The goal of our project "Dissecting Natural Mechanisms for Genome Content Variation and the Impact on Phenotypic Variation" was to understand genomic variation that exists between cultivars (i.e. varieties) within a species with regard to what genes are present in each cultivar and how the presence or absence of genes in a genome impact the phenotypic traits of a cultivar. There are a portion of genes that are present in all cultivars within a species, termed 'core genes', and another portion of genes that are present in only some cultivars within a species, termed 'dispensable genes'. There are many ways these dispensable genes can come to exist in a genome, but the relative contribution of each mechanism is not well understood, nor is the importance of these dispensable genes to trait variation within a species. In this project we sequenced the genomes of over 500 different maize cultivars to document the presence or absence of each gene in the genome in each of these cultivars. We studied signatures in the genome that indicate the likely origin of dispensable genes, and we linked this variation in gene content across cultivars to phenotypic trait variation. We found that while there are approximately 40,000 genes in any given maize cultivar, collectively across the species there are well over 100,000 genes that vary relative to their presence in any given cultivar. We evaluated many potential mechanisms that generate this variation and demonstrate 1) there is substantial variability in copy number of tandem duplicate genes due to unequal recombination and 2) transposable elements contribute significantly to the dynamic gene content in maize as they move throughout the genome. In contrast, differential fractionation, which are non-shared gene loss events that occur between cultivars following a whole-genome duplication event, played a more limited role in generating genome content variation. When linking this genetic variation to phenotypic trait variation, we demonstrated that genome-wide association analyses using both single nucleotide polymorphisms and structural variations (e.g. presence/absence of whole genes or transposons) can improve the power of quantitative mapping studies.  For example, we identified specific gene content variants associated with important phenotypic traits, including 1) the presence/absence of the sugary enhancer1 gene that generates the super sweet flavors of fresh market sweet corn varieties, and 2) variation in the pericarp color1 genethat underlies variation in seed color. Further, we documented genome content complementation between the two major heterotic groups in US commercial corn germplasm that contributes to the superior performance of hybrid varieties over their inbred parents. This has important implications in plant breeding decisions as demonstrated in a simulation study we conducted. 

The genomic variation present among the cultivars also drives phenotypic variation at the molecular level, specifically of metabolites. We focused on metabolites that comprise the cuticular waxes within the cuticle, which covers the external epidermal surfaces of aerial plant tissues to provide a protective barrier against environmental stresses. We observed substantial natural variation in cuticular wax load and composition on maize silks, which are flower parts that facilitate pollination and therefore corn yield. Joint statistical analysis of weather parameters and silk cuticular wax composition suggests that precipitation patterns late in plant development, and solar radiation earlier in development impact cuticular wax composition. This work enhances our understanding of how weather modulates cuticular wax composition in genotype-specific manners. Finally, genome-wide association analyses of cuticular wax compositions across the cultivars identified novel candidate genes enriched for roles in regulatory mechanisms at the transcriptional, co-transcriptional, translational, and post-translational levels. Also implicated were protein-coding genes associated with known enzymatic functions in cuticular wax biosynthesis, and cuticular wax transport mechanisms. Collectively, these results have impact on future maize breeding programs targeting cuticle deposition as a means of enhanced stress response.

The successful completion of this project has provided important insights into the dynamics of intraspecies genomic variation and the impacts on phenotypic trait variation. This project successfully trained 6 post-docs, 7 graduate students, 45 undergraduate students, and 8 high school students in quantitative genetics, genomics, phenomics, biochemistry, and metabolomics, and 59 of the 66 individuals trained on this project were from groups traditionally underrepresented in STEM fields. All raw data generated throughout this project were deposited at NCBI SRA (sequence data) and the PMR (surface lipid profiles). Results of this project have been widely disseminated to the community through 22 peer-reviewed publications and numerous invited presentations. 

Last Modified: 01/07/2024
Modified by: Candice N Hirsch