Systems Genetics of Crowding Tolerance in Brassica rapa

The demand placed on arable land to produce enough food, fuel, and fiber is increasing. One way to increase crop yields per acre is to grow plants at higher densities. However, when plants are grown close together they compete for light resources by altering growth and development, which can have negative impacts on yield. Genetic variation for this shade avoidance response exists in many crop species, suggesting a path forward for yield improvement. In order to understand the genetic basis for variation in response to crowding, a Recombinant Inbred Line (RIL) population of Brassica rapa segregating for response to shade was grown in crowded and uncrowded field conditions. Physiological and developmental phenotypes were collected and RNA-seq libraries were made from shoot meristem tissue. SNPs were called from the RNA-seq reads and a new genetic map was constructed with <1 cM resolution. This saturated map significantly refined quantitative trait loci (QTL) regions for physiological traits compared to an existing map. The RNA-seq data was then used to map expression QTL (eQTL). Notably, some eQTL co-localized with physiological QTL regions, and gene co-expression network analysis identified subnetworks that correlated with physiological traits. Together this information can be used to understand the basis of the physiological QTL. There were three trans-eQTL hotspots showing significant genotype by environment interactions for the transcripts under their control. Current work to narrow down candidate genes includes a promoter enrichment analysis of eQTL hotspot regions and a Bayesian modeling framework that integrates genotype, co-expression networks, and physiological traits.