Genetic Mechanisms of Genome Changes.

Progress of sequencing technologies has generated huge genomic sequences, which provides great opportunity to address fundamental questions about the genome itself. One prominent phenomenon is the variation of genome-wide base composition between species, for example, Eudicots (like Arabidopsis) typically have significantly higher AT in their genomes than Monocots (like Rice). By investigating the Base Composition across SNP sites (BCS) within species, our research group has discovered a conserved pattern of BCS among individuals. i.e., modern varieties of rice, maize, soybean, and grape all have significantly higher BCS value than their ancestors. This consistent pattern across multiple species indicates an underlying genetic mechanism for the variation of BCS, an ideal indicator of genome changes accumulated through evolution. Arabidopsis, with small genome size and available genetic resources, is a feasible system to dissect the genetic mechanisms. By analyzing the 300 Arabidopsis genomes, we identified one locus at chromosome 5 strongly associated with the BCS variation through Genome Wide Association Studies (GWAS). To pinpoint the underlying gene, a set of Near-Isogenic Lines (NILs) are used for functional assays. These NILs were developed from two parents harboring different alleles at the GWAS signal. Research discoveries in genetic mechanisms for the genome itself will broadly enrich our understanding of genomics, genetics, and evolution.