Download Comparative Genomics Of The Compositae With An

Comparative Genomics Of The Compositae With An Emphasis On
Disease Resistance In Lettuce.
Richard Michelmore, The Genome Center, University of California, Davis, USA
The Compositae is one of the largest and most diverse families of flowering
plants, comprising 10% of all known Angiosperm species. The family is cosmopolitan,
occupies diverse ecological niches, and produces numerous biologically and
economically important secondary chemicals, e.g. rubber and insecticides. The
Compositae contains over 40 major and minor crops, including lettuce (one of the top ten
US crops) and sunflower (one of the world’s most important oilseed crops), as well as
many noxious weeds and species with novel biochemistries. The Compositae Genome
Project (CGP; http://compgenomics.ucdavis.edu) is exploiting the crop and weed
diversity in the Compositae to examine the genetic changes underlying parallel
phenotypic changes that have accompanied the origins of multiple crops and weeds.
Over the past ten years the CGP has been developing genomics resources for the family.
The initial focus was on EST sequencing, particularly for lettuce and sunflower. These
efforts were expanded to include 21 species, resulting in over 848,000 ESTs. Current
efforts include complete transcriptome analysis of an additional 25 species as well as
gene space sequencing of key species using next-generation sequencing. Over 35,000
unigenes were identified in lettuce and used to construct a high density Affymetrix
oligonucleotide array. This was used to analyze the segregation of Single Position
Polymorphisms in a core mapping population of Recombinant Inbred Lines, resulting in
an ultra-dense, transcript-based genetic map of lettuce containing over 13,000 unigenes
as well as to assess allelic variation across diverse germplasm of Lactuca spp. This map
has been used to identify candidate genes for numerous traits of agricultural importance,
particularly disease resistance. RNAi is being used for functional validation of candidate
genes for disease resistance. The ultra-dense map will also provide a scaffold for
ordering and validation of genome assemblies.