Progress 03/01/08 to 02/28/11
Outputs
Progress Report Objectives (from AD-416) To enhance understanding of and access to the genetic diversity in wild and landrace relatives of tomato and potato, and contribute to the same for other euasterid plant species, five objectives are proposed: 1. Document relative diversity in and relationships among a core germplasm set of wild and cultivated tomato and potato species as revealed by DNA sequences of COSII genes. 2. Help orient the utilization of tomato and potato diversity by re- evaluating grouping concepts based on unbiased measures given by COSII markers. 3. Identify and describe putative regions of positive and negative selection throughout tomato and potato genomes and relate these to known domestication loci or mapped phenotypic traits, focusing on COSII markers linked to domestication loci (Appendix 1). 4. Facilitate comparative mapping in the Solanaceae by mapping 300 single-copy COSII (to include the 48 above) in potato, lulo, sweet potato, and carrot 5. Make these data publicly available on the SGN bioinformatics platform (http://sgn.cornell.edu/). Approach (from AD-416) USDA and Univ. Wisconsin (Ane) activity. Assessment of genetic and allelic diversity and phylogenetic relationships, with 24 COSII (four per linkage group), across 59 individuals to include cultivated and wild tomato and potato species and outgroups, and a nested diversity assessment in tomato and potato. All of the sequencing will be with a single individual per accession except for a nested study inside the S. peruvianum/S. brevicaule study that will use five clones of each of five individuals for five accessions of S. peruvianum and five clones for five individuals of five accessions in the S. brevicaule complex. The USDA will also sequence parents of one potato mapping population for the 420 COSII markers to be placed on the potato linkage map, and the mapping parents of lulo, sweetpotato and carrot to be provided by cooperators, for their inclusion in diversity and phylogenetic assessment. Some of these species will be the same as those used in the potato AFLP and SSR studies as mentioned above for comparative diversity assessments. CIP activity. 420 COSII will be mapped in a reference population of potato. Emphasis will be given to the tomato/potato inverted regions, and to QTL regions for domestication and resistance traits across Solanaceae. SNPs and indels identified in the above sequencing of 420 COSII will be mapped in a reference population of potato as CAPs, SSCP or simple PCR, using the most informative progeny subset and ordered using IntiMap software. Scoring will be extended to the full mapping population of >100 individuals, once reliable polymorphisms are detected and position preliminarily assigned. JoinMap software version 3.0 will be used for linkage analysis and map calculations to develop a consensus of both parental maps. We will also recover and compile raw data supporting prior publications from genetic and QTL mapping using this population. Cornell Univ activity. Database and bioinformatics. The Sol Genomics Network (SGN) will generate primers, experimental conditions, and sequence for the 24 COSII markers in this study, and up to the same number of sequences from mapping parents of each of three other crop species in the Euasterid II clade. In addition, marker sequences, experimental conditions, and polymorphism information will be stored in the SGN database and a web query interface provided. The maps generated will be added to the SGN mapping database and available through the SGN comparative mapviewer. With this viewer, different genetic maps in the SGN database can be compared dynamically. The newly developed maps will therefore be available for comparison with tomato, pepper, eggplant, and Arabidopsis. Trees and alignments will be shown through our tree-browser and alignment viewer software. We will also create a special SGN portal that will contain introductions to SGN features and COSII for a breeder's perspective on the best utility of the data deposited at SGN. This is the final report for the project 3655-21000-050-01R terminated in February 2011. This work was funded by a United States Department of Agriculture (USDA) Competitive grant and involved three subcontracts. Various components of this project are reported individually in subcontracts; project 3655-21000-050-04S involving genetic mapping, project 3655-21000-050-05S involving bioinformatics construction of markers and their storage on the Solanaceae Genomics, and project 3655- 21000-050-06G involving phylogenetic analyses. The bioinformatics work identified 420 markers from which we mapped about 300. The mapping work mapped these markers to potato, using a combination of (initially) conventional mapping strategies and later in- silico mapping (possible because of the availability of a potato genomic sequence), and the phylogenetic analysis involved examining the utility of 24 single copy conserved orthologs for phylogenetic analysis of potato and tomato diploids and potato polyploids. The overall utility of this project involved a much better genetic map of markers of use to potato breeders, the development of a technique to separate out allelic variants by a process involving single strand conformation polymorphism, and improved phylogenetic resolution of potato and tomato. The project was monitored through in person discussions, phone calls, and e-mail exchanges.
Impacts
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Publications
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report Objectives (from AD-416) To enhance understanding of and access to the genetic diversity in wild and landrace relatives of tomato and potato, and contribute to the same for other euasterid plant species, five objectives are proposed: 1. Document relative diversity in and relationships among a core germplasm set of wild and cultivated tomato and potato species as revealed by DNA sequences of COSII genes. 2. Help orient the utilization of tomato and potato diversity by re- evaluating grouping concepts based on unbiased measures given by COSII markers. 3. Identify and describe putative regions of positive and negative selection throughout tomato and potato genomes and relate these to known domestication loci or mapped phenotypic traits, focusing on COSII markers linked to domestication loci (Appendix 1). 4. Facilitate comparative mapping in the Solanaceae by mapping 300 single-copy COSII (to include the 48 above) in potato, lulo, sweet potato, and carrot 5. Make these data publicly available on the SGN bioinformatics platform (http://sgn.cornell.edu/). Approach (from AD-416) USDA and Univ. Wisconsin (Ane) activity. Assessment of genetic and allelic diversity and phylogenetic relationships, with 24 COSII (four per linkage group), across 59 individuals to include cultivated and wild tomato and potato species and outgroups, and a nested diversity assessment in tomato and potato. All of the sequencing will be with a single individual per accession except for a nested study inside the S. peruvianum/S. brevicaule study that will use five clones of each of five individuals for five accessions of S. peruvianum and five clones for five individuals of five accessions in the S. brevicaule complex. The USDA will also sequence parents of one potato mapping population for the 420 COSII markers to be placed on the potato linkage map, and the mapping parents of lulo, sweetpotato and carrot to be provided by cooperators, for their inclusion in diversity and phylogenetic assessment. Some of these species will be the same as those used in the potato AFLP and SSR studies as mentioned above for comparative diversity assessments. CIP activity. 420 COSII will be mapped in a reference population of potato. Emphasis will be given to the tomato/potato inverted regions, and to QTL regions for domestication and resistance traits across Solanaceae. SNPs and indels identified in the above sequencing of 420 COSII will be mapped in a reference population of potato as CAPs, SSCP or simple PCR, using the most informative progeny subset and ordered using IntiMap software. Scoring will be extended to the full mapping population of >100 individuals, once reliable polymorphisms are detected and position preliminarily assigned. JoinMap software version 3.0 will be used for linkage analysis and map calculations to develop a consensus of both parental maps. We will also recover and compile raw data supporting prior publications from genetic and QTL mapping using this population. Cornell Univ activity. Database and bioinformatics. The Sol Genomics Network (SGN) will generate primers, experimental conditions, and sequence for the 24 COSII markers in this study, and up to the same number of sequences from mapping parents of each of three other crop species in the Euasterid II clade. In addition, marker sequences, experimental conditions, and polymorphism information will be stored in the SGN database and a web query interface provided. The maps generated will be added to the SGN mapping database and available through the SGN comparative mapviewer. With this viewer, different genetic maps in the SGN database can be compared dynamically. The newly developed maps will therefore be available for comparison with tomato, pepper, eggplant, and Arabidopsis. Trees and alignments will be shown through our tree-browser and alignment viewer software. We will also create a special SGN portal that will contain introductions to SGN features and COSII for a breeder's perspective on the best utility of the data deposited at SGN. This project reports on the overall USDA National Research Initiative (NRI) grant. A total of 428 conserved orthologous sequences (COS) have been developed for the project. The single strand conformational polymorphism (SSCP) technique was developed to separate all the alleles reducing the amount of cloning. We optimized the polymerase chain reaction (PCR) conditions for 388 COS. We are well along with finishing the sequencing phase of our project and are writing papers on the phylogenetic aspects. In one project, we finished sequencing alleles of six COS sequences of 54 accessions of 11 polyploid species, by SSCP that we optimized in the Wisconsin laboratory and are writing up the results of this study. Two separate studies that were completed this year and are in press used five COS. One of these studies examined 199 accessions of 66 species in a group of mostly diploid species in the Solanum Piurana Group. The second study sequenced 72 accessions from 22 species from series Conicibaccata and 42 additional accessions from related series. Another study in press and completed this year used deoxyribonucleic acid (DNA) sequences of the gene granule-bound starch synthase (GBSSI) or waxy gene to examine relationships of all four cultivated potato species. The sequences of all of these are deposited or being deposited in GenBank. For the COSII mapping phase of this project, sequencing was completed for 90% of the potato and tomato mapping populations, 60% of the sweet potato populations, and is being generated for carrot. Monitoring of this project is accomplished by telephone conversations among the partners at the USDA, the University of Wisconsin, the International Potato Center, and the Boyce Thompson Research Institute.
Impacts
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Publications
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report Objectives (from AD-416) To enhance understanding of and access to the genetic diversity in wild and landrace relatives of tomato and potato, and contribute to the same for other euasterid plant species, five objectives are proposed: 1. Document relative diversity in and relationships among a core germplasm set of wild and cultivated tomato and potato species as revealed by DNA sequences of COSII genes. 2. Help orient the utilization of tomato and potato diversity by re- evaluating grouping concepts based on unbiased measures given by COSII markers. 3. Identify and describe putative regions of positive and negative selection throughout tomato and potato genomes and relate these to known domestication loci or mapped phenotypic traits, focusing on COSII markers linked to domestication loci (Appendix 1). 4. Facilitate comparative mapping in the Solanaceae by mapping 300 single-copy COSII (to include the 48 above) in potato, lulo, sweet potato, and carrot 5. Make these data publicly available on the SGN bioinformatics platform (http://sgn.cornell.edu/). Approach (from AD-416) USDA and Univ. Wisconsin (Ane) activity. Assessment of genetic and allelic diversity and phylogenetic relationships, with 24 COSII (four per linkage group), across 59 individuals to include cultivated and wild tomato and potato species and outgroups, and a nested diversity assessment in tomato and potato. All of the sequencing will be with a single individual per accession except for a nested study inside the S. peruvianum/S. brevicaule study that will use five clones of each of five individuals for five accessions of S. peruvianum and five clones for five individuals of five accessions in the S. brevicaule complex. The USDA will also sequence parents of one potato mapping population for the 420 COSII markers to be placed on the potato linkage map, and the mapping parents of lulo, sweetpotato and carrot to be provided by cooperators, for their inclusion in diversity and phylogenetic assessment. Some of these species will be the same as those used in the potato AFLP and SSR studies as mentioned above for comparative diversity assessments. CIP activity. 420 COSII will be mapped in a reference population of potato. Emphasis will be given to the tomato/potato inverted regions, and to QTL regions for domestication and resistance traits across Solanaceae. SNPs and indels identified in the above sequencing of 420 COSII will be mapped in a reference population of potato as CAPs, SSCP or simple PCR, using the most informative progeny subset and ordered using IntiMap software. Scoring will be extended to the full mapping population of >100 individuals, once reliable polymorphisms are detected and position preliminarily assigned. JoinMap software version 3.0 will be used for linkage analysis and map calculations to develop a consensus of both parental maps. We will also recover and compile raw data supporting prior publications from genetic and QTL mapping using this population. Cornell Univ activity. Database and bioinformatics. The Sol Genomics Network (SGN) will generate primers, experimental conditions, and sequence for the 24 COSII markers in this study, and up to the same number of sequences from mapping parents of each of three other crop species in the Euasterid II clade. In addition, marker sequences, experimental conditions, and polymorphism information will be stored in the SGN database and a web query interface provided. The maps generated will be added to the SGN mapping database and available through the SGN comparative mapviewer. With this viewer, different genetic maps in the SGN database can be compared dynamically. The newly developed maps will therefore be available for comparison with tomato, pepper, eggplant, and Arabidopsis. Trees and alignments will be shown through our tree-browser and alignment viewer software. We will also create a special SGN portal that will contain introductions to SGN features and COSII for a breeder's perspective on the best utility of the data deposited at SGN. Significant Activities that Support Special Target Populations This project reports on the overall USDA National Research Initiative (NRI) grant. In 2008, we screened 40 Conserved orthologous sequence (COS) and generated sequences for 24 of them in 11 wild potato species, 13 wild tomato species and 6 outgroups; and 489 sequences were deposited in GenBank. In 2009, 388 additional pairs of primers were designed for 388 COS, which makes a total of 428 COS. The single strand conformational polymorphism (SSCP) technique was developed to separate all the alleles reducing the amount of cloning. Up to date, we have optimized the polymerase chain reaction (PCR) conditions for 114 of these COS. Sequences were generated for 28 of the 388 new COS in 24 tomato and diploid wild potato species; they are being edited and are going to be submitted to GenBank soon. In addition, we sequenced 4 COS in 53 accessions of 11 wild potato polyploid species; the sequences currently are being edited. To investigate domestication loci, sequences were generated for 3 COS in 25 wild potato and 25 wild tomato accessions, they are being edited and are going to be submitted to GenBank soon. To date, we have amplified 88 COS in the parents of the potato and tomato mapping populations and their alleles are being separated in SSCP. On the other hand, by the case of sweet potato and carrot, using the same set of potato and tomato primers, we were successful generating PCR products only in 45% and 25% of the cases respectively. Now we are separating their alleles by SSCP. Monitoring of this project was done by a site visit by post-doctoral researcher to the International Potato Center during May-July 2009 for the mapping work, will be meeting with cooperator at the Plant and Animal Genome meetings in January 2010, and by bi-weekly meetings at the University of Wisconsin.
Impacts
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Publications
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