Large-scale resequencing has been undertaken to identify allelic variants in rice. Most of agronomic traits, which are called complex traits, are usually controlled by multiple genes and affected by various environmental conditions. Although a lot of quantitative trait locus (QTL) and genes related to rice complex traits have been cloned and functionally characterized, genetic basis and regulatory mechanisms underlying these complex traits are still unclear. Unlocking genetic diversity of Oryza species will provide insights into genomics of rice complex traits and rice breeding. We have implemented an integrated approach of genome-wide association study (GWAS) and phenomics with functional analysis to catch up agronomic trait genes or QTLs in a diverse cultivated rice population. This approach informs that the associated loci with the agronomic traits such as panicle length, grain sizes, grain weight and grain filling rate can be further characterized through expressional profiling, in-depth genome analysis, transgenic study, genome editing, and population genetic analysis. Allelic genetic variations responsible for complex traits can be effectively explored.
Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. We have developed an integrated genomic and forward genetic approach to construct a genome map for elite hybrid rice varieties and their inbred parental lines. We identified that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. The large data of genomics and phenomics from the well-designed populations enabled us, for the first time, to identify the genetic contributors and find out the exact causes of heterosis using “a composite interval-mapping method”. For the individual yield components, the heterozygous state of the heterosis-related genes generally acted through the way of dominance complementation. These results inform on the genomic architecture of heterosis for yield traits in rice, which will be useful information for crop improvement program.