The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) generates more damage to soybean [Glycine max (L.) Merr.] than any other parasite in most soybeanproducing countries. The use of SCN-resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN-resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift in nematode virulence to overcome the resistance. Furthermore, PI 88788 and other sources of resistance characterized to date belong to maturity groups (MGs) III and higher, making them less attractive to develop early maturing soybean varieties (MGs 0-000). In this work, we performed a quantitative trait loci (QTL) analysis of the SCNresistant soybean accession PI 494182 (MG 0). A recombinant inbred lines (RILs) population ('Costaud' × PI 494182) segregating for SCN resistance was challenged with SCN (H. glycines [HG] type 0) and genotyped via genotyping-by-sequencing (GBS) to produce a genetic map. Six resistance QTL were identified, including a potentially new resistance locus on chromosome 07. A subset of the RIL population was confronted to a HG type 2.5.7 SCN population and some of these exhibited resistance toward this type. Whole-genome sequencing of PI 494182 and Costaud allowed us to determine the alleles and their copy number for three candidate genes: GmSNAP11, GmSNAP18 (Rhg1), and GmSHMT08 (Rhg4). Finally, we determined that selecting for PI 494182 alleles at some SCN-resistance QTL could entail linkage drag (decrease in protein concentration and 100-seed weight, increase in oil concentration). This work provides useful markers for introgressing SCN resistance in early maturing soybean varieties.

Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size (n<300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limitations affect both the resolution and extent of genome coverage of such maps. Consensus genetic maps overcome the limitations of individual genetic maps by merging the information from multiple segregating populations derived from a greater diversity of parental combinations, thus increasing the number of recombination events and reducing the number of monomorphic regions. The aim of this study was to construct a high-density consensus genetic map for SNP markers obtained through a genotyping-by-sequencing (GBS) approach. Individual genetic maps were generated from six F_4:5 mapping populations (n=278-365), totaling 1857 individuals. The six linkage maps were then merged to produce a consensus map comprising a total of 16,311 mapped SNPs that jointly cover 99.5% of the soybean genome with only two gaps larger than 10 cM. Compared to previous soybean consensus maps, it offers a more extensive and uniform coverage.