Advances in genotyping technology, such as genotyping by sequencing (GBS), are making genomic prediction more attractive to reduce breeding cycle times and costs associated with phenotyping. Genomic prediction and selection has been studied in several crop species, but no reports exist in soybean. The objectives of this study were (i) evaluate prospects for genomic selection using GBS in a typical soybean breeding program and (ii) evaluate the effect of GBS marker selection and imputation on genomic prediction accuracy. To achieve these objectives, a set of soybean lines sampled from the University of Nebraska Soybean Breeding Program were genotyped using GBS and evaluated for yield and other agronomic traits at multiple Nebraska locations. Genotyping by sequencing scored 16,502 single nucleotide polymorphisms (SNPs) with minor-allele frequency (MAF) > 0.05 and percentage of missing values ≤ 5% on 301 elite soybean breeding lines. When SNPs with up to 80% missing values were included, 52,349 SNPs were scored. Prediction accuracy for grain yield, assessed using cross validation, was estimated to be 0.64, indicating good potential for using genomic selection for grain yield in soybean. Filtering SNPs based on missing data percentage had little to no effect on prediction accuracy, especially when random forest imputation was used to impute missing values. The highest accuracies were observed when random forest imputation was used on all SNPs, but differences were not significant. A standard additive G-BLUP model was robust; modeling additive-by-additive epistasis did not provide any improvement in prediction accuracy. The effect of training population size on accuracy began to plateau around 100, but accuracy steadily climbed until the largest possible size was used in this analysis. Including only SNPs with MAF > 0.30 provided higher accuracies when training populations were smaller. Using GBS for genomic prediction in soybean holds good potential to expedite genetic gain. Our results suggest that standard additive G-BLUP models can be used on unfiltered, imputed GBS data without loss in accuracy.

The colocalization of two resistance (R) genes on chromosome 13 of soybean (Glycine max (L.) Merrill) that confer resistance against the soybean aphid (Aphis glycines) and soybean mosaic virus (SMV) gives rise to a very unique R-avr tritrophic incompatible interaction system that goes across biological kingdoms. In this tritrophic system, the insect is the only natural vector of the virus and soybean is a host-plant for both pests/pathogen. The almost unavoidable co-evolution of pathogen-vector with that of the R-genes in soybean plants through an endless arms race to avoid each other’s defense-attack mechanisms raises interesting questions. The objectives of this work were to (i) develop double-resistant recombinant inbred lines (RILs) with a Rag2-Rsv1-h gene haplotype in coupling phase using resistance alleles from two different genetic sources (PI 243540 (Rag2) and Suweon 97 (Rsv1-h)), (ii) confirm phenotypically the resistant reaction against both pests in double-resistant RILs, and (iii) dissect the Rag2-Rsv1-h region with molecular markers and investigate the potential for structural variation. We observed a recombination event in identified double-resistant F3:5 RILs in a region of chromosome 13 ca. 21 kb long (between positions 30,297,227 and 30,318,949 in Wm82.a2.v1) that lies between the reported locations of the Rsv1-h and Rag2 genes (29,815,463--29,912,369 and 30,412,581--30,466,533 intervals, respectively, based on Wm82.a2.v1), indicating the double-resistant haplotype is in coupling phase. The tight LD estimates obtained between haplotype markers underscored the physical proximity of the two resistance genes. Only 10 recombinant haplotype classes (excluding double heterozygotes) were observed among the 51 that were possible with a four loci haplotype. The 10 recombinant classes represented 15 out of 192 screened individuals. A joint SMV-aphid phenotypic greenhouse screen allowed us to identify the best aphid biotype 1 and SMV-G1, double resistant haplotype class in recombinant progeny. Our molecular marker results agree with previous fine-mapping reports and preclude the presence of resistance genes other than Rag2 and Rsv1-h in double-resistant RILs. A comparative genomic hybridization analysis revealed no obvious structural variants in the region. To our knowledge, this is the first report of double-resistant Rag2-Rsv1-h soybean RILs that used a plant-insect-pathogen tritrophic system for germplasm enhancement. The co-occurrence of Rag and Rsv genes in a region that clusters resistance genes on chromosome 13 may be a unique feature of domesticated soybean. The recombinant genotypes will be useful in breeding to develop soybean cultivars with resistance to both the vector and the virus. The parental and recombinant genotypes may be helpful in future studies to elucidate interesting evolutionary questions regarding vector, host, and virus tritrophic systems.