Progress 10/01/12 to 09/30/17
Outputs
Target Audience:The target audiences for this project have included botanists throughout the world who are interested in results of our systematic studies of horticultural crop plants and wild relatives, especially those with interests in the areas of phylogenetic systematics, taxonomy, crop plant evolution, and domestication. Additional target audiences are campus colleagues who request my assistance with taxonomic questions and phylogenetic analyses and international collaborators including faculty and students from universities in various countries, several of whom have visited UC Davis for periods of one week to a year throughout the project performance period. In addition, two subprojects were focused specifically on the California flora, for which the target audiences included land managers, state agencies, conservation organizations,and environmental consultants. The first was a rare plant survey for the Knoxville Wildlife Area, funded by the California Department of Fish and Wildlife, for which the target audience includes the California Department of Fish and Wildlife, the Napa Land Trust, the California Native Plant Society, and students and volunteers participating in the project. The second was a project entitled "Clarifying the conservation status of northern California black walnut (Juglans hindsii) using molecular markers," funded by the UC Davis Genetic Resources Conservation Program, for which the target audience includes botanists from the California Native Plant Society, the California Department of Fish and Wildlife, county governments, consultants, and landowners throughout the state. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?During the project period, I served as major professor for the following graduate students: Jennifer Petersen Ph.D. 2012 Siew Wai Chin Ph.D. 2012 Daniel Park Ph.D. 2014 Kai Battenberg Ph.D. 2017 Jorge Perez-Zabala Ph.D. in progress Christopher Adlam Ph.D. in progress Oscar Hinojosa Ph.D. in progress Alexandra Towns M.S. 2012 Javier Jauregui Lazo M.S. 2014 In addition, several current and past UC Davis undergraduate and graduate students participated as volunteers in field surveys and related herbarium work for the KWA rare plant survey project, which was a great benefit to the project and also provided them with valuable experience in practicing plant identification skills. The following visiting international scholars worked with me in association with the project: Ademola Aina (Nigeria) Khadijeh Alekasir (Iran) Huijuan Jing (China) Mahmoud Kiani (Iran) Ki-Ryong Park (Korea) Humaira Shaheen (Pakistan) Eyasu Wada (Ethiopia) Hyosig Won (Korea) Baohuan Wu (China) How have the results been disseminated to communities of interest?Results have been disseminated formally through publications, reports, presentations at professional meetings, and invited talks during international visits (China, Mexico, Philippines), and informally through email exchanges, telephone conversations, and discussions at research group meetings (e.g., annual the USDA Juglans Crop Germplasm Committee meetings). In April, 2016, I co-led (with UC Davis Herbarium Assistant Curator Daniel McNair) a field trip for the Davis Botanical Society to the Knoxville Wildlife Area, where we have been conducting rare plant and general floristic surveys for the California Department of Fish and Wildlife. This was a public outreach event for the DBS, a support organization for the UC Davis herbarium and Botanical Conservatory, attended by about 20 people. It helped make people aware of the floristic diversity of the KWA. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The general goals of the project are to document diversity and investigate diversification in horticultural crop plants and their wild relatives. We use phylogenetic analyses of molecular and morphological data, as well as phylogeographic and population genetic approaches, to address taxonomic and evolutionary questions, sometimes incorporating ethnobotanical data to explore interactions between plants and people. Major accomplishments include: 1. Phylogeny, character evolution, and historical biogeography of the stone-fruit genus, Prunus (Rosaceae): with Ph.D. student Siew-Wai Chin and collaborators Jun Wen (Smithsonian Institution) and Liang Zhao (Northwest A&F University, China), partly funded by NSF. Phylogenetic analyses of plastid DNA and nuclear gene sequences for a broad sampling of Prunus species support the hypothesis that early hybridization events within the genus gave rise to the ancestors of extant raceme-bearing species generally classified in subgenera Laurocerasus and Padus. Reconstructions of ancestral areas in conjunction with clade dating indicate that Prunus originated in eastern Asia in the late Paleocene, with subsequent dispersals to Southeast Asia, western Asia, Europe, and Africa and multiple migrations into the New World 2. Domestication status and origins of cultivated forms of caimito (star apple), Chrysophyllum cainito (Sapotaceae): with Ph.D. student Jennifer Petersen and collaborator Ingrid Parker, partly funded by UC Davis Academic Senate. Phylogeographic studies of nuclear and plastid DNA sequences and evidence from microsatellite markers supported the hypothesis that domesticated forms of caimito likely originated in the area that is now Panama and were dispersed northward to Mexico and the Antilles via human activity, refuting the prevailing hypothesis that caimito originated in the West Indies. 3. Incipient domestication in the locally important crop plant `huaya India' (Melicoccus oliviformis, Sapindaceae) on the Yucatán Peninsula: with Dr. Jaime Martinez Castíllo and others at Centro de Investigación Científica de Yucatán, Mexico, partly funded by UC Mexus. The goals of this project, initiated in 2017, are to investigate the process of incipient domestication of M. oliviformis on the Yucatán Peninsula, where it has been used for centuries for its edible fruits. Ethnobotanical approaches will be used to document traditional methods of management, criteria for selection, and historical movements of this plant by Maya communities. Morphological and biochemical characterizations of fruits from wild and cultivated trees will be used to identify traits that have been subjected to human selection. Analyses of variation at 30 microsatellite loci will be used to compare levels of genetic diversity in wild and cultivated trees. 4. Clarifying the conservation status of northern California black walnut (Juglans hindsii) using microsatellite markers: with collaborators Heath Bartosh (Nomad Ecology), Roxanne Bittman (California Department of Fish and Wildlife), and John Preece (USDA-ARS National Clonal Germplasm Repository), partly funded by the National Clonal Germplasm Repository. The project sought to investigate the degree to which J. hindsii has hybridized with other species. This has important conservation implications because the species is currently listed by the California Native Plant Society as seriously endangered in California based on the largely untested assumption that most populations, both natural and planted by people, consist primarily of hybrids. We analyzed genotypes at 10 microsatellite loci for 160 apparently wild trees of J. hindsii from one county in southern Oregon and 10 counties in northern and southern California, including representatives of putative original native populations, as well as several Paradox hybrids, 10-20 standards for each of the five North American black walnut species, and six standards for J. regia. Our analyses indicated that about two-thirds of the putatively wild J. hindsii sampled represent genetically pure members of that species, while the remaining trees show evidence of past hybridizations with one or more of the other North American black walnut species. These results suggest that J. hindsii should not be considered a rare species. 5. Rare plant surveys in the Knoxville Wildlife Area (KWA), Napa County: with UC Davis graduate Ninh Khuu and several volunteers, partly funded by the California Department of Fish and Wildlife. In 2015 and 2016, we conducted rare plant surveys in the southern Knoxville Wildlife Area (KWA )in Napa County. The project resulted in documentation of populations of 19 rare plant taxa, primarily from habitats with serpentinite-derived soils, and production of an updated plant list for the KWA. In addition, it motivated molecular phylogenetic analyses to determine the taxonomic identity of individuals potentially assignable to the federally endangered species Sidalcea keckii. Nucleotide sequence data from the nuclear ribosomal ITS region supported the conclusion that plants found in the KWA that are morphologically similar to S. keckii are, in fact, more closely related to, and may be conspecific with, the more widely distributed species S. diploscypha. These individuals may represent an undescribed taxon (perhaps a subspecies of S. diploscypha or a separate species) or possibly descendants of hybrids between the two species or their ancestors. Further study is needed. 6. Additional projects with UC Davis graduate students and campus colleagues Daniel Park's (PhD, 2014) innovative dissertation research (supported in part by an NSF Doctoral Dissertation Improvement Grant) explored the evolutionary ecology of invasive species using Asteraceae in Mediterranean climates as the study system and specifically addressing the question of whether successful invaders are more or less closely related to native taxa than expected by random chance. Daniel's results support the former conclusion, contra Darwin's naturalization hypothesis. Kai Battenberg's (Ph.D. 2017), co-advised with Alison Berry, used comparative transcriptomics to investigate the evolutionary origin of root-nodule symbiosis in angiosperms that engage in symbiotic nitrogen fixation, and provided evidence for the homology of all root nodules as well as for the two-step hypothesis for the origin of symbiotic nitrogen fixation in flowering plants. I contributed to data analyses and manuscript writing for projects led by campus colleagues, including Michael Grieneisen, Terry Murphy, Sharman O'Neill, and the late Kentaro Inoue. 7. Projects with visiting international scholars Projects undertaken in collaboration with international visiting scholars have included studies of: genetic diversity and conservation of olive (Olea europaea, Oleaceae) germplasm on a global scale, with Isabel Trujillo (Spain); systematics and diversity of Fritillaria (Lilaceae) in Iran with Mahmoud Kiani (Iran); studies of systematics and diversity of Ornithogalum (Apsaragaceae) in Iran with Khadijeh Alekasir (Iran); phylogeny of Pyrus (Rosaceae) with several collaborators in China; genetic diversity of cocoyam (Xanthosoma spp., Araceae) with Eyasu Wada (Ethiopia); genetic diversity of African yam bean (Sphenostylis stenocarpa, Fabaceae) with Ademola Aina(Nigeria); floristics and ethnobotany of the Thal Desert with Humaira Shaheen(Pakistan). Additional international collaborations resulted from my participation in the project "Biodiversity surveys in Indonesia and discovery of health and energy solutions," (2008-2013), which was supported by an International Cooperative Biodiversity Group (ICBG) grant funded by lead agency NIH, with contributions from USDA, NSF, and DOE. I contributed to botanical aspects of the project, documenting the floristic diversity of the Mekongga Mountains, Southeast Sulawesi, with Elizabeth Widjaja and others (Indonesia).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
O'Neill, S. D., Bui, A. Q., Potter, D., and Zhang, X. S. 2017. Pollination of orchid flowers: quantitative and domain-specific analysis of ethylene biosynthetic and hormone-induced gene expression. International Journal of Plant Sciences 178: 188-210.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Murphy, T. R., and Potter, D. 2017. Genetic distinctions among oaks in the University of California, Davis Arboretum: contributions to oak phylogeny. International Oaks 28: 59-72.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Battenberg, K., Lee, E. K., Chiu, J. C., Berry, A. M., and Potter, D. 2017. OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement.�BMC Bioinformatics 18: 310.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Kiani, M., Mohammadi, S., Babaei, A., Sefidkon, F., Naghavi, M. R., Ranjbar, M., Razavi, S. A., Saeidi, K., Jafari, H., Asgarig, D., and Potter, D. 2017. Iran supports a great share of biodiversity and floristic endemism for�Fritillaria�spp. (Liliaceae): a review. Plant Diversity 39: 245-262.
|
Progress 10/01/15 to 09/30/16
Outputs
Target Audience:The general target audiences continue to include botanists throughout the world who are interested in results of our systematic studies of horticultural crop plants and wild relatives, campus colleagues who request my assistance with taxonomic questions and phylogenetic analyses, and international collaborators including faculty and students from universities in various countries, several of whom have visited UC Davis for periods of one week to several months during the review period. More specifically, two sub-projects were largely completed during the review period: 1) a rare plant survey for the Knoxville Wildlife Area, funded by the California Department of Fish and Wildlife, for which the target audience includes the California Department of Fish and Wildlife, the Napa Land Trust, the California Native Plant Society, and students and volunteers participating in the project; 2) a project entitled "Clarifying the conservation status of northern California black walnut (Juglans hindsii) using molecular markers," funded by the UC Davis Genetic Resources Conservation Program, for which the target audience includes botanists from the California Native Plant Society, the California Department of Fish and Wildlife, county governments, consultants, and landowners throughout the state. The objective of the project is to investigate the degree to which J. hindsii has hybridized with other species. The project builds upon our past work on the parentage of Paradox hybrid rootstocks, and on recent genetic testing done for landowners in Napa County, which have relied on DNA sequence data; the use of microsatellite markers, which sample a broader range of the nuclear genome, should provide more sensitive detection of past hybridizations with other species. The target audiences named are interested in the results because J. hindsii is currently listed by the California Native Plant Society as seriously endangered in California based on the largely untested assumption that most populations, both natural and planted by people, consist primarily of hybrids. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Several current and past UC Davis undergraduate and graduate students participated as volunteers in field surveys and related herbarium work for the KWA rare plant survey project, which was a great benefit to the project and also provided them with valuable experience in practicing plant identification skills. How have the results been disseminated to communities of interest?Results have been disseminated formally through publications and reports and informally through conversations and email exchanges. In addition, I presented preliminary results of the Juglans hindsii project at at a meeting of the walnut Thousand Cankers Disease taskforce for Napa County in February, 2016, and at the USDA Juglans Crop Germplasm Committee (CGC) meeting in July, 2016. In April, 2016, I co-led (with UC Davis Herbarium Assistant Curator Daniel McNair) a field trip for the Davis Botanical Society to the Knoxville Wildlife Area, where we have been conducting rare plant and general floristic surveys for the California Department of Fish and Wildlife. This was a public outreach event for the DBS, a support organization for the UC Davis herbarium and Botanical Conservatory, attended by about 20 people. It helped make people aware of the floristic diversity of the KWA. What do you plan to do during the next reporting period to accomplish the goals?1. Conduct further analyses (morphological and molecular genetic) to elucidate the status of Sidalcea keckii in northern California, in order to confirm and expand the results reported in the KWA rare plant survey report, which were based on a limited number of samples. 2. Fully complete analyses and writing up of results of Juglans hindsii project. 3. Begin new projects, including: a) A study of genetic diversity of African yam bean (Sphenostylis stenocarpa, Fabaceae) accessions from Nigeria, to be conducted by Mr. Ademola Aina, a Ph.D student from Nigeria, supported in part by a Borlaug-LEAP fellowship for Mr. Aina, who is a visiting scholar in my lab Jan. - May 2017. b) A study molecular phylogenetic study of the genus Ornithogalum (Asparagaceae), focusing on species native to Iran, being conducted by Ms. Khadijeh Alekasir, a visiting scholar from Iran working in my lab Sept. 2016 - Aug. 2017. c) A study of the process of incipient domestication in the edible fruit-bearing tree species "huaya India" (Melicoccus oliviformis, Sapindaceae) on the Yucatán Peninsula, Mexico. The project, which will involve collection and analysis of ethnobotanical, morphological, biochemical, and molecular genetic data, is a collaboration with Dr. Jaime Martinez Castillo at the Centro de Investigación Científica de Yucatán (CICY) in Mérida, Meixico, which has been funded by the U C Mexus - CONACYT Collaborative Research Grants Program.
Impacts
What was accomplished under these goals?
As noted above, data collection and analyses for two sub-projects were largely completed during the review period: 1) Our rare plant survey of the Knoxville Wildlife Area (KWA), funded by the California Department of Fish and Wildlife (CDFW) and the Napa Land Trust, focused on land parcels added to the KWA since 2008, especially locations in the western (upper) ends of both the Nevada Creek and Zim Zim Creek drainages, both of which are areas with serpentinite-derived soils. Our survey resulted in documentation of populations of 19 rare plant taxa, of which one has a California Native Plant Society (CNPS) rank of 1B.1, seven have a rank of 1B.2, three have a rank of 4.2, and eight have a rank of 4.3. As expected, most of these were found in the serpentine habitats (serpentine seeps, grasslands, barrens, and chaparral) in the upper Zim Zim and Nevada Creek drainages. Estimated population sizes, GPS points, habitat descriptions, photographs, and voucher specimens were taken to document the occurrences. In addition, collections were made of non-rare plant taxa not previously recorded for the KWA. We documented occurrence of 87 taxa in the KWA that were not included in the last published plant list, produced by Jake Ruygt in 2005. We used nucleotide sequence data from the nuclear ribosomal ITS regionDNA sequence data toto investigate the identity of individual plants potentially assignable to the federally endangered species Sidalcea keckii. Results of those analyses support the conclusion that plants found in the Knoxville Wildlife Area that are morphologically similar to S. keckii are, in fact, more closely related to, and may be conspecific with, the more widely distributed species S. diploscypha. All information was included in the final project report provided to the CDFW. 2) For the project entitled "Clarifying the conservation status of northern California black walnut (Juglans hindsii) using molecular markers," funded by the UC Davis Genetic Resources Conservation Program, genotypes at ten microsatellite loci were generated for 227 trees, 60 representing standards for the five native North American black walnut species and the cultivated walnut (J. regia), 162 representing wild trees morphologically assignable to J. hindsii, collected from throughout California and in southern Oregon, and five wild trees morphologically identified as Paradox hybrids (J. hindsii X J. regia). The results indicated that about two thirds of the wild trees identified as J. hindsii in the field are, in fact, genetically pure members of that species, while the remaining third have contributions from one or more of the other native North American species (but not J. regia) in their backgrounds (first-, second-, third-. or fourth-generation hybrids). The results suggest that listing of J. hindsii as a rare species by CNPS may not be appropriate. A manuscript describing these results is in preparation. Also during this review period, Eyasu Wada, a visiting Ph.D. scholar from Ethiopia, completed his analyses of genetic diversity among cocoyam (Xanthosoma sagittifolium, Araceae) cultivars from his country, using microsatellite markers. He has returned to Ethiopia and is working on a manuscript for publication describing those results combined with those from his ethnobotanical studies of the species.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Zhao, L., Jiang, X.W., Zuo, Y.J., Liu, X.L., Chin, S.W., Haberle, R., Potter, D., Chang, Z.Y. and Wen, J. 2016. Multiple events of allopolyploidy in the evolution of the racemose lineages in Prunus (Rosaceae) based on integrated evidence from nuclear and plastid data. PLoS ONE 11(6): e0157123. doi:10.1371/journal.pone.0157123.�
- Type:
Other
Status:
Published
Year Published:
2016
Citation:
Potter, D. 2016. Reivew of: Flora of North America: North of Mexico. Volume 9: Magnoliophyta: Picramniaceae to Rosaceae. Edited by Flora of North America Editorial Committee. Oxford and New York: Oxford University Press. $95.00. xxiv + 713 p. + 1 pl.; ill.; index. ISBN: 978-0-19-534029-7. 2014. Review published in Quarterly Review of Biology 91: 103.
|
Progress 10/01/14 to 09/30/15
Outputs
Target Audience:The target audiences continue to include botanists throughout the world who are interested in results of our systematic studies of horticultural crop plants and wild relatives (e.g., our phylogenetic analyses of the stone-fruit genus Prunus), campus colleagues who request my assistance with taxonomic questions and phylogenetic analyses, and international collaborators from various countries whom I have visited and/or who have visited UC Davis for periods of 1 week to several months during thie review period. In addition, newly initiated subprojects during the review period include: 1) a rare plant survey for the Knoxville Wildlife Area, funded by the California Department of Fish and Wildlife, for which the target audience includes the California Department of Fish and Wildlife, the Napa Land Trust, the California Native Plant Society, and students and volunteers participating in the project; 2) a project entitled "Clarifying the conservation status of northern California black walnut (Juglans hindsii) using molecular markers," funded by the UC Davis Genetic Resources Conservation Program, for which the target audience is botanists from the California Native Plant Society, the California Department of Fish and Wildlife, county governments, consultants, and landowners throughout the state. The objective of the project is to investigate the degree to which J. hindsii has hybridized with other species. The project builds upon our past work on the parentage of Paradox hybrid rootstocks, and on recent genetic testing done for landowners in Napa County, which have relied on DNA sequence data; the use of microsatellite markers, which sample a broader range of the nuclear genome, should provide more sensitive detection of past hybridizations with other species. The target audiences named are interested in the results because J. hindsii is currently listed by the California Native Plant Society as seriously endangered in California based on the largely untested assumption that most populations, both natural and planted by people, consist primarily of hybrids. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Several undergraduate and graduate students and volunteers from the community have assisted with field and herbarium work related to rare plant surveys in the Knoxville Wildlife Area. Visiting graduate students from Ethiopia and China worked in my lab and/or the UC Davis herbarium. A UC Davis undergraduate intern worked in the lab with the student from Ethiopia and gained lab research experience. How have the results been disseminated to communities of interest?During this period, dissemination of results has occurred primarily through conversations, email exchanges, and informal meetings with members of the target audience groups, in order to discuss research needs, plans, and results. Several scientific papers are expected to result from the efforts described above within the next year. In addition, I gave a presentation entitled "UC Davis Center for Plant Diversity: Research Experience and Opportunities" for an International Symposium on Biodiversity, SMART/Precision Agriculture and Cooperative Extension at the University of Southern Mindanao, Kabacan, Cotabato, Philippines, on September 21, 2015. What do you plan to do during the next reporting period to accomplish the goals?Continue gathering data for the Knoxville rare plant survey project; analyze and report (in oral and written formats) results from that project and the Juglans hindsii project. Continue to foster international collaborations. Continue to seek funding to support costs of supplies and support personnel needed in order to be able to conduct research. Develop new subprojects on taxonomy and distribution of California rare plants and on phylogeny and diversity of other crop plants and their wild relatives.
Impacts
What was accomplished under these goals?
Two new subprojects were initiated with grants from other sources. The first, from the USDA National Clonal Germplasm Repository, Davis ($15,000), entitled "Clarifying the conservation status of northern California black walnut (Juglans hindsii) using molecular markers," builds upon our past work on the parentage of Paradox hybrid rootstocks to investigate the degree to which J. hindsii has hybridized with other species. This has important conservation implications because the species is currently listed by the California Native Plant Society as seriously endangered in California based on the largely untested assumption that most populations, both natural and planted by people, consist primarily of hybrids. Thanks to the efforts of several collaborators, more than 200 samples have been collected and data analyses should be complete within the next several months. One season of field work has been completed for the second project, "Rare plant surveys of the southern Knoxville Wildlife Area," funded by the California Department of Fish and Wildlife ($25,000); the second and final season is planned for 2016. The project has provided great opportunities for involving students and volunteers. My students, collaborators, and I have continued to work on resolving phylogenetic analyses across Prunus. Ph.D. student Jorge Perez Zabala has nearly completed his dissertation, which focuses on taxonomy, phylogeny, and diversification of the neotropical species of the genus, which have been very poorly sampled in previous phylogenetic studies. Collaborator Jun Wen (Smithsonian Institution) and one of her associates have led an effort, to which my former postdoc. Rosemarie Haberle (now on the faculty at Pacific Lutheran University), my former student Siew-Wai Chin (now a researcher with Singapore National Gardens), and I have contributed, to conduct new phylogenetic analyses of nuclear gene sequences from species across the genus in order to refine and test our hypothesis, based on Siew-Wai's dissertation work, of hybrid, allopolyploid origins of most of the Old and New World tropical, plus a few temperate, lineages of Prunus. I have also continued to cultivate international collaborations. In June-July, 2015, I participated in a plant-collecting trip in northwestern China with collaborators from South China Agricultural University, aimed primarily at collecting wild Prunus; I hosted visiting scholars from China, Korea, and Ethiopia. The last was a Ph.D. student from Addis Ababa University who conducted analyses of genetic diversity of landraces of the tuber crop Xanthosoma sagittifolium from his country using microsatellite markers. The USDA National Clonal Germplasm Repository - Davis generously provided lab space and technical assistance for him to generate the data and I assisted him with data analysis and interpretation. Finally, I gave a presentation entitled "UC Davis Center for Plant Diversity: Research Experience and Opportunities" for an International Symposium on Biodiversity, SMART/Precision Agriculture and Cooperative Extension at the University of Southern Mindanao, Kabacan, Cotabato, Philippines. The talk was given during a visit in September, 2015, sponsored by Associate Dean Jim Hill in the office of International Programs of the College of Agricultural and Environmental Sciences, to discuss potential collaborative research on biodiversity with colleagues at the University of Southern Mindanao.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Day, P. M., Potter, D., and Inoue, K. 2014. Evolution and targeting of Omp85
homologs in the chloroplast outer envelope membrane. Frontiers in Plant
Science 5: 535.
|
Progress 10/01/13 to 09/30/14
Outputs
Target Audience: The target audiences included those who read papers my students, collaborators, and I have published on systematics of Prunus and other Rosaceae and on Chrysophyllum cainito (Sapotaceae), as well as researchers, nurseries, developers, and government agency employees who are interested in our work on molecular markers to distinguish species and hybrids in the walnut genus (Juglans). During this period, I also visited collaborators at Sun Yat-Sen University ,in Guangzhou, China, where I participated in field work with professors and students, gave a talk at Sun Yat-Sen University on our work on Prunus, and gave a talk at the Sichuan Forestry Academy in Chengdu on our work on walnuts. I also gave a guest lecture on traditional and scientific classification systems to Dr. Michelle Stevens's Ethnoecology class at California State University - Sacramento, and a public talk on "Phylogeny, Taxonomy and Recent Name Changes in the California Flora" for the Sacramento Valley Chapter of the California Native Plant Society. Finally, I participated in an open house at the UC Davis herbarium in conjunction with UC Davis Biodiversity Museum Day, for which I set up a display and talked to visitors about the value of herbaria and herbarium specimens and their use in research. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? During the reporting period, I have served as major professor for two MS students and three PhD students. The subjects of their research projects include systematics of two genera in Rosaceae, Prunus and Acaena, the evolution of invasiveness in Asteraceae, and the evolution of the nitrogen-fixing symbiosis in angiosperms. These students have been trained in plant identification, plant nomenclature, examination of morphological characters of plants, including herbarium specimens, phylogenetic analysis, and molecular approaches in systematics (DNA extraction, PCR, sequencing, and sequence analysis). In addition, a Ph.D. student from China, interested in systematics of Sorbus (Rosaceae), worked in my lab as a visiting scholar for 9 months during the period. How have the results been disseminated to communities of interest? Results have been disseminated via publications, listed above, and presentations listed in "Target Audiences." What do you plan to do during the next reporting period to accomplish the goals? Continue to supervise graduate students as they complete their thesis and dissertation research and assist them with publishing results. Continue work, including field collections, lab work, and data analyses, on species delimitation in Juglans and Holodiscus. Proceed with DNA sequence analyses of species of Rosaceae collected in China to incorporate into phylogenetic analyses of selected groups, especially Prunus and Spiraea. Continue to seek additional funding opportunities to support field and lab research.
Impacts
What was accomplished under these goals?
In addition to publications and outreach activities mentioned above, I participated in field work to collect samples of Juglans species from localities in northern California, in preparation for a study that will use DNA sequences and microsatellite markers to test the hypothesis that the northern California black walnut, J. hindsii, is widely distributed and that its genetic purity is not threatened by gene flow from other species. I also collected material of the genus Holodiscus, for which I authored the treatment in the second edition of The Jepson Manual, that we will for molecular studies to test taxon delimitation in that genus. Different authors, including myself, have interpreted the morphological variation present in California in several different ways taxonomically and a new variety was recently described from a serpentine soil area Sonoma County which shares greater similarity in some morphological characters to plants from the Sierra Nevada and Great Basin than to Sonoma County plants from non-serpentine soils. Molecular evidence may help establish is correct classification. As noted above, I also visited collaborators at Sun Yat-Sen University in Guangzhou, China, with whom I participated in field trips in Shaanxi and Sichuan Provinces, where we collected herbarium specimens and leaf material for DNA analysis of a diversity of native species, focusing on genera in Rosaceae including Aruncus, Malus, Prunus, Pyrus, Sorbaria, Sorbus, and Spiraea.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Trujillo, I., Ojeda, M. A., Urdiroz, N. M., Potter, D., Barranco, D., Rallo, L., and Diez, C. M. 2014. Identification of the Worldwide Olive Germplasm Bank of C�rdoba (Spain) using SSR and morphological markers. Tree Genetics & Genomes 10: 141-155.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Petersen, J. J., Parker, I. M., and Potter, D. 2014. Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama. Ecology and Evolution 4: 539 -553.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Petersen, J. J., Parker, I. M., and Potter, D. 2014. Ten polymorphic microsatellite primers in the tropical tree caimito, Chrysophyllum cainito (Sapotaceae). Applications in Plant Sciences 2:1300079. DOI: http://dx.doi.org/10.3732/apps.1300079.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Shaheen, H., Qureshi, R., Akram, A., Gulfraz, M., and Potter, D. 2014. A preliminary floristic checklist of Thal Desert, Punjab, Pakistan. Pakistan Journal of Botany 46: 13-18.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Chin, S.-W., Shaw, J., Haberle, R., Wen, J., and Potter, D. 2014. Diversification of almonds, peaches, plums and cherries - Molecular systematics and biogeographic history of Prunus (Rosaceae). Molecular Phylogenetics and Evolution 76: 34-48.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Grieneisen, M. L., Zhan, Y., Potter, D., and Zhang, M. 2014. Biodiversity, taxonomic infrastructure, international collaboration, and new species discovery. BioScience 64: 322-332.
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
Zheng, X., Cai, D., Potter, D., Postman, J., Liu, J., and Teng, Y. 2014. Phylogeny and evolutionary histories of Pyrus L. revealed by phylogenetic trees and networks based on data from multiple DNA sequences. Molecular Phylogenetics and Evolution. 80: 54 -65.
|
Progress 01/01/13 to 09/30/13
Outputs
Target Audience: During this reporting period, the primary target audiences have been those who read papers we have published or intend to publish (in preparation during the review period), i.e., mostly researchers and instructors at academic institutions. I also routinely respond to inquiries from students and faculty at other institutions who have questions about our work on Rosaceae systematics, as well as questions from researchers, nurseries, developers, and government agency employees who are interested Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? During the reporting period, I have served as major professor for two MS students and three PhD students. The subjects of their research projects include systematics of particular genera within Rosaceae, ethnobotany of the Osage Indians, the evolution of invasiveness in Asteraceae, and the evolution of the nitrogen-fixing symbiosis in angiosperms. These students have been trained in plant identification, plant nomenclature, examination of morphological characters of plants, including herbarium specimens, phylogenetic analysis, and molecular approaches in systematics (DNA extraction, PCR, sequencing, and sequence analysis). Two of them participated in our initial efforts in next-generation sequencing (see above). In addition, several undergraduates worked in the lab assisting the graduate students, and four visiting international scholars, two from China and two from Pakistan, all interested in various aspects of plant systematics and/or ethnobotany, conducted research in my lab for periods of 6 months to a year. How have the results been disseminated to communities of interest? For this reporting period, the primary means of dissemination of results has been through journal publications. What do you plan to do during the next reporting period to accomplish the goals? I will continue to supervise my graduate students as they complete their thesis and dissertation research and write up the results. These should result in publications that provide important contributions to knowledge of the diversity, phylogeny and classification of Prunus and to the taxonomy, phylogeny, and biogeography of Acaena, a primarily southern hemisphere genus of Rosaceae with centers of diversity in Chile and New Zealand, as well as to understanding of the evolution of invasiveness, a major ecological problem, and the evolution of symbiotic nitrogen fixation, a phenomenon of tremendous agricultural and ecological importance. We will also continue to seek funding to support our studies of phylogeny of Maleae and evolution of the pome fruit type.
Impacts
What was accomplished under these goals?
A major emphasis during this reporting period has been on writing manuscripts based on past research on systematics of the general Prunus (Rosaceae) and Chrysophyllum (Sapotaceae). As a result, several manuscripts are expected to be published during the next review period. Two papers were published during this period, one reporting results of ethnobotanical research conducted by a former MS student in Niger for her thesis, the other reporting results of phylogeographic studies in Pyrus. My participation in the writing of the latter paper grew out of my collaborations with two Chinese labs, both of which have sent visiting scholars to my lab (see below). I also assisted those scholars and two from Pakistan with other research and writing. We have conducted DNA-based identifications of walnut trees for several researchers. This is important because some closely related species and hybrids cannot be reliably distinguished based on morphology alone. Finally, we generated next-generation sequence data from about 200 single-copy loci for species in 12 genera of the apple tribe (Maleae, Rosaceae), as well as from transcriptomes of developing fruits of two species in the tribe. These served as preliminary data for a full proposal to NSF to study the phylogeny of Maleae and the evolution of the pome, the unique fruit type found in the tribe. That proposal was not funded, but we recently submitted a pre-proposal for an improved, more focused version of the same project and we are hopeful that we will be invited to submit a full proposal again, and that it will be successful this time.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Liu, J., Sun, P., Zheng, X., Potter, D., Li, K., Hu, C., and Teng Y. 2013. Genetic structure and phylogeography of Pyrus pashia L. (Rosaceae) in Yunnan Province, China, revealed by chloroplast DNA analyses. Tree Genetics & Genomes 9: 433-441.
- Type:
Journal Articles
Status:
Published
Year Published:
2013
Citation:
Towns, A. M., Potter, D., and Idrissa, S. 2013. Cultivated, caught, and collected: defining culturally appropriate foods in Tall�, Niger, Development in Practice 23: 169-183.
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Progress 01/01/12 to 12/31/12
Outputs
OUTPUTS: Graduate student Siew-Wai Chin completed his Ph.D. dissertation on phylogeny, evolution, and biogeography of Prunus, in June2012. His research is a major component of a long-term collaborative project with Jun Wen (Smithsonian Institution) and Joey Shaw (University of Tennessee - Chattanooga) on systematics of the genus, in which current Ph.D. student Jorge Perez-Zabala is also participating. Jorge is studying taxonomy and phylogeny of the South American species of Prunus, with a particular focus on climatic drivers of diversification. I was the speaker for a multi-authored oral presentation about our latest results on this project, including many of Siew-Wai's findings, at the Botany2012 meetings in Columbus Ohio in July. Graduate student Daniel Park also gave a talk on his dissertation research invasive Asteraceae (see below) at those meetings. I have continued to host international visiting scholars, for periods of 3 months to 1 year, in my lab, and two international Ph.D. students participated in work in my lab during 2012: Jing Liu, from Jejiang University (China), and Mahmoud Khourank, from Tehran University (Iran). These opportunities foster international collaborations on systematics of Rosaceae and other groups. In April 2012, I taught a one-day workshop entitled "Introduction to the Second Edition of The Jepson Manual" at California State University - Chico, sponsored sponsored by the Friends of the Chico State Herbarium. Participants included educators, agency and amateur botanists, and professional consultants. The workshop provided an overview of the principles of phylogenetic systematics and botanical nomenclature, explanations of why and how new evidence about phylogenetic relationship can result in taxonomic changes, descriptions of examples of name changes that have occurred at the family and genus levels between the first and second editions of The Jepson Manual, as well as a practice session using the keys in the second edition. Participants were provided with handouts of the presentations and supplementary information and electronic copies were made available on request. Additional research projects in my lab during the review period include the completion of Shannon Still's Ph.D. research on phylogeny and taxonomy of the California poppies and relatives (tribe Eschscholtzieae, family Papaveraceae), collaborative projects with Chinese scientists in the Rosaceous genera Photinia and Pyrus, and current Ph.D. student Daniel Park's innovative studies using community phylogenetic approaches to investigate patterns of relationship between native and exotic taxa in California Asteraceae, supported in part by an NSF Doctoral Dissertation Improvement Grant. PARTICIPANTS: Individuals who worked on the project during the reporting period include the following: UC Davis Ph. D. Students: Siew-Wai Chin, Jorge Perez-Zabala, Daniel Park. Visiting International Ph.D. Students: Jing Liu (Zhejiang University, China), Mahmoud Khorank (Tehran University, Iran). Collaborators in the US: Jun Wen (Smithsonian Institution), Joey Shaw (University of Tennessee-Chattanooga). TARGET AUDIENCES: As described under Outputs, I presented an overview of results of our ongoing collaborative phylogenetic, evolutionary, and biogeographic analyses of the genus Prunus (Rosaceae, Amygdaloideae) at the Botany 2012 meetings, which were attended by a broad range of investigators and students of Plant Biology from throughout the US and some international participants. I also led a workshop on "Introduction to the Second Edition of The Jepson Manual" at CSU - Chico, which was attended by educators, agency and amateur botanists, and consultants. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Prunus comprises 200-400 species of trees and shrubs, including many of the most economically important fruit crops of temperate regions. Best known from the temperate zone of the Northern Hemisphere, the genus is also well represented in tropical regions in Asia and the Americas. Phylogenetic analyses of plastid DNA provide support for the following: 1) a clade comprised of members of subgenera Prunus (with section Microcerasus cherries embedded), Amygdalus, and Emplectocladus; 2) a clade comprising most members of subgenus Cerasus; 3) a clade comprising clades 1) and 2); and 4) a clade comprised of tropical and temperate members of subgenera Laurocerasus and Padus (with genus Maddenia embedded). In contrast, analyses of nuclear ribosomal ITS sequences provide support for Clades 1) and 2), but not 3) and 4), and some topologies resolve Cerasus as more closely related to temperate members of Laurocerasus and Padus than to Clade 1). In addition, the ITS data suggest that the tropical African, American, and southeast Asian species form several distinct and geographically consistent clades. Taken together with the fact that documented chromosome counts indicate that subgenera Laurocerasus and Padus are polyploid groups, our results suggest that an early hybridization in the genus, involving an ancestral cherry on the paternal side and another early-diverging lineage on the maternal side, gave rise to the common ancestor of extant Laurocerasus and Padus. Reconstructions of ancestral areas in conjunction with clade dating indicate that the genus originated in eastern Asia in the late Paleocene and that the proposed hybridization event that resulted in the divergence of clades 3) and 4) in the plastid phylogeny occurred in the same area in the early Eocene. Subsequent diversification of clade 1) included at least two separate dispersals into North America, most likely via the Bering land bridge. Diversification of clade 4) involved dispersals into southeast Asia and Africa, as well as at least two to the New World, one most likely via the North Atlantic land bridge, the second possibly via the Bering land bridge and extending into Central and South America. Our study includes greater representation of tropical taxa than in previous analyses, but increased sampling from some areas is needed to test these hypotheses. Morphological and anatomical studies of the distinctive and diagnostic leaf glands that occur in diverse forms and positions in species of Prunus resulted in classification of the glands into two major types: Class 1, extrafloral nectaries, and Class 2, resin-secreting colleters. Class 1 is further divided based on gland position and form into Class 1A (raised, marginal) and Class 1B (flat, laminar). We hypothesize that the derived flat glands evolved due to adaptive loss of leaf serrations in warmer climates, while the plesiomorphic glandular teeth were indirectly selected for in cooler climates due to an adaptive advantage of serrated margins. Finally, we showed that the dark punctate spots that occur on the abaxial surfaces of some tropical species are in fact cork warts, derived from stomata, which do not form a glandular function.
Publications
- Journal Articles: Chin, S.-W., Lutz, S., Wen, J., and Potter, D. 2013. The bitter and the sweet: inference of homology and evolution of leaf glands in Prunus (Rosaceae) through anatomy, micromorphology and ancestral character state reconstruction. International Journal of Plant Sciences 174: 27-46.
- Still, S. M., and Potter, D. 2013. California poppy conundrums: insights into relationships within tribe Eschscholtzieae (Papaveraceae). Systematic Botany: in press.
- Abstract: Chin, S.-W., J. Wen, J. Shaw, R. Haberle, J. Perez-Zabala, and D. Potter. 2012. Phylogeny and historical biogeography of Prunus (Rosaceae, Amygdaloideae). Presented at Botany2012, Columbus, Ohio, July 7-11, 2012.
- Park, D., and Potter, D. 2012. Weed profiling: a molecular phylogenetic approach to Darwin's naturalization hypothesis. Presented at Botany2012, Columbus, Ohio, July 7-11, 2012.
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: I presented an overview of results of our ongoing collaborative phylogenetic, evolutionary, and biogeographic analyses of the genus Prunus (Rosaceae, Amygdaloideae) in an invited plenary lecture at Wild Crops 2011: 1st International Symposium on Wild Relatives of Subtropical and Temperate Fruit and Nut Crops, held in Davis in March, 2011. I also contributed an introductory chapter on the botany, diversity, taxonomy, evolution, economic importance, and research interests of Prunus to a forthcoming book on stone fruit breeding and genomics. Graduate student Jennifer Petersen completed her Ph.D. dissertation, which documents her research on two species in the family Sapotaceae that are native to Mesoamerica and cultivated for their edible fruits throughout the tropics. Her work includes studies of the origins of cultivated forms of Chrysophyllum cainito, known as 'caimito' or 'star apple', based on evidence from microsatellite markers and DNA sequences, and investigations into the effects of management practices on genetic diversity of Manilkara zapota, known as 'chicozapote' or 'sapodilla,' based ethnobotanical interviews and microsatellite evidence. In 2011, I taught two workshops entitled "Phylogeny, Taxonomy, and Name Changes in the California Flora", one in February at UC Berkeley, sponsored by the Friends of the Jepson Herbarium, and one in March at UC Davis, sponsored by the Davis Botanical Society. Participants included educators, agency and amateur botanists, and professional consultants. The workshops provided an overview of the principles of phylogenetic systematics and botanical nomenclature, explanations of why and how new evidence about phylogenetic relationship can result in taxonomic changes, and descriptions of examples of name changes that have occurred at the family and genus levels between the first and second editions of The Jepson Manual. Participants were provided with handouts of the presentations and supplementary information and electronic copies were made available on request. I also gave a talk on this topic for the Mt. Lassen chapter of the California Native Plant Society in Chico in December. PARTICIPANTS: Individuals who worked on the project during the reporting period include the following: UC Davis Ph. D. Students: Siew-Wai Chin, Jorge Perez-Zabala, Jennifer Petersen, Daniel Park. Collaborators in the US: Ingrid Parker (UC Santa Cruz), Jun Wen (Smithsonian Institution), Joey Shaw (University of Tennessee-Chattanooga). TARGET AUDIENCES: As described under Outputs, I presented an overview of results of our ongoing collaborative phylogenetic, evolutionary, and biogeographic analyses of the genus Prunus (Rosaceae, Amygdaloideae) in an invited plenary lecture at Wild Crops 2011: 1st International Symposium on Wild Relatives of Subtropical and Temperate Fruit and Nut Crops, held in Davis in March, 2011. The audience was an international group of researchers, including plant breeders, germplasm resource managers, and other plant biologists. In 2011, I taught two workshops entitled "Phylogeny, Taxonomy, and Name Changes in the California Flora", which were attended by educators, agency and amateur botanists, and consultants. I also gave a talk on this topic for the Mt. Lassen chapter of the California Native Plant Society in Chico in December. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Our research in Prunus is contributing to improved understanding of the historical biogeography, morphological character evolution, and taxonomy of this large and very important genus. Our phylogenetic analyses of maternally inherited chloroplast DNA have provided support for the following: 1) a clade comprised of members of subgenera Prunus (with section Microcerasus cherries embedded), Amygdalus, and Emplectocladus; 2) a clade comprising most members of subgenus Cerasus; 3) a clade comprising clades 1) and 2); and 4) a clade comprised of tropical and temperate members of subgenera Laurocerasus and Padus (with genus Maddenia embedded). In contrast, analyses of nuclear ribosomal ITS sequences provide support for Clades 1) and 2), but not 3) and 4), and some topologies resolve Cerasus as more closely related to temperate members of Laurocerasus and Padus than to Clade 1). In addition, the ITS data suggest that the tropical African, American, and southeast Asian species form several geographically consistent clades that may have diverged early in the evolution of the genus. Taken together with the fact that documented chromosome counts indicate that subgenera Laurocerasus and Padus are polyploid groups, our results suggest that an early hybridization in the genus, involving an ancestral cherry on the paternal side and an early-diverging, probably raceme-bearing lineage on the maternal side, gave rise to the common ancestor of extant Laurocerasus and Padus. Phylogenetic and phylogeographic studies of Chrysophyllum cainito show that its closest relative is C. argenteum and that domesticated forms of the former species likely originated in the area that is now Panama and were dispersed northward to Mexico and the Antilles via human activity, rather than having been domesticated in the West Indies as previously thought. The results are significant in demonstrating one of the first cases in which a plant was domesticated in southern Mesoamerica and in being one of the first studies of this type in Sapotaceae. In the Yucatan Peninsula of Mexico, human-managed trees of Manilkara zapota retain high levels of the genetic diversity found in wild trees in the same area, a result that has important implications for germplasm conservation.
Publications
- Petersen, J. J., Parker, I. M., and Potter, D. 2012. Origins and close relatives of a semi-domesticated neotropical fruit tree: Chrysophyllum cainito L. (Sapotaceae). American Journal of Botany (in press).
- Potter, D. 2012. Basic information on the stone fruit crops. Chapter 1 in: Abbott, A. G. and Kole, C., eds. Genetics, Genomics and Breeding of Stone fruits. Science Publishers, Enfield, New Hampshire, and CRC Press, Boca Raton, Florida (in press).
- Potter, D., Chin, S.-W., Haberle, R., Perez-Zabala, J., Shaw, J., Widjaja, E. A., and Wen, J. 2011. Phylogeny and biogeography of Prunus (Rosaceae): implications for lineage-based conservation. Plenary lecture presented at Wild Crops 2011: 1st International Symposium on Wild Relatives of Subtropical and Temperate Fruit and Nut Crops, Davis, California, March 19-23, 2011.
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Collaborative phylogenetic and evolutionary analyses of the genus Prunus (Rosaceae, Amygdaloideae) based on DNA sequence data, including investigations of biogeographic history and morphological character evolution, have continued, as have studies of origins of cultivated forms of Chrysophyllum cainito (Sapotaceae), based on evidence from microsatellite markers and DNA sequences. A collaborative study of Photinia and closely related genera (Rosaceae, Pyrinae) was completed. New studies initiated during the reporting period include: 1) analyses of diversity of olive (Olea europaea, Oleaceae) cultivars represented in the germplasm collections of the Olive World Germplasm Bank at the Universidad de Cordoba, Spain and the USDA National Clonal Germplasm Repository in Davis, based on microsatellite markers; and 2) analyses of variation in DNA sequences and expression patterns of several genes putatively involved in leaf morphogenesis (orthologs of PHANTASTICA, KNOX, and LEAFY) in Spiraea and related genera of Spiraeeae (Rosaceae), which together exhibit a diversity of leaf morphologies from simple entire, to variously lobed and toothed, to highly dissected, to pinnately compound. I have also contributed to studies of genetic diversity of walnut (Juglans regia) populations in Iran being conducted by collaborators in that country. All of the treatments I authored for the second edition of The Jepson Manual, as well as the rest of the Rosaceae treatments for which I served as family editor, were completed and are now posted on line, with the hard copy of the new manual scheduled for publication by the end of 2011. In 2010, I taught two workshops entitled "Phylogeny, Taxonomy, and Upcoming Name Changes in the California Flora", one at UC Davis (March 6), sponsored by the Davis Botanical Society, and one at UC Berkeley (April 3), sponsored by the Friends of the Jepson Herbarium. Participants included educators, agency and amateur botanists, and professional consultants. The workshops provided an overview of the principles of phylogenetic systematics and botanical nomenclature, explanations of why and how new evidence about phylogenetic relationship can result in taxonomic changes, and descriptions of examples of name changes that have occurred at the family and genus levels between the first and second editions of The Jepson Manual. Participants were provided with handouts of the presentations and supplementary information and electronic copies were made available on request. PARTICIPANTS: Individuals who worked on the project during the reporting period include the following: UC Davis Ph. D. Students: Siew-Wai Chin, Jorge Perez-Zabala, Jennifer Petersen. Visiting Ph.D. Students: Syed Aneel Gilani (Quaid-I-Azam University, Islamabad, Pakistan), Guo Wei (Sun Yat-sun University, Guangzhou, China). Visiting Scholar: Isabel Trujillo (University of Cordoba, Sapin). Collaborators in the US: Ingrid Parker (UC Santa Cruz), Jun Wen (Smithsonian Institution), Joey Shaw (University of Tennessee-Chattanooga). International Collaborators: Dalibor Ballian (University of Sarajevo, Sarajevo, Bosnia and Herzegovina), Mehdi Sharifani (Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran). TARGET AUDIENCES: As described under Outputs, in 2010, I taught two workshops entitled "Phylogeny, Taxonomy, and Upcoming Name Changes in the California Flora", which were attended by educators, agency and amateur botanists, and consultants. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
Phylogenetic analyses of nuclear ribosomal ITS and plastid ndhF sequences, with an expanded sampling of tropical species of subgenus Laurocerasus compared to previous studies and the inclusion of three Maddenia, species confirmed previous results that Maddenia is nested within Prunus and supported the formal transfer of all species previously classified in the former genus to the latter. Results of phylogenetic analyses of relationships among 23 Prunus species collected from different regions of Pakistan, based on nuclear ITS sequences, were concordant with those from previous phylogenetic studies of the genus, with species belonging to subgenera Padus, Laurocerasus, and Cerasus, except those belonging to section Microcerasus, forming a clade sister to species from subgenera Prunus and Amygdalus and members of subgenus Cerasus section Microcerasus. Pollen grains of six species of Prunus collected from various parts of Northern Pakistan were characterized micromorphologically using scanning electron microscopy. Variation was observed in shape and exine sculpturing, and the variations were found to be useful for species identification. Phylogenetic analyses of Photinia sensu lato and several related genera based on two chloroplast DNA regions and nrITS sequences indicated that Stranvaesia should be merged into Photinia, while Pourthiaea and Aronia should be delimited as two separate genera. Incongruence between chloroplast and nuclear data supported the hypothesis of a hybrid origin of the genus Heteromeles, which comprises a single species in western North America, with a recent ancestor of extant Photinia implicated as the probable male parent. Comparisons of morphological and chemical traits revealed significant differences between cultivated and wild forms of Chrysophyllum cainito in Panama, interpreted as a signature of domestication, but corresponding differences have not been detected with molecular markers to date, suggesting that human selection acted on multiple wild genotypes and/or that there is ongoing gene flow between wild and cultivated trees.
Publications
- Chin, S.-W., Wen, J., Johnson, G,. and Potter, D. 2010. Merging Maddenia with the morphologically diverse Prunus (Rosaceae). Botanical Journal of the Linnaean Society 164:236-245.
- Gilani, S. Y., Qureshi, R. A., Khan, A. M., and Potter, D. 2010. Morphological characterization of the pollens of the selected species of genus Prunus Linn. from northern Pakistan. African Journal of Biotechnology 9:2872-2879.
- Gilani, S. Y., Qureshi, R. A., Khan, A. M., and Potter, D. 2010. A molecular phylogeny of selected species of genus Prunus L. (Rosaceae) from Pakistan using the internal transcribed spacer (ITS) spacer DNA. African Journal of Biotechnology 9:4867-4872.
- Parker, I. M., Lopez, I., Petersen, J. J., Anaya, N., Cubilla-Rios, L., and Potter, D. 2010. Domestication syndrome in caimito (Chrysophyllum cainito L.): fruit and seed characteristics. Economic Botany 64:161-175.
- Potter, D. 2011b. Rosaceae treatments in: Baldwin, B. et al. eds, The Jepson Manual: Vascular Plants of California, Second Edition, University of California Press, Berkeley (in press). On-line versions currently available at: http://ucjeps.berkeley.edu/tjm2/review/treatments/rosaceae_all.html
- Guo, W., Yu, Y., Shen, R.-J., Liao, W.-B., Chin, S.-W., and Potter, D. 2011. A phylogeny of Photinia sensu lato (Rosaceae) and related genera based on nrITS and cpDNA analysis. Plant Systematics and Evolution 291:91-102.
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Progress 01/01/09 to 12/31/09
Outputs
OUTPUTS: The primary goals of our studies are to understand genetic diversity within and phylogenetic relationships among cultivated and wild plant species in selected taxonomic groups and to use the information to examine patterns of character evolution and historical biogeography, as well as to revise classifications, including species delimitations and generic and higher-level circumscriptions, when appropriate. The taxonomic groups of particular interest include tribe Spiraeeae and genus Prunus of the family Rosaceae, Juglans (Juglandaceae), and Chrysophyllum (Sapotaceae). The methods used to address these issues include development and application of molecular markers, including nucleotide sequence data and microsatellite or simple sequence repeat (SSR) markers, useful for phylogeny reconstruction and studies of genetic diversity. For questions concerning phylogenetic relationships among species and higher-level taxa, nucleotide sequence data are generated for both nuclear and chloroplast genes and spacers. Regions of interest are amplified by PCR and, if necessary, cloned, and the products are sequenced. The resulting data are analyzed phylogenetically using parsimony, maximum likelihood, and Bayesian approaches to produce hypotheses of evolutionary relationship in the form of phylogenetic trees. Characters of interest are mapped onto these trees in order to examine evolutionary transformations. For lower-level studies involving genetic diversity and relationships within species and among closely related species, SSR markers are used. The resulting data are analyzed using distance and Bayesian clustering approaches. Taxonomic changes are proposed where multiple sources of data strongly support the conclusion that existing classifications do not accurately reflect phylogenetic relationships. Results are disseminated via presentations in university classes and seminars, public workshops, at regional, national and international professional meetings, and through publications in scientific journals, books, and newsletters. In addition, we host international scholars in our lab and provided internship opportunities for undergraduate students. I also collaborate with various colleagues on and off campus who are interested in conducting phylogenetic studies in connection with their research. PARTICIPANTS: The project has contributed extensively to undergraduate and graduate student training and fostering of international collaborations. Several undergraduate students have assisted with research for this project. The project has provided training for four Ph.D. students in the Potter lab at UC Davis: Mr. Siew-Wai Chin, Mr. Jorge Andres Perez Zabala, Ms. Jennifer Petersen, and Mr. Shannon Still, and for two international graduate students visiting our lab: Mr. Syed Aneel Gilani (Quaid-I-Azam University, Islamabad, Pakistan), and Mr. Guo Wei (Sun Yat-sun University, Guangzhou, China). TARGET AUDIENCES: Because of the size, economic and ecological importance, and wide distribution, of Rosaceae, phylogenetic studies of the family are of broad interest to horticulturists, agency workers, environmental consultants, and amateur botanists worldwide. This is especially true in California: our state is the nation's leading producer of most rosaceous fruit, nut, and ornamental crops and the family is very well represented in our native flora. I am family editor for Rosaceae for the Jepson Flora Project, including the second edition of the Jepson Manual: Higher Plants of California (TJM2), a reference that is extensively used by members of the aforementioned groups in California. Our work on molecular marker development and phylogenetic relationships in Juglans has relevance to breeding and identification of J. regia cultivars and walnut rootstocks. I incorporate examples from my research related to these projects in my classroom teaching (California Floristics, Ethnobotany, Plant Biology Graduate Group Core Course, and a Freshman Seminar: Perspectives on Plant Diversity) and in public workshops and talks on the impacts of phylogeny on taxonomy, emphasizing examples from the California flora. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Our systematic studies of Prunus have continued to focus on the tropical Asian and American taxa, the subject of an NSF-funded collaboration with Jun Wen (Smithsonian Institution) and Joey Shaw (University of Tennessee-Chattanooga), and including the participation of our collaborator Elizabeth Widjaja (Indonesia), graduate student Chin Siew Wai and former postdoc. Rosemarie Haberle. We continue to find support for the following: 1) a clade comprised of members of subgenera Prunus, Amygdalus, and Emplectocladus; and 2) a clade comprised of temperate members of subgenera Laurocerasus and Padus. Intriguingly, ITS data suggest that the newly collected tropical African, American, and Southeast Asian species form several geographically consistent clades that may have diverged early in the evolution of the genus, forming successive sisters to the two main clades mentioned above. The Asian species formerly assigned to genus Pygeum evidently comprise a monophyletic group (but the African P. africana is excluded); it is nonetheless probably nested within Prunus. In September, 2009, Jorge Perez, an assistant professor at the Universidad Nacional de Colombia, joined my lab as a Ph.D. student through the Plant Biology Graduate Group. Mr. Perez is already has considerable experience with taxonomic studies of neotropical Prunus and will pursue further studies of that group for his Ph.D. dissertation research. Two other international students participated in research in my lab as visiting scholars: Mr. Syed Aneel Gilani (Quaid-I-Azam University, Islamabad, Pakistan), interested in diversity and phylogeny of the Amygdalus group (almonds and relatives) in Prunus and Mr. Guo Wei (Sun Yat-sun University, Guangzhou, China), interested in phylogeny and taxonomy of the genus Photinia, a member of Rosaceae tribe Pyreeae, the tribe that includes apples, pears, and other pome-bearing members of the family. Because of my experience in research on the genus, I was invited I was invited to contribute a chapter on Prunus to a forthcoming book on wild crop relatives. I also continue to serve as Rosaceae family editor for the forthcoming second edition of The Jepson Manual; during the past year, I have completed my editing of most of the 25 generic treatments authored by others and also finalized the ten generic treatments for which I am serving as primary author. My lab has continued to provide species identifications of Paradox and black walnut (Juglans spp.) rootstock samples provided by nurseries and growers. With graduate student Jennifer Petersen and collaborator Ingrid Parker (UC Santa Cruz), I have continued studies of the origins and domestication of Chrysophyllum cainito, known as caimito or star apple, widely cultivated throughout the tropics; a publication describing our examinations of phenotypic differences between wild and cultivated forms of the species in Panama has been submitted to Economic Botany, and manuscripts describing the results of molecular analyses are in preparation. Finally, I contributed phylogenetic studies of antioxidant biosynthetic pathway and phytochrome genes to publications by campus colleagues.
Publications
- Journal articles: Zheng, C. C., Potter, D., and O'Neill, S. D. 2009. Phytochrome gene expression and phylogenetic analysis in the short-day plant Pharbitis nil (Convolvulaceae): differential regulation by light and an endogenous clock. American Journal of Botany 96:1319-1336.
- Ikegami, A., Akagi, T., Potter, D., Yamada, M., Sato, A., Yonemori, K., Kitajima, A., and Inoue, K. 2009. Molecular identification of 1-Cys peroxiredoxin and anthocyanidin/flavonol 3-O-galactosyltransferase from proanthocyanidin-rich youg fruits of persimmon (Diospyros kaki Thunb.). Planta 230:841-855.
- Abstracts: Petersen, J., Parker, I. M., and D. Potter. 2008. Out of Panama Microsatellite variation suggests a southern Central American origin of the star apple, Chrysophyllum cainito L. Poster presentation at Harlan II: An International Symposium "Biodiversity in Agriculture: Domestication, Evolution, & Sustainability." Davis, California, September 14-18, 2008. Abstracts, p. 26.
- Chin, S.-W., Haberle, R. C., Wen, J., Shaw, J., and D. Potter. 2008. Phylogeny and diversity of Prunus (Rosaceae). Poster presentation at Harlan II: An International Symposium "Biodiversity in Agriculture: Domestication, Evolution, & Sustainability." Davis, California, September 14-18, 2008. Abstracts, p. 30.
- Shaw, J., Wen, J., Haberle, R., Chin, S. W., and D. Potter 2009. Phylogeny of 130 Prunus L. (Rosaceae) species using three cpDNA regions. Botany & Mycology 2009, Snowbird, Utah, July 25-29, 2009. http://2009.botanyconference.org/engine/search/index.phpfunc=detail& aid=933
- Book chapter: Potter, D. 2010 (In press). Prunus. In: Kole, C., ed. Wild Crop Relatives: Genomic & Breeding Resources, Volume 6: Wild Relatives of Temperate Fruits. Springer, Heidelberg, Berlin, New York, Tokyo.
- Newsletter article: Potter, D. 2009. Stalking wild stone fruits in Indonesia. Lasthenia, Newsletter of the Davis Botanical Society, no. 31, p. 5.
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: The origins, genetic diversity, and evolutionary relationships among many horticultural crop plants and their wild relatives remain poorly understood. The purpose of this study is to add to a growing body of molecular genetic data that can help elucidate relationships in several plant groups that include important horticultural crop species, and to use the information to revise classifications of those groups as necessary. The primary objectives of our studies are: 1) to develop molecular markers, including nucleotide sequence data and microsatellite or simple sequence repeat (SSR) markers, useful for phylogeny reconstruction and studies of genetic diversity in horticultural crop plants and their wild relatives, especially in tribe Spiraeeae and genus Prunus of Rosaceae, Juglans (Juglandaceae), and Chrysophyllum (Sapotaceae); 2) to increase sampling and continue to seek to obtain better phylogenetic resolution in Prunus and Chrysophyllum; 3) to examine the evolution of particular genetic, morphological, and ecological characters, such as self-incompatibility genes and leaf gland morphology in Prunus and characters associated with cultivation and domestication in Chrysophyllum and patterns of historical biogeography, in the groups of interest; 4) to use the information from the first three objectives to revise, as necessary, the taxonomies of the groups in question. For questions concerning phylogenetic relationships among species and higher-level taxa, nucleotide sequence data are generated for both nuclear and chloroplast genes and spacers. Regions of interest are amplified by PCR and, if necessary, cloned, and the products are sequenced. The resulting data are analyzed phylogenetically to produce hypotheses of evolutionary relationship in the form of phylogenetic trees. Characters of interest are mapped onto these trees in order to examine evolutionary transformations. For lower-level studies involving genetic diversity and relationships within species and among closely related species, SSR markers are used. The resulting data are analyzed using distance and Bayesian clustering approaches. Taxonomic changes are proposed where multiple sources of data strongly support the conclusion that existing classifications do not accurately reflect phylogenetic relationships. Results are disseminated via presentations at regional, national and international professional meetings and publications in scientific journals and books. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
Our recent systematic studies of Prunus have been focused on the tropical Asian and American taxa, the subject of an NSF-funded collaboration with Jun Wen (Smithsonian Institution) and Joey Shaw (University of Tennessee-Chattanooga), and including the participation of graduate student Chin Siew Wai and postdoc. Rosemarie Haberle. One paper resulting from this work was published this year. In Novemer, 2008, Wen and Potter traveled to Indonesia and spent two weeks on the island of New Guinea and one week on the island of Java, collecting material (herbarium specimens and leaves for DNA extraction) of native species of Prunus for inclusion in this study. We were accompanied by Elizabeth Widjaja (Herbarium Bogoriense). The project will provide a rigorous modern systematic study and revised taxonomic treatments for a large, taxonomically complex, and economically very important genus of angiosperms. A paper describing work done in my lab several years ago by Marie Pairon, a visiting student from Belgium, was published this year. The paper describes her work to develop genome-specific microsatellite markers for the allotetraploid Prunus serotina, native to North America but introduced and naturalized in parts of Europe; these markers will be useful for future studies of the population biology of this species. As a result of my interest in phylogeny and evolution of Prunus, I have continued to participate in collaborative research on the evolution of genes associated with fruit softening, a project led by Cameron Peace, and gametophytic self-incompatibility, in collaboration with Amy Iezzoni (Michigan State University), Tatsuya Tsukamoto (University of Arizona), and Ryutaro Tao (Kyoto University). One paper resulting from each of these studies was published this year. Because of my experience in research on family-level phylogenetic relationships and classification of Rosacae, I was invited to contribute a chapter on those subjects to the McGraw Hill 2009 Yearbook of Science & Technology. I also continue to serve as Rosaceae family editor for the forthcoming second edition of The Jepson Manual. My lab continues to provide species identifications of Paradox and black walnut (Juglans spp.) rootstock samples provided by nurseries and growers. Graduate student Jennifer Petersen, collaborator Ingrid Parker (UC Santa Cruz), and I are pursuing systematic, evolutionary, and ethnobotanical studies of cultivated and wild species of Chrysophyllum, focusing on the origins of C. cainito, known as caimito or star apple, widely cultivated throughout the tropics. Intriguingly, our preliminary results suggest a Panamanian origin for this species, in contrast to the West Indian origin previously reported in the literature. We presented our results at the Harlan II Symposium held at UC Davis in September and at the Second International Meeting of Sapotaceae Researchers, held in Geneva, Switzerland in October. Our work on Chrysophyllum is contributing to understanding of the systematics of a large and important tropical plant family while addressing compelling questions about domestication processes in tropical tree fruits.
Publications
- Tsukamoto, T., Potter, D., Tao, R., Vieira, C. P., Vieira, J., and Iezzoni, A. F. (2008) Genetic and molecular characterization of three novel S-haplotypes in sour cherry (Prunus cerasus L.). Journal of Experimental Botany 59: 3169-3185.
- Potter, D. 2009. Rosaceae (rose family). McGraw Hill 2009 Yearbook of Science & Technology: (in press)
- Pairon, M., Potter, D., and Jacquemart, A-L. Detection and characterization of genome-specific microsatellite markers in the allotetraploid Prunus serotina. (2008) Journal of the American Society of Horticultural Science 133: 390-395.
- Shulaev, V., Korban, S. S., Sosinski, B., Abbott, A. G., Aldwinckle, H. S., Folta, K. M., Iezzoni, A., Main, D., Arus, P., Dandekar, A. M., Lewers, K. Brown, S. K., Davis, T. M., Gardiner, S. E., Potter, D., and Veilleux, R. E. 2008. Multiple models for Rosaceae genomics. Plant Physiology 147: 985-1003.
- Wen, J., Berggren, S. T., Lee, C.-H., Ickert-Bond, S., Yi, T.-S., Yoo, K.-O., Xie, L., Shaw, J., and Potter. D. (2008) Phylogenetic inferences in Prunus (Rosaceae) using chloroplast ndhF and nuclear ribosomal ITS sequences. Journal of Systematics and Evolution 46: 322-332.
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Progress 01/01/07 to 12/31/07
Outputs
The genus Prunus is a primary focus of phylogenetic, taxonomic, and evolutionary studies in my lab. Our most recent efforts have been focused on the tropical Asian and American taxa, the subject of an NSF-funded collaboration with Drs. Jun Wen (Smithsonian Institution) and Joey Shaw (University of Tennessee-Chattanooga). Preliminary results of these studies were presented by graduate student Chin Siew Wai at the Flora Malesiana conference held in Leiden, The Netherlands, in June, and by Dr. Shaw and postdoc. Rosemarie Haberle (two separate presentations) at the Botany and Plant Biology 2007 meetings held in Chicago in July. As a result of my interest in phylogeny and evolution of Prunus, I have continued to participate in collaborative research on the evolution of genes associated with fruit softening, a project led by Dr. Cameron Peace, and gametophytic self-incompatibility, in collaboration with Drs. Amy Iezzoni (Michigan State University), Tatsuya Tsukamoto
(University of Arizona), and Ryutaro Tao (Kyoto University). I presented results of the latter project at the Chicago meetings. Also at those meetings, students in my lab gave presentations on their systematic studies of grapes (Vitis; Eric Wada), California poppies (Eschscholzia; Shannon Still), and the star apple or caimito (Chrysophyllum cainito; Jennifer Petersen), a tree fruit widely grown in the New World tropics. I gave two invited lectures on the topic By any other name: how phylogenies affect taxonomy, with examples from the California flora, one as the keynote speaker for the first meeting of the recently formed Northern California Botanists group, held in Chico in January, and the second to a meeting of the Eldorado Chapter of the California Native Plant Society, held in Placerville in May. In these lectures I gave an introduction to phylogenetic principles, an overview of how results of phylogenetic analyses can be incorporated into classification systems, and I then went
through several examples of how recent advances in our understanding of phylogenetic relationships of vascular plants will result in changes in taxonomic treatments, especially at the family level, in the forthcoming second edition of The Jepson Manual. We have continued to provide species identifications of Paradox and black walnut (Juglans spp.) rootstock samples provided by nurseries and growers.
Impacts
Our systematic studies of Prunus are leading toward a phylogenetically based infrageneric classification of Prunus, similar to our recently published phylogenetically based new infrafamilial classification of Rosaceae, and to taxonomic revisions of tropical Asian Prunus including the Pygeum group. The project will provide a rigorous modern systematic study and new taxonomic treatments for a large, taxonomically complex genus of angiosperms performed by a team of researchers with complementary expertise and extensive experience with the group. The project also represents an important contribution to the study of angiosperm biogeography. Our work on phylogeny of genes involved in self-incompatibility in Prunus is providing insights into the evolution of breeding systems in angiosperms. The lectures I have given on the affects of phylogenetic evidence on plant classifications have given me opportunities to help those who deal with plant identification in the field in
connection with public education, making policy decisions related to development and conservation, and/or recreation to understand the intellectual basis for the changes, some of which are quite significant and surprising, that will be forthcoming in one of the most important reference volumes used by professional and amateur botanists in California. Our work on walnuts is providing stakeholders with information about the degree to which genetic backgrounds of the trees influence their field performance.
Publications
- Aradhya, M. K, Potter, D., Gao, F., and Simon, C. J. (2007) Simon Molecular phylogeny of Juglans (Juglandaceae): a biogeographic perspective. Tree Genetics & Genomes 3: 363-378.
- Ortega, O. R., Duran, E., Arbizu, C., Ortega, R., Roca, W., Potter, D., and Quiros, C. F. (2007) Pattern of genetic diversity of cultivated and non-cultivated mashua, Tropaeolum tuberosum, in the Cusco region of Peru. Genetic Resources and Crop Evolution 54:807-821.
- Peace, C.P., Callahan, A., Ogundiwin, E.A., Potter, D., Gradziel, T.M., Bliss, F.A. and Crisosto, C.H. (2007) Endopolygalacturonase genotypic variation in Prunus. Acta Hort. (ISHS) 738: 639-646.
- Potter, D, and Still, S. (2007) Phylogenetic position of Kelseya based on molecular data. Kelseya, Newsletter of the Montana Native Plant Society, Vol. 7 (4): 6-7.
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Progress 01/01/06 to 12/31/06
Outputs
Graduate student S. W. Chin and postdoc. R. Haberle joined my lab as part of our NSF-funded project on phylogeny, taxonomy, and biogeography of Prunus. They and collaborator J. Shaw have extracted DNA and begun nucleotide sequencing of material collected by collaborator J. Wen on trips to Asia and South America. Graduate student E. Wada has supervised three undergraduates working on our lab's portion of the USDA-funded project 'Candidate Genes for Fruit Softening in Prunus,' headed by C. Peace, in which the roles of our lab group are: 1) to survey the allelic diversity of endo-PG genes in peach; and 2) to examine phylogeny of these genes across Prunus and Rosaceae. I began a collaboration with Dr. A. Iezzoni examining phylogenetic relationships among genes encoding the pistil (SRNase) and pollen (SFB) determinants of self-incompatibility in Prunus. Graduate student J. Petersen, in collaboration with Dr. I. Parker, has continued her work on phylogeography and evolution
of Chrysophyllum cainito (Sapotaceae). Our collaborative NSF proposal for this project was rated highly by reviewers but was not funded due to insufficient preliminary data. We were awarded a UC Davis faculty research 'insurance' grant for this project, which has provided funding to allow Ms. Petersen and several undergraduates to increase the preliminary data; we plan to resubmit the proposal in 2007. We have provided species identifications of Paradox and black walnut (Juglans spp.) rootstock samples from several areas in California where unusually high mortality in walnut orchards occurred in 2006.
Impacts
Systematic studies of horticulturally important families such as Rosaceae and genera such as Prunus and Spiraea, and phylogenetic analyses of genes involved in fruit ripening and self-incompatibility have implications for germplasm conservation and crop plant improvement. Research in Chrysophyllum provides opportunities to examine evolutionary dynamics of plant-people interactions.
Publications
- Bortiri, E., Vanden Heuvel, B., and Potter, D. 2006. Phylogenetic analysis of morphology in Prunus reveals extensive homoplasy. Plant Systematics and Evolution 259:53-71.
- Oh, S.-H. and Potter, D. 2006. Description and phylogenetic position of a new, angiosperm family, Guamatelaceae, inferred from chloroplast rbcL, atpB, and matK sequences. Systematic Botany: in press (2007).
- Potter, D., Eriksson, T., Evans, R. C., Oh, S., Smedmark, J., Morgan, D. R., Kerr, M., Robertson, K. R., Arsenault, M., Dickinson, T. A., and Campbell, C. S. 2006. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution: in press(2007).
- Potter, D., Still, S. M., Grebenc, T., Ballian, D., Bozic, G., Franjae, J., and Kraigher, H. Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data. Plant Systematics and Evolution: in press (2007).
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Progress 01/01/05 to 12/31/05
Outputs
We have initiated a four-year NSF-funded project in collaboration with Drs. Jun Wen and Joey Shaw to examine phylogeny, taxonomy, and biogeography of the large, economically important genus Prunus, emphasizing the tropical American and especially the southeast Asian species, which have been very poorly represented in previous systematic and evolutionary studies of the genus. Family-level studies of DNA sequence variation across Rosaceae have also continued in collaboration with researchers at several labs in the US and internationally. Results of the most recent collaborative efforts of this group were presented in a Rosaceae symposium at the XVI International Botanical Congress in Vienna in July, 2005 and a publication reporting those results, in which a new subfamilial and tribal classification for the family will be proposed, is in preparation. In conjunction with the same symposium, graduate student Shannon Still and I prepared a poster presentation of recently
initiated studies of phylogeny and biogeography of the tribe Spiraeeae, which includes the large genus Spiraea and several smaller genera. For the IBC in Vienna, I also was invited to participate in a symposium on Character Coding in Phylogenetic Inference, in which I gave a presentation, co-authored with John Freudenstein (Ohio State University) about current views, including our own, on the relationships among characters, phylogenies, and classifications. The presentation was subsequently published in the journal Taxon. Another recently initiated area of research, with graduate student Jennifer Petersen, involves systematic studies in the genus Chrysophyllum (Sapotaceae), focussing on one of the species that is cultivated for its edible fruits, specifcially C. cainito, the caimito or star apple. The primary goal of our research in this group is to examine the origins of the cultivated taxon and its relationships to wild species in order to understand the role that humans have played
in shaping character evolution and influencing geographic distributions in this genus. We are collaborating with Ingrid Parker (U C Santa Cruz) who is interested in the question of whether or not C cainito is invasive in areas of Central America, especially Panama. Recently, I began a collaboration with Roxanne Bittman, botanist for California Department of Fish and Game with the objective of using molecular markers to address the question of whether or not Juglans hindsii should be considered invasive in areas along the northern Sacramento River. We intend to achieve this by comparing levels of genetic diversity in populations from those areas and putative native populations in Napa and Contra Costa Counties. I have also collaborated with colleagues in the Department of Plant Sciences who are incorporating phylogenetic analyses in their research on biochemical evolution. I am a collaborator on a USDA-funded project headed by Cameron Peace entitled Candidate Genes for Fruit Softening
in Prunus. The role of my lab group in this project is to survey the allelic diversity of endo-PG genes in peach and to examine phylogeny of these genes across Prunus and Rosaceae.
Impacts
The focus on Rosaceae in general is motivated in part by the tremendous economic importance of that family, including the fact that the majority of temperate fruit crops are classified there. Our studies of genetic diversity and relationships within horticulturally important genera such as Prunus, Spiraea, and Vitis (dissertation research of Ph.D. student Eric Wada) have implications for germplasm conservation and breeding. The results of the research on Juglans hindsii should have important implications for management of this native California species. Research in Chrysophyllum provides many opportunities to study evolutionary issues related to plant domestication.
Publications
- Inoue, K and Potter, D. 2004. The chloroplastic protein translocation channel Toc75 and its paralog OEP80 represent two distinct protein families and are targeted to the chloroplastic outer envelope by different mechanisms. The Plant Journal 39:354-365.
- Oh, S.-H. and Potter, D. 2005. Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of cpDNA, rDNA, and Leafy. American Journal of Botany 92(1):179-192.
- Dangl, G. S., Woeste, K., Mallikarjuna, K., Keohmstedt, A., Simon, C., Potter, D., Leslie, C. A. and McGranahan, G. 2005. Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut. Journal of the American Society for Horticultural Science 130(3):348-354.
- Inoue, K., Potter, D., Shipman, R.L., Perea, J.V. and Theg, S.M. 2005. Involvement of a type I signal peptidase in biogenesis of chloroplasts-towards identification of the enzyme for maturation of the chloroplast protein translocation channel, pp. 933-935. In: Photosynthesis: Fundamental Aspects to Global Perspectives, A. van der Est and D. Bruce (eds.), Allen Press, Lawrence.
- Aradhya, M. K., Potter, D., and Simon, C. J. 2005. Cladistic biogeography of Juglans (Juglandaceae) based on chloroplast DNA intergenic spacer sequences, pp. 143-170. In: Darwins Harvest, New Approaches to the Origins, Evolution, and Conservation of Crops, T. Motley, N. Zerega, and H. Cross (eds.), Columbia University Press, New York.
- Gao, M., Li, G., Potter, D., McCombine, W. R., and Quiros, C. F. 2005. Comparative analysis of methylthioalkylmalate snythase (MAM) gene family and flanking DNA sequences in Brassica oleracea and A. thaliana. Plant Cell Reports: in press.
- Potter, D. and Freudenstein, J. V. 2006 Character-based phylogenetic Linnaen classification: taxa should be both ranked and monophyletic. Taxon 141: in press.
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Progress 01/01/04 to 12/31/04
Outputs
e have largely completed our NSF-funded project in collaboration with Dr. David Benson to examine diversity and phylogenetic relationships among the actinorhizal Rosaceae and to compare those with patterns of diversity and relationship among the Frankia strains found in root nodules of the plants. Our previous analyses revealed a surprising lack of diversity among Frankia strains nodulating members of Rosaceae in California. Several hypotheses could explain this result: 1) dominance of one or a few closely related strains over a broad geographic range resulting in reduced diversity of strains in the soil; 2) current strong selection by the host plants resulting in reduced diversity of strains in nodules; 3) current strong selection by the environment eliminating diverse strains from the soil; 4) a past evolutionary bottleneck that reduced the diversity of strains in this part of the world. Postdoctoral associate Brian Vanden Heuvel developed a method for amplifying
Frankia genes directly from soil samples. Cloning and sequencing of these genes from several sites at which actinorhizal members of Rosaceae occur revealed that the majority of strains present in the soil were very closely related to those found in the nodules, but a few more divergent strains were present at each location. These results support the first hypothesis. Along with undergraduate Sarina Lambert, Dr. Vanden Heuvel optimized microsatellite primers for studies of intraspecific variation within and among species of Cercocarpus. Several of these markers were applied to a study of the Cercocarpus ledifolius complex, which includes three taxa that are distinguished primarily based on leaf shape and size. Several hypotheses could account for the existence of these three taxa: 1) they represent three separate lineages; 2) there are two distinct lineages, with large and small leaves respectively, with the intermediates representing hybrids; 3) there is just one lineage with local
genetically and/or environmentally determined variation. We collected leaf tissue from throughout the geographic distribution of the species complex, and found that microsatellite variation does not correspond to taxonomic boundaries based on leaf morphology, supporting the third hypothesis. Graduate student Jennifer Petersen has begun molecular phylogenetic studies in the large tropical plant family Sapotaceae, which includes numerous wild, cultivated, and semi-domesticated species that produce edible fruits. Her dissertation project will be a phylogenetic study of tribe Chrysophylleae with an emphasis on the origins and variation of cultivated forms of C. cainito, the star apple, widely cultivated in Latin America and considered native to the Greater Antilles. Using DNA provided by the staff at the Royal Botanic Gardens Kew and material she collected in Costa Rica during the summer of 2003, Ms. Petersen has been examining DNA sequence variation in this group for several genes
commonly used in phylogenetic studies. Because she has detected low levels of sequence variability, she has also begun to investigate the utility of microsatellite primers developed for other species of Sapotaceae.
Impacts
The research on the diversity of Frankia in soil compared to that in nodules is an important contribution to the understanding of the evolution of symbiotic nitrogen fixation in plants. The work on taxonomic variation in Cercocarpus contributes to improving the classification of an ecologically important genus of shrubs in western North America. We are beginning work in Sapotaceae, a taxonomically difficult family of considerable economic and ecological importance in tropical areas which, to date, has been little studied from a molecular phylogenetic perspective. The family provides many opportunities to study evolutionary issues related to plant domestication.
Publications
- Vanden Heuvel, B. D., Benson, D. R., Bortiri, E., and Potter, D. 2004. Low genetic diversity among Frankia sp. strains nodulating sympatric populations of actinorhizal species of Rosaceae, Ceanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae) west of the Sierra Nevada (California). Canadian Journal of Microbiology: in press.
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Progress 01/01/03 to 12/31/03
Outputs
Postdoctoral associate Brian Vanden Heuvel has continued to work on our NSF-funded project, in collaboration with Dr. David Benson at the University of Connecticut, to examine diversity and phylogenetic relationships among the actinorhizal Rosaceae and to compare those with patterns of diversity and relationship among the Frankia strains infecting the plants. The main goal of the project is to assess the degree to which coevolution and cospeciation have occurred between plant hosts and their bacterial symbionts. During the summer of 2003, undergraduate Sarina Lambert joined the project; her summer employment was funded by an REU supplement to the NSF grant, and she has continued as a student assistant this academic year. Our analyses have revealed a surprising lack of diversity among Frankia strains on Rosaceae in California, but somewhat more diversity in other areas and we are continuing to investigate patterns of diversity in this group. Concomitantly, we have
generated phylogenies for the plants based on several gene sequences. Dr. Vanden Heuvel presented results of both aspects of this study at professional meetings in summer of 2003, and we are preparing results of both of these aspects of the project for publication. Most recently, with the assistance of Riaz Ahmad from Dr. Steve Southwick's lab, Dr. Vanden Heuvel has developed microsatellite primers for this group, which will be useful for testing hypotheses of interspecific hybridization within two of the genera, Cercocarpus and Purshia. I have also collaborated with Mr. Ahmad and Dr. Southwick on molecular marker development projects for stonefruit (Prunus spp.). Pedro Martinez-Gomez, a visiting scientist from Spain who worked in Dr. Tom Gradziel's lab and ours, completed and published molecular phylogenetic studies of varieties of peach and almond and closely related wild species. I assisted with phylogenetic analyses. Graduate student Sang-Hun Oh completed his dissertation research
on phylogeny and evolution of tribe Neillieae of Rosaceae. Dr. Joseph Rohrer, University of Wisconsin-Eau Claire, who spent a sabbatical leave in 2002 in our lab, examining diversity and phylogeny of species of North American plums, has published a paper resulting from that research. Our molecular marker development work in walnut, in collaboration with Dr. Chuck Simon and Dr. Malli Aradhya at the USDA's National Clonal Germplasm Repository, is largely complete and two manuscripts resulting from that work are in preparation.
Impacts
Our research on actinorhizal Rosaceae will help clarify the taxonomy of ecologically important shrubs in the western U. S., provide a detailed phylogeny of one major lineage within Rosaceae, and improve our understanding of the evolution of symbiotic nitrogen fixation in plants. Our work on molecular marker development in several fruit and nut crops and their wild relatives has relevance to plant breeding and germplasm conservation.
Publications
- Oh, Sang-Hun and Potter, Daniel. 2003. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Molecular Phylogenetics and Evolution 29:203-215.
- Martinez-Gomez, P., Arulsekar, S., Potter, D., and Gradziel, T.M. 2003. An extended interspecific gene pool available to peach and almond breeding as characterized using simple sequence repeat (SSR) markers. Euphytica 131:313-322.
- Martinez-Gomez, P., Arulsekar, S. Potter, D., and Gradziel, T.M. 2003. Relationships among peach, almond, and related species as detected by simple sequence repeat markers. Journal of the American Society for Horticultural Science 128(5):667-671.
- Rohrer, J. R., Ahmad, R., Potter, D., and Southwick, S. M. 2004. Microsatellite analysis of relationships among North American plums (Prunus sect. Prunocerasus, Rosaceae). Plant Systematics and Evolution: in press.
- Ahmad. R., Potter, D. and Southwick, S. M. 2004. Genotyping of peach and nectarine cultivars by molecular markers. J. Amer. Soc. Hort. Sci. 129 (2): in press.
- Ahmad. R., Potter, D.. and Southwick, S. M. 2004. Identification and characterization of plum and pluot cultivars by microsatellite markers. Hort Sci and Biotechnology. 79(2): in press.
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Progress 01/01/02 to 12/31/02
Outputs
At a symposium on Rosaceae held at the Botany2002 meetings this past summer, we presented results of phylogenetic analyses of species representing all major groups within the family, based on combined molecular data from our lab and several others. The group of researchers also met to discuss future plans to complete phylogenetic work on Rosaceae and to develop a new tribal classification for the family. In the same symposium, graduate student Sang-Hun Oh presented the results of his dissertation research on phylogeny and biogeography of tribe Neillieae, and we presented data to show that the monotypic genus Guamatela, formerly classified in that tribe, does not belong there and in fact is not even a member of Rosaceae but should instead be placed in the order Crossosomatales, perhaps in its own family. Further investigation of the position of this enigmatic taxon is in progress. Field collections of several small rosaceous genera of the western U.S. (Coleogyne,
Kelseya, Petrophyton) were made this past summer so that the phylogenetic positions of these taxa within the family can be established. Preliminary data have been generated and will be included in future analyses. Brian Vanden Heuvel, a postdoctoral associate hired to work on our collaborative project with Dr. David Benson, University of Connecticut, to examine patterns of co-speciation between actinorhizal species of Rosaceae (members of the genera Cercocarpus, Chamaebatia, Cowania, Dryas, and Purshia) and the nitrogen-fixing actinomycete bacteria (Frankia spp.) with which they form symbiotic relationships, joined our lab in June, 2002. He has made several field trips to collect root nodules from these species and other actinorhizal plants (Ceanothus spp., Rhamnaceae) in the western United States and Mexico. He has proceeded with developing a phylogeny for the actinorhizal Rosaceae based on molecular data and with analyzing the genetic diversity of the Frankia strains in the nodules
he has collected. Results to date indicate extremely low diversity of Frankia strains across host taxa, including Ceanothus spp., throughout the geographic region surveyed, which contrasts with results of previous studies of other plant groups. We are also developing microsatellite markers for the actinorhizal Rosaceae in order to facilitate studies of genetic diversity of the plants. Graduate student Esteban Bortiri has completed his dissertation research on phylogeny and evolution across the genus Prunus. Dr. Joseph Rohrer, University of Wisconsin ? Eau Claire, spent a sabbatical leave in our lab examining diversity and phylogeny of species of North American plums, while Antonio Reales Moya, visiting graduate student from the University of Murcia, Spain, pursued a similar project with European plums.
Impacts
As a result of collaborative phylogenetic studies in several labs, we are close to proposing a new intrafamilial classification for Rosaceae, which includes many temperate fruit crops. Our studies of genetic diversity in wild and cultivated Prunus have relevance to breeding and germplasm conservation. Our work on actinorhizal Rosaceae has implications for our understanding of the evolution of symbiotic nitrogen fixation in plants.
Publications
- Bortiri, E., Oh, S.-H., Gao, F., and Potter, D. 2002. The phylogenetic utility of nucleotide sequences of sorbitol 6-phosphate dehydrogenase in Prunus (Rosaceae) American Journal of Botany: 89: 1697-1708.
- Oh, S.-H., and Potter, D. 2003. Phylogenetic utility of the second intron of LEAFY in Neillia and Stephanandra (Rosaceae) and implications for the origin of Stephanandra. Molecular Phylogenetics and Evolution: in press.
- Potter, D. 2003. Molecular phylogenetic studies in Rosaceae. In: Sharma, A. K., and Sharma, A., eds. "Plant Genome: Biodiversity and Evolution, Volume 1: Phanerogams". Science Publishers, Inc. Enfield, New Hampshire. In press.
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Progress 01/01/01 to 12/31/01
Outputs
Results from our phylogenetic analyses of DNA sequence variation in chloroplast matK and trnL-trnF genes across Rosaceae have been accepted for publication. We have continued to investigate the phylogenetic utility of several protein-encoding nuclear genes in the family. A collaborative project with Dr. David Benson, University of Connecticut, to examine patterns of co-speciation between actinorhizal species of Rosaceae (members of the genera Cercocarpus, Chamaebatia, Cowania, Dryas, and Purshia) and the nitrogen-fixing actinomycete bacteria (Frankia spp.) with which they form symbiotic relationships, has been funded by the National Science Foundation. Preliminary work on this project has included collecting root nodules from several species in California and New Mexico and proceeding with gathering molecular data to generate a phylogeny for the plant species in this group. Graduate student Sang-Hun Oh has proceeded with phylogenetic and biogeographic studies of the
tribe Neillieae, while graduate student Esteban Bortiri has continued his work on Prunus. Dr. Pedro Martinez-Gomez, a visiting scientist from Spain working with Dr. Tom Gradziel, has completed collaborative work in our lab on variation among cultivars of almond (Prunus dulcis) and peach (Prunus persica) and related species using simple sequence repeat (SSR) markers.
Impacts
As a result of studies in our lab and several others, we are developing a detailed understanding of evolutionary relationships among taxa of Rosaceae, which include the majority of temperate fruit crops. Studies of variability among and within species of Prunus have relevance to plant breeding and germplasm conservation for these crops. Our examination of co-speciation between actinorhizal Rosaceae and nitrogen-fixing Frankia will have important implications for our understanding of the evolution of symbiotic nitrogen fixation and of symbioses in general.
Publications
- Potter, D., Gao, F., Bortiri, P. E., Oh, S.-H., and Baggett, S. 2001. Phylogenetic relationships in Rosaceae inferred from chloroplast matK and trnL-trnF nucleotide sequence data. Plant Systematics and Evolution: in press.
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Progress 01/01/00 to 12/31/00
Outputs
The results of our phylogenetic analyses of nuclear ITS and chloroplast trn sequences from species of Prunus have been accepted for publication. Results from our phylogenetic analyses of DNA sequence variation in nuclear genes encoding polygalacturonase inhibitor proteins (PGIPs) and chloroplast matK genes across Rosaceae have been submitted for publication. We have continued to investigate variation in sequences of nuclear genes encoding sorbitol 6-phosphate dehydrogenase (S6PDH), dihydroflavonol reductase (DFR), and polyphenol oxidase (PPO). A grant proposal on this research submitted to the Systematic Biology Program of the National Science Foundation (NSF) was recommended for funding but not at high enough priority to receive an award this year; a revised proposal is under preparation. In collaboration with Dr. David Benson, University of Connecticut, we have initiated studies of the phylogeny of actinorhizal species of Rosaceae (members of the genera Cercocarpus,
Chamaebatia, Cowania, Dryas, and Purshia). Members of these species form symbiotic relationships with nitrogen-fixing bacteria that inhabit nodules on the plants' roots. Our goal is to use the resulting data to examine coevolution between the plant hosts and the nodulating actinomycetes (Frankia spp.). A proposal to support this research has been submitted to NSF. Phylogenetic and biogeographic studies of the tribe Neillieae have been continued by graduate student Sang-Hun Oh, who has been awarded an NSF Doctoral Dissertation Improvement grant. His work has important implications for studies of the biogeographic history of North America and eastern Asia.
Impacts
Phylogenetic analyses of species of Prunus and other genera of Rosaceae are needed to establish stable and informative classifications for these economically important taxa, which include the majority of temperate fruit crops. The resulting hypotheses will also be used to address evolutionary and biogeographic questions and to provide information important for plant breeders. Several of the genes we are studying are physiologically and ecologically significant.
Publications
- Dobritsa, S., D. Potter, and A. Berry. 2001. Hopanoid lipids in Frankia: identification of squalene-hopene cyclase gene sequences. Canadian Journal of Microbiology: in press.
- Bortiri, E., S. Oh, J. Jiang, S. Baggett, A. Granger, C. Weeks, M. Buckingham, D. Potter, and D. Parfitt. 2001. Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Systematic Botany: in press.
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Progress 01/01/99 to 12/31/99
Outputs
The results of our phylogenetic analyses of nuclear ITS and chloroplast trn sequences from species of Fragaria have been accepted for publication. Results from our phylogenetic analyses of DNA sequence variation in nuclear genes encoding polygalacturonase inhibitor proteins (PGIPs) and chloroplast matK genes across Rosaceae were presented at the XVI International Botanical Congress this summer. Our results agree with many of those of phylogenetic studies of other genes in other labs and suggest that the subfamilial classification of Rosaceae requires revision. All of the existing classifications include some tribes and subfamilies that are clearly paraphyletic or polyphyletic. Our data resolved a sister relationship between the Spiraeoid genus Porteranthus and Maloideae sensu lato. In our studies and all others published to date, support for the relationships among major clades within Rosaceae remains weak; we are examining variation in three additional nuclear genes
and in chloroplast trn genes and spacers in order to investigate whether better resolution can be obtained. The three nuclear genes are those encoding sorbitol 6-phosphate dehydrogenase (S6PDH), dihydroflavonol reductase (DFR), and polyphenol oxidase (PPO), respectively. Phylogenetic studies of lower-level taxonomic groups within Rosaceae (the tribe Neillieae and the genera Exochorda and Prunus) have been continued by two graduate students and a postdoc. in the lab; all three presented posters at the Botanical Congress. We have submitted several proposals to the Systematic Biology Program of the National Science Foundation for grants to support this research.
Impacts
Phylogenetic analyses of chloroplast and nuclear gene sequences for species from all tribes of Rosaceae have confirmed some previously published results and have provided new insights. Robust hypotheses of phylogenetic relationship are needed to address evolutionary questions and to establish a stable classification system for this economically important family, which includes the majority of temperate fruit crops.
Publications
- Bortiri, E., Oh, S., Baggett, S., Buckingham, M., and Potter, D. 1999. Phylogeny and systematics of the genus Prunus L. (Rosaceae). Abstracts from the XVI International Botanical Congress, August 1-7, 1999, St. Louis, MO, p. 706.
- Gao, F., van der Maesen, L. J. G., and Potter, D. 1999. Phylogenetic analysis of the Exochorda complex (Rosaceae) based on morphological and molecular data. Abstracts from the XVI International Botanical Congress, August 1-7, 1999, St. Louis, MO, p. 434.
- Oh, S., and Potter, D. 1999. Phylogenetic relationships of the tribe Neillieae (Rosaceae) based on ITS sequences. Abstracts from the XVI International Botanical Congress, August 1-7, 1999, St. Louis, MO, p. 434.
- Potter, D., Gao, F., Oh, S., and Baggett, S. 1999. Molecular phylogenetic studies in Rosaceae. Abstracts from the XVI International Botanical Congress, August 1-7, 1999, St. Louis, MO, p. 39.
- Potter, D., Luby, J. J., and Harrison, R. E. 2000. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Systematic Botany: In press.
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Progress 01/01/98 to 12/31/98
Outputs
We have continued our examination of variation in DNA sequences from several genes across Rosaceae. Phylogenetic analyses of sequences of genes encoding polygalacturonase inhibitor proteins (PGIPs) are nearly complete, as is a study of variation in the chloroplast gene matK. Results from both studies are generally consistent with published results from analyses of the chloroplast gene rbcL, with a few notable differences. Both genes support the hypothesis that one or more Spiraeoid ancestors were involved in the origin of subfamily Maloideae. In general, chromosome number is a more reliable indicator of relationship than is fruit type within the family. We have also continued to amplify, clone, and sequence fragments of genes encoding NADP-dependent sorbitol 6-phosphate dehydrogenase (S6PDH) from representative Rosaceae. We have used sequence data from the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, and from the trnL intron and the trnL-trnF
spacer of chloroplast DNA, to examine relationships among species of Fragaria, Prunus (in collaboration with Dan Parfitt), Vitis (in collaboration with Andy Walker), and Lycianthes (in collaboration with Ellen Dean). A paper describing the work on Fragaria has been submitted for publication. The results of the Prunus studies suggest that some traditionally recognized taxonomic groups within the genus are not monophyletic.
Impacts
(N/A)
Publications
- PARFITT, D.E., JIANGYOU, J., WEEKS, C.F., GRANGER, A.R., AND POTTER, D. 1999. Taxonomic evaluation of 31 PRUNUS species from chloroplast DNA sequence data. Poster presented at the Plant and Animal Genome VII Conference, San Diego, CA, Jan. 17-21, 1999.
- DEAN, E.A. AND POTTER, D. 1998. A phylogeny of Lycianthes series MEIZONODONTAE (SOLANACEAE) based on morphological and molecular characters. Annual Meeting of the Botanical Society of America, Baltimore, Maryland, USA, Aug. 2-6, 1998. American Journal of Botany
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Progress 01/01/97 to 12/01/97
Outputs
We are examining variation in DNA sequences of two classes of nuclear genes in Rosaceae. They encode, respectively, polygalacturonase inhibitor proteins (PGIPs)and NADP-dependent sorbitol 6-phosphate dehydrogenase (S6PDH). Results of phylogenetic analyses of PGIP sequences from representatives of all subfamilies of Rosaceae were consistent with those published for chloroplast rbcL gene sequence data. Part of the S6PDH gene, including an intron,was amplified and sequenced from most of these species. The intron was too variable to align across all taxa, but it should be useful for examining relationships at lower taxonomic levels. Analysis of only the coding regions from representative woody Rosaceae provided less resolution than the PGIP analysis, but several of the same clades were supported. Both genes support the hypothesis that one or more Spiraeoid ancestors were involved in the origin of Maloideae. A grant proposal to expand these studies has been submitted to
NSF. We have used sequence data from the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA, and from the trnL intron and the trnL-trnF spacer of chloroplast DNA, to examine relationships among species of Fragaria. Variability is relatively low within the genus, but ITS data provide greater resolution than was published for chloroplast DNA restriction site data. A survey of ITS variation among about 18 North American species of Prunus indicated that ITS data provide substantial phylogenetic resolution in that genus.
Impacts
(N/A)
Publications
- POTTER, D. 1997. Variation and phylogenetic relationships of nucleotide sequences for putative genes encoding polygalacturonase inhibitor protein (PGIPs) among taxa of Rosaceae. American Journal of
- POTTER, D., LUBY, J.J., AND HARRISON, R.E. 1997. Phylogenetic relationships in Fragaria L. (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. American Journal of Botany
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