- Plants to be Studied:
  Tomato, especially Solanum lycopersicum and Solanum pennellii.

- Project Objectives:
  Plants acquire the bulk of their energy from light capture by leaves, and leaf shape has direct consequences on the efficiency of light capture and photosynthetic carbon fixation. As a result, leaf shape must be optimized in response to variation in light quality. To understand the genetic programs controlling fundamental developmental processes, genetic networks regulating both environmental response and morphological form must be integrated. This proposal uses a genomics approach to understand natural variation in leaf morphology and light response, and to investigate the mechanism by which these two genetic networks are integrated to ensure optimal developmental pattern.

- Experimental Approaches:
  To elucidate developmental networks, we are using a "genetical genomics" approach, taking advantage of near isogenic mapping lines (NILs) where regions of the S. pennellii genome have been introgressed into S. lycopersicum. Importantly, the parental species vary significantly in both light response and leaf complexity. We are sequencing the parental line transcriptomes to deep coverage to acquire genome-wide mRNA sequence and SNP information. The resulting data will be used to expand the tomato UniGene set and to develop a dense genome-wide marker database for S. lycopersicum and S. pennellii. The NIL population will be phenotyped for leaf development and light-response traits and characterized for genome-wide transcript levels and genotypes by massively parallel short-read sequencing. Construction of genetic networks regulating leaf morphology and light development from this genotype, phenotype, and trancript profile data will be coupled with genetic and transgenic approaches to identify central regulators of development and developmental variation. The resulting network will then be used as a guide to survey natural variation found in additional wild tomato accessions.