SCN resistance. To do so, a population of recombinant inbred lines named QS13073 was generated from a biparental cross between an SCN-susceptible cultivar (S12-A5) and an SCN-resistant accession (PI 507354, also named Tokei 421). Using four mapping algorithms (SMA, ICIM, GCIM, and R/qtl2), seven loci, including rhg1a and Rhg4-a, involved in the resistance to SCN Hg type 5.7 were identified. To the best of our knowledge, two QTL (Chr.10-QTL and Chr.19-QTL) were novel, while three others (Chr.07-QTL, Chr.14-QTL, and Chr.20-QTL) were previously identified by other researchers. Based on statistical analyses, two loci, Chr.10-QTL and Chr.20-QTL, seemed to be partially viable alternatives to the rhg1a and Rhg4-a loci, as they were demonstrated to be effective in the Rhg1 and/or Rhg4 susceptible backgrounds. Using a four-step prediction pipeline, seven candidate genes ( Glyma.07G196800, Glyma.07G199700, Glyma.07G203300, Glyma.07G206200, Glyma.14G019600, Glyma.14G025800, and Glyma.20G197600) were identified in the narrow regions of Chr.07-QTL, Chr.14-QTL, and Chr.20-QTL. Based on these predictions and a thorough literature review, we consider that Glyma.07G196800, Glyma.07G203300, and Glyma.07G206200 are the best candidates for Chr.07-QTL. In conclusion, our study strengthens our understanding of the genetic loci underlying SCN resistance and diversifies the single nucleotide polymorphism marker catalog currently available to breeders.