| Abstract Detail
Translational Genomics - Morning Francis, David [1], Yang, Wencai [2], van der Knaap, Esther [1], van Deynze, Allen [3]. Translational genomics in tomato: marker discovery for breeding. WE are developing Single Nucleotide Polymorphisms (SNPs) as molecular markers for application in cultivated tomato (S. lycopersicum). Implementing SNP-based marker technology has the potential to dramatically alter approaches to both gene discovery and genetic characterization. Our strategies for marker discovery include analysis of polymorphisms in EST databases, de novo sequencing across introns, and hybridization to a custom oligonucleotide array to detect single feature polymorphisms (SFPs). We are developing a panel of molecular markers for application within domesticated germplasm (http://www.tomatomap.net). These markers have been used to genotype a core collection (n = 99) of S. lycopersicum varieties representing heirloom (19), fresh market (23), and processing germplasm (39). Greenhouse varieties (3), land races (5) and wild species accessions from S. lycopersicum var cerasiformae, S. pimpinellifolium, S. pennellii, and S. habrochaites are also included in the core collection. A variety of indexes and clustering proceedures were used to analayze population structure within the cultivated germplasm. These analyses reveal sub-populations consistent with market class differentiation (P = 0.0001) and adaptation to arid or humid growing environments (P = 0.003). Eigenvectors from principle components analysis were used to identify markers and genes that are most informative for differentiating germplasm. These analysis can be performed in a hierarchical fassion, an approach which may elucidate the evolutionary history of individual genes. In addition the markers have been applied to the rational design of hybrids and to association mapping within the context of an elite x elite breeding program.
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Related Links:
database for SSR and SNPs polymorphic within cultivated tomato germplasm
1 - The Ohio State University, Horticulture and Crop Science, 1680 Madison Ave., Wooster, OH, 44691
2 - China Agricultural University, Vegetable Sciences, College of Agronomy and Biotechnology, No.2 Yuanmingyuan Xi Lu, Beijing, 100094, China
3 - University of California, Seed Biotechnology Center, Davis, CA, 95616, USA
Keywords:
SNP
microarray
association mapping
structure.
Session: SAT05-5
Location: Hall of Ideas Room I/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 9:30 AM
Abstract ID:238 |
