Comparative Genomics of Domestication Traits in Lettuce and Sunflower

COMPARATIVE GENOMICS OF DOMESTICATION TRAITS IN LETTUCE AND SUNFLOWER

Sponsoring Institution

National Institute of Food and Agriculture

Project Status

TERMINATED

Funding Source

OTHER GRANTS

Reporting Frequency

Annual

Accession No.

0186480

Grant No.

00-52100-9609

Project No.

CA-D*-PLS-6794-CG

Proposal No.

2000-04292

Multistate No.

(N/A)

Program Code

(N/A)

Project Start Date

Sep 15, 2000

Project End Date

Sep 30, 2004

Grant Year

2000

Project Director
Michelmore, R. W.

Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671

Performing Department
PLANT SCIENCES

Non Technical Summary
We will develop permanent resources for functional and comparative genomics of lettuce and sunflower. This consortium will capitalize on the wealth of knowledge being developed for Arabidopsis.Wild and domesticated forms of lettuce and sunflower are dramatically different. The lack of information on the genetic basis of these differences and their linkage relationships has slowed introgression of useful traits from wild germplasm. We will study the genes underlying agriculturally important, qualitative and quantitative traits by conducting parallel genetic analyses on lettuce and sunflower to dissect the genetic basis of traits that distinguish domesticated from wild forms of lettuce and sunflower. We will (i) generate an extensive expressed sequence tag (EST) databases from two different genotypes each of lettuce and sunflower (~80,000 total), (ii) determine the extent of synteny among sunflower, lettuce and Arabidopsis by mapping known sequences in lettuce and sunflower and by comparison to the genomic sequence of Arabidopsis, (iii) conduct quantitative trait locus (QTL) and candidate gene analyses of domestication traits, and (iv) develop a genetic approach to the control of expression levels of candidate genes. We will determine the genetic bases and linkage relationships of metabolic and morphological changes associated with domestication. This will allow the development of PCR-based markers for high-throughput genetic analyses. It will show the extent of synteny between the two major divisions within the Compositae and with Arabidopsis for sequenced genes and QTLs.

Animal Health Component

(N/A)

Research Effort Categories

Basic

50%

Applied

50%

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	1430	1080	50%
201	1844	1080	50%

Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1844 - Sunflower; 1430 - Greens and leafy vegetables;

Field Of Science
1080 - Genetics;

Goals / Objectives
To establish an extensive EST database for sunflower and lettuce. To develop high density genetic maps for both lettuce and sunflower based on known transcribed sequences. To determine the level of synteny between lettuce and sunflower and to Arabidopsis. To establish correlations between several agriculturally important traits and candidate genes.

Project Methods
An extensive EST database of approximately 80,000 sequences will be developed by sequencing 50,000 clones from each of lettuce and sunflower. The sequences will be made publicly accessible over the www in the compositdb database. The libraries will be made from several tissues of each of two genotypes that have been used as the parents for the core mapping populations of each species. Sequences derived from the two parents will be compared to identify single nucleotide polymorphism markers. A large numbers of markers sufficient to saturate the genome will be developed and mapped. Macro- and micro-synteny between lettuce, sunflower and Arabidopsis will be analyzed on the basis of preservation of linkage blocks along the chromosomes of these species. The progeny from the cultivar x wild progenitor mapping populations will be analyzed for a broad range of traits involved in domestication and of agricultural importance to identify the underlying quantitative trait loci (QTL). As genes determining agriculturally important traits become identified in other species, homologs from lettuce and sunflower will be identified in the EST database and mapped relative to QTLs determining agricultural traits. The experimental feasibility of analyzing QTLs determining expression level polymorphisms will be analyzed using microarrays of selected sequences.

Progress 09/15/00 to 09/30/04

Outputs
The Compositae Genome Project (CGP) is a multi-institutional collaboration that had four objectives: 1) Establish an extensive EST database for sunflower and lettuce. 2) Develop high density genetic maps for both species based on transcribed sequences. 3) Determine the extent of synteny between lettuce and sunflower and to Arabidopsis. 4) Establish correlations between several agriculturally important traits and candidate genes. We have developed an extensive EST database containing over 68,000 and 44,000 sequences from lettuce and sunflower respectively. These sequences were derived from a total of 40 cDNA libraries from several tissues of each of two genotypes that have been used as the parents for the core mapping populations of each species. These sequences and extensive analyses are displayed on the public project website (http://compgenomics.ucdavis.edu). Ancillary software developed for the project are also available from this site. Sequences derived from the two parents of our cultivar x wild progenitor mapping population have been compared to identify single nucleotide polymorphisms. RIL progeny from this mapping population have been analyzed in multiple locations and years for a broad range of traits involved in domestication and of agricultural importance; this has identified numerous quantitative trait loci (QTL) underlying these traits. Homologs from lettuce and sunflower of genes determining agriculturally important traits identified in other species have been identified in the EST database and mapped relative to QTLs determining agricultural traits. Macro and micro synteny between lettuce, sunflower and Arabidopsis has been analyzed to identify preserved linkage blocks along the chromosomes of these species. To facilitate this we identified a set of COS (Conserved Orthologous Sequence) markers as well as clusters of contiguous genes in Arabidopsis with ESTs in our database.

Impacts
The Compositae Genome Project provides genomic information for sunflower and lettuce that is being used for the improvement of both species as well as the exploitation of knowledge resulting from the sequencing and detailed characterization of Arabidopsis. In addition, it has contributed genetic, physiological and phenotypic information to the general syntenic consideration that is developing for plants.

Publications

Gedil, M.A., Slabaugh, M.B., Berry, S., Johnson, R., Michelmore, R.W., Miller, J., Gulya, T., Knapp, S.J. (2001). Candidate disease resistance genes in sunflower cloned using conserved nucleotide binding site motifs: genetic mapping and linkage to the Pi1 gene for resistance to downy mildew. Genome 44:205-212.
Kozik, A., Kochetkova, E., Michelmore, R.W. (2002). GenomePixelizer a visualization program for comparative genomics within and between species. Bioinformatics 18:335-336.

Progress 01/01/03 to 12/31/03

Outputs
The Compositae Genome Project (CGP) is a multi-institutional collaboration that has four objectives: 1) Establish an extensive EST database for sunflower and lettuce. 2) Develop high-density genetic maps for both species based on transcribed sequences. 3) Determine the extent of synteny between lettuce and sunflower and to Arabidopsis. 4) Establish correlations between several agriculturally important traits and candidate genes. We have developed an extensive EST database containing over 68,000 and 44,000 sequences from lettuce and sunflower respectively. These sequences were derived from a total of 40 cDNA libraries from several tissues of each of two genotypes that have been used as the parents for the core mapping populations of each species. These sequences and extensive analyses are displayed on the project website (http://compgenomics.ucdavis.edu). Ancillary software developed for the project are also available from this site. Sequences derived from the two parents have been compared to identify single nucleotide polymorphisms. The progeny from the cultivar x wild progenitor mapping populations have been analyzed for a broad range of traits involved in domestication and of agricultural importance to identify the underlying quantitative trait loci (QTL). As genes determining agriculturally important traits become identified in other species, homologs from lettuce and sunflower are being identified in the EST database and mapped relative to QTLs determining agricultural traits. Macro- and micro-synteny between lettuce, sunflower and Arabidopsis is being analyzed to identify preserved linkage blocks along the chromosomes of these species. To facilitate this we identified a set of COS (Conserved Orthologous Sequence) markers as well as clusters of contiguous genes in Arabidopsis with ESTs in our database.

Impacts
The Compositae Genome Project provides genomic information for sunflower and lettuce that is being in improvement of both species as well as the exploitation of knowledge resulting from the sequencing and detailed characterization of Arabidopsis. In addition, it will contribute genetic, physiological and phenotypic information to the general syntenic consideration that will develop for plants.

Publications

Michelmore, R.W. (2003). Impact zone: genomics and breeding for durable disease resistance. Current Opinion in Plant Biology 6:397-404.
Cannon S.B., Kozik A., Chan B., Michelmore R., Young N.D. 2003 DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology-discovery, and visualization. Genome Biology. In Press

Progress 01/01/02 to 12/31/02

Outputs
The Compositae Genome Project (CGP) is a multi-institutional collaboration that has four objectives: 1) Establish an extensive EST database for sunflower and lettuce. 2) Develop high-density genetic maps for both species based on transcribed sequences. 3) Determine the extent of synteny between lettuce and sunflower and to Arabidopsis. 4) Establish correlations between several agriculturally important traits and candidate genes. We have developed an extensive EST database containing over 68,000 and 44,000 sequences from lettuce and sunflower respectively. These sequences were derived from a total of 40 cDNA libraries from several tissues of each of two genotypes that have been used as the parents for the core mapping populations of each species. These sequences and extensive analyses are displayed on the project website (http://compgenomics.ucdavis.edu). Ancillary software developed for the project are also available from this site. Sequences derived from the two parents have been compared to identify single nucleotide polymorphisms. The progeny from the cultivar x wild progenitor mapping populations have been analyzed for a broad range of traits involved in domestication and of agricultural importance to identify the underlying quantitative trait loci (QTL). As genes determining agriculturally important traits become identified in other species, homologs from lettuce and sunflower are being identified in the EST database and mapped relative to QTLs determining agricultural traits. Macro- and micro-synteny between lettuce, sunflower and Arabidopsis is being analyzed to identify preserved linkage blocks along the chromosomes of these species. To facilitate this we identified a set of COS (Conserved Orthologous Sequence) markers as well as clusters of contiguous genes in Arabidopsis with ESTs in our database.

Impacts
The Compositae Genome Project provides genomic information for sunflower and lettuce that is being in improvement of both species as well as the exploitation of knowledge resulting from the sequencing and detailed characterization of Arabidopsis. In addition, it will contribute genetic, physiological and phenotypic information to the general syntenic consideration that will develop for plants.

Publications

Kozik, A., Kochetkova, E., Michelmore, R.W. (2002). GenomePixelizer - a visualization program for comparative genomics within and between species. Bioinformatics 18:335-336.
Kozik, A., Michelmore, R.W., Knapp, S.J., Matvienko, M., S., Rieseberg, L., Lin, H., van Damme, M., Lavelle, D., Chevalier, P., Ziegle, J., Ellison, P. Kolkman, J., Slabaugh, M.S., Livingston, K., Zhou, Lai, Z., Church, S., Edberg, S., Jackson, L., Bradford, K., et al. (2002). Lettuce and Sunflower ESTs from the Compositae Genome Project. http://compgenomics.ucdavis.edu/.

Progress 01/01/01 to 12/31/01

Outputs
There are three objectives: 1) To map transcribed genes in both lettuce and sunflower. 2) To integrate the gene-based genetic maps with existing maps of PCR-based and morphological markers. 3) To determine partially the extent of synteny between lettuce, sunflower, and Arabidopsis. In collaboration with S. Knapp at the Oregon State University, and Loren Reiseberg, Indiana University, we will map sequenced-based markers in lettuce and sunflower using existing, well-characterized, single populations of each species. An extensive EST database of at least 80,000 sequences is being developed by sequencing over 50,000 clones from each of lettuce and sunflower. The sequences will be made publicly accessible over the www in the compositdb database. A total of 40 cDNA libraries have been made from several tissues of each of two genotypes that have been used as the parents for the core mapping populations of each species. The main sequencing phase has just been completed. Sequences derived from the two parents will be compared to identify single nucleotide polymorphism markers. Large numbers of markers sufficient to saturate the genome will be developed and mapped. Macro- and micro-synteny between lettuce, sunflower and Arabidopsis will be analyzed on the basis of preservation of linkage blocks along the chromosomes of these species. The progeny from the cultivar x wild progenitor mapping populations will be analyzed for a broad range of traits involved in domestication and of agricultural importance to identify the underlying quantitative trait loci (QTL). As genes determining agriculturally important traits become identified in other species, homologs from lettuce and sunflower will be identified in the EST database and mapped relative to QTLs determining agricultural traits. The experimental feasibility of analyzing QTLs determining expression level polymorphisms will be analyzed using microarrays of selected sequences.

Impacts
This will allow information generated in sunflower and lettuce to be used in improvement of both species as well as the exploitation of information resulting from the sequencing and detailed characterization of Arabidopsis. In addition, it will contribute genetic, physiological and phenotypic information to the general syntenic map that will develop for plants.

Publications

Kozik, A., Kochetkova, E., Michelmore, R.W. GenomePixelizer (2002)- a visualization tool for comparative genomics within and between species. Bioinformatics. In Press.