Genetic architecture of antibiosis and antixenosis aphid resistance in soybean and elucidation of the molecular effect of pyramiding Rag1 and Rag2 resistance genes

Soybean aphids are a major problem to soybean growers worldwide and they cause great yield losses. In the United States, soybean aphids can cause yield losses of up to 50% especially on susceptible varieties. Yield losses attributed to feeding by soybean aphids can be reduced by cultivating resistant soybean varieties. In recent years, certain biotypes of soybean aphids that can colonize resistant soybean plants have been reported, suggesting the continued need for identification of novel sources of aphid resistance to include in plant breeding programs. While gene pyramiding, in which certain resistant soybean genotypes carry more than one aphid resistance gene has been effectively used to mitigate the problem of virulent aphid biotypes on resistant soybean, the molecular mechanisms of increased resistance in soybean genotypes with multiple genes is still unknown. Research presented in this dissertation utilized a genome-wide association study (GWAS) to identify novel sources of soybean aphid resistance and characterize the genetic architecture of aphid resistance in a diverse panel of USDA soybean accessions. Using RNA-seq, the molecular mechanisms of increased resistance that results from pyramiding two aphid-resistance genes (Rag1 and Rag2) in one soybean genotype (Rag1Rag2) were elucidated. In the GWAS project, we identified significant Single Nucleotide Polymorphisms (SNPs) located in genomic regions of four soybean chromosomes that contained prospective candidate genes associated with aphid resistance. Two chromosomes have never been reported before. Identification of novel resistance sources allows the possibility of using the accessions and SNPs for marker assisted selection in plant breeding programs, reducing the time needed to develop resistant soybean genotypes. Our RNA-seq study revealed that pyramiding the two aphid-resistance genes in one soybean genotype resulted in a synergistic effect on resistance to soybean aphids at the molecular level. Specifically, there were sets of differentially expressed genes that were present in the Rag1Rag2 response but absent in the Rag1-alone or Rag2-alone response, indicating activation of different defense pathways in Rag1Rag2 soybean genotype compared to genotypes with individual genes. This project allowed the identification of aphid-responsive genes that can be targeted in future functional genomics studies to validate their role in resistance to soybean aphids