"The soybean aphid, an invasive species, has been posing a substantial threat on soybean production in North America since its first discovery in 2000. Two novel aphid-resistance quantitative loci (QTLs) were previously revealed as controlling aphid resistance in the wild soybean, Glycine soja 85-32. Therefore, the first objective was to validate these QTLs under different genetic backgrounds. Using single nucleotide polymorphism (SNP) markers, discovered from whole genome resequencing data or mined from the SoySNP50K iSelect BeadChip, two aphid-resistance QTLs were successfully validated and designated Rag6 and Rag3c, respectively. The second objective was to fine map these two loci and identify structural variants within the candidate genes. Rag6 was refined to a 49-kb interval with four candidate genes, including three clustered nucleotide-binding site leucine-rich repeat (NBS-LRR) genes and an amine oxidase encoding gene. Rag3c was refined to a 150-kb interval with eleven candidate genes, two of which are a LRR gene and a lipase gene. By aligning the sequencing reads from the whole genome exome-capture of the resistant source to the soybean reference genome (aphid-susceptible), structural variants (including frame shifts, deletions and nonsynonymous coding changes) were identified within the candidate genes of Rag6 and Rag3c, and new SNPs and insertion/deletions were discovered in the exon regions. The variability and dynamics of aphid population limits the effectiveness of host-resistance gene(s). Therefore, the third objective was to develop and evaluate soybean advanced breeding lines integrated with different aphid-resistance genes. Based on the responses from the indicator lines, Biotype 3 was determined as a major component of aphid populations collected in Michigan during 2015 - 2016. The different performance of Rag-'Jackson' and Rag1-'Dowling' along with the breakdown of resistance in plant introductions (PIs) 567301B and 567324 may be explained by Biotype 3 or an unknown virulent biotype establishing in Michigan. Lines with rag1c, Rag3d, Rag6, Rag3c+Rag6, rag1b+rag3, rag1c+rag4, rag1c+rag3+rag4, rag1c+Rag2+rag3+rag4 and rag1b+rag1c+rag3+rag4 demonstrated strong and consistent resistance in five trials across 2015 - 2017. Due to the variability of virulent aphid populations, different combinations of Rag genes may perform differently across geographies. However, advanced breeding lines pyramided with three or four Rag genes will likely provide broader and more durable resistance to diverse and dynamic aphid populations across many geographic regions."--Pages ii-iii.
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