My current research in the Sinha Lab, and in collaboration with the Maloof Lab, uses tomato as a model to study the genetic basis of natural variation and environmental response. Central to this work is the use of 76 near-isogenic introgression lines (NILs), each harboring an introgressed segment of the wild tomato Solanum pennellii genome in an otherwise domesticated tomato background. Together, the introgressed segments of the 76 lines span the entire genome, and finding a phenotypic difference between a NIL and domesticated tomato indicates that the responsible genes controlling the trait lie in the introgressed region.
The transcriptomes of the NILs are analyzed using next-generation sequencing techniques, under simulated sun and foliar shade. Because each NIL contains a single introgressed segment, differentially-expressed genes can be classified as cis- or ¬trans-regulated. Such a comprehensive dataset allows not only genetic x environmental effects to be discerned, but the outlines of a transcriptional network, as defined by evolutionary changes between two species.
My main contribution to this project has been to develop statistical methods to not only precisely measure leaf shape amongst introgression lines, but to analyze patterns of gene expression between wild tomato species and tissues, integrating information at evolutionary, developmental, and environmental response levels. Ultimately, my analyses seek to use developmental modeling to comprehensively describe phenotype and correlate it with genotypic and transcriptomic information to find the genetic basis of phenotypic differences between domesticated and wild tomato species.