SYSTEMATIC STUDIES OF HORTICULTURAL CROP PLANTS AND THEIR WILD RELATIVES

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: COMPLETE
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 1013393
• Project Start Date: Oct 1, 2017
• Project End Date: Sep 30, 2022
• Program Code: [(N/A)]- (N/A)

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

Performing Department
Plant Sciences

Non Technical Summary
This project supports the mission of the Agricultural Experiment Station by addressing the Hatch Act area(s) of: plant and animal production, protection, and health. Systematics is the branch of biology concerned with understanding the origins and distribution of organismal diversity and using that information to elucidate evolutionary processes and develop robust classification systems. Basic research issues that are addressed by systematic studies in general include the elucidation of fundamental biological processes such as how species originate and diversify and the evolution of important, genetic, biochemical, morphological, and ecological features, in particular groups. Systematic studies of crop plants and their wild relatives further yield insight into the effects of cultivation, domestication, and human selection on plant evolution. Systematic studies are important to germplasm conservation and genetic improvement programs and to management and conservation of natural ecosystems. Many economically important crop plant species belong to larger taxonomic groups whose phylogenetic relationships are not well understood and whose classifications require revision. Many of these groups also have considerable ecological importance and they can include many wild species that exhibit potentially useful characteristics. By examining variation within and among crop species and their wild relatives and their relationships to one another, phylogenetic and evolutionary studies can furnish information relevant to issues such as which varieties or species, and from which geographic regions, should be given high priority for conservation. These studies also provide information about the evolution of agriculturally and environmentally important characteristics, such as pollination and dispersal syndromes, breeding systems, defense mechanisms, and invasiveness. Finally, the classification systems resulting from systematic studies provide a context for all other basic and applied biological research, and classifications that are based on current understanding of evolutionary relationships have maximum power to convey biologically meaningul information in addition to an organizational framework.

Animal Health Component

(N/A)

Research Effort Categories

Basic

100%

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
201	2499	1060	25%
202	2499	1060	25%
206	2499	1060	50%

Knowledge Area
206 - Basic Plant Biology; 202 - Plant Genetic Resources; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
2499 - Plant research, general;

Field Of Science
1060 - Biology (whole systems);

Keywords

evolution

systematics

taxonomy

phylogeny reconstruction

biogeography

classification

ethnobotany

domestication

rosaceae

prunus

sapindaceae

melicoccus

Goals / Objectives
1) To continue to investigate species delimitations, phylogenetic relationships, and patterns of character evolution and historical biogeography in major horticultural crop plants and their wild relatives, as exemplified by our work on Rosaceae, including Prunus and Pyrus.2) To continue to investigate domestication status, genetic diversity, and geographic and phylogenetic origins of locally important tropical edible fruit crops, as exemplified by our work on Chrysophyllum (Sapotaceae) and Melicoccus (Sapindaceae). 3) To continue to investigate the conservation status, geographic distributions, levels of genetic diversity, and potential for hybridization with other species, of selected plant taxa native to the California Floristic Province, especially taxa considered rare, as exemplified by our work on Juglans hindsii. 4) To continue to investigate the taxonomic circumscriptions, geographic distributions, and levels of genetic diversity of selected plant taxa native to the California Floristic Province, as exemplified by our work on Holodiscus and Sidalcea.5) To continue collaborative research with international visiting scholars from various countries, as exemplified by our work on Fritillaria and Sphenostylis.

Project Methods
Plant materials will be obtained from a variety of sources, including field collections in the wild, nurseries, germplasm collections, botanical gardens and arboreta, and herbarium specimens. Morphological characters will be evaluated and scored by examination of fresh and herbarium specimens. Methods for molecular phylogenetic (interspecific level), phylogeographic, and population genetic (infraspecific level) analyses, including selection of appropriately variable marker types and genomic regions, DNA extraction, PCR amplification of targeted regions, cloning, sequencing, alignment, and data analysis, will follow procedures described in previous publications (e.g.,Chin et al. 2014, Petersen et al. 2014, Zhao et al. 2016). A range of methods, including parsimony and model-based (maximum likelihood, Bayesian) approaches, will be employed for exploring species delimitations, phylogeny reconstruction, and investigations of character evolution and historical biogeography. Taxonomic decisions will incorporate information from analyses of morphological and molecular data with careful attention to nomenclatural issues. To date, we have primarily used "traditional" approaches to determining genotypes, such as Sanger sequencing and PCR amplification of microsatellite regions using taxon-specific primers, but we have recently ventured into high-throughput approaches such as comparative transcriptomics and genotyping-by-sequencing. As funding allows, we will continue to use these newer approaches, which provide significantly larger amounts of data from across the genome.

Progress 10/01/19 to 09/30/20

Outputs
Target Audience:Readers of plant systematics and other botanical journals in which I publish papers; professional botanists including faculty members, researchers, government agency workers, and consultants;amateur botanists; undergraduate and graduate students at UC Davis and elsewhere; agencies and organizations concerned with plant conservation (e.g., California Native Plant Society, California Department of Fish and Wildlife, San Francisco Public Utilities Commission); students and teachers at St. Patrick - St. Vincent Catholic High School (Vallejo), who participated in a project described herein, and Summit Public Schools (San Jose), for whom I gave a presentation in winter 2020. Changes/Problems:Restrictions on access to lab facilities and the need to pivot rapidly to teaching two lab courses on-line in spring 2020 due to the COVID19 pandemic resulted in somewhat reduced research activity and productivity. What opportunities for training and professional development has the project provided?The following graduate students worked in my lab during the reporting period. Graduate program, degree objective, and research topic are listed for each student: Chris Adlam, Ecology, Ph.D. (completed in 2020): traditional vegetation management, especially the use of fire in forest management, by native Americans, and its relationship to US Forest Service policies. Chenjiao Deng, Horticulture and Agronomy, M.S. (in progress): clarifying taxonomic identities of populations ofSidalceafrom the North Coast Range. Abbey Hart, Ecology M.S. (in progress): Regeneration of culturally significant plant species in Tásmam Koyóm in collaboration with the Maidu Summit Consortium.Intersection of ecological restoration, climate change adaptation and Indigenous sovereignty and land management. Oscar Hinojosa, Plant Biology Ph.D. (in progress): Phylogeny and taxonomy of the marigold tribe (Tageteae, Asteraceae). Reed Kenny, Ecology Ph.D. (in progress): Systematics and ethnobotany of the rush family, Juncaceae. Deniss Martinez, Ecology Ph.D. (in progress): understanding how California Native Nations navigate power differentials in natural resource stewardship collaborations, addressing questions of Indigenous science, environmental justice, and governance. Angelica Sauceda, Horticulture and Agronomy M.S. (in progress):Investigations in the germination ecology and propagation of three serpentine endemics of the San Francisco Peninsula. Rachel Spaeth, Horticulture and AgronomyPh.D. (in progress):Genetic complexity of inter- and intra- specific hybrid plums (Prunusspp.)introduced by world famous horticulturist Luther Burbank over 100 years ago. Mark Uleh, Horticulture and AgronomyPh.D. (in progress): Systematics and evolution of miraculin (a taste-altering protein that makes sour foods taste sweet) production in the miracle berry (Synsepalum dulcificum, Sapotaceae) and relatives in tropical Africa. How have the results been disseminated to communities of interest?Through publications in scientificjournals, presentations at professional meetings, articles in newsletters, and talks for high school students visiting the UC Davis herbarium. What do you plan to do during the next reporting period to accomplish the goals?Continue and work towards completion and publication of studies descried above: 1. Collaboration with Summer Ragosta,Heath Bartosh, and St. Patrick - St. Vincent Catholic High School to document floristic diversity in Solano County. 2. Phylogenomic analyses ofPrunustotest current ideas about the evolution and classification of the genus, in particular the hypothesis of multiple allopolyploid hybrid origins of the Laurocerasus-Padus group. 3. Comparative transcriptome analyses of members of Rosaceae tribe Spiraeeae with contrasting leaf morphologies. 4. Comparative genomic analyses of the three species ofFremontodendron. 5. Continued support of graduate student projectsin progress described above.

Impacts
What was accomplished under these goals? Research accomplishments during the review period include the following: 1. Publication of several papers resulting from ongoing international collaborations with researchers in Pakistan and China (two of whom were visiting scholars in my lab in previous years) were published. These include taxonomic and phylogenetic studies of the large, complex, and economically important generaArtemisia(Asteraceae),Pulsatilla(Ranunculaceae), andPhotinia(Rosaceae). 2. Publication of a paper describing ourpartnership with Dr. Summer Ragosta, a botanist and environmental science teacher and Heath Bartosh, lead botanist of the Solano County Flora Project, in which students in Dr. Ragosta's classes at the ethnically diverse St. Patrick - St. Vincent Catholic High School in Vallejo conducted floristic surveys and plant collections in an open space area in Vacaville.The project, which was funded by the school and the Toomey Foundation, will continue in 2021 with additional collections. 3. MS student Chenjiao Deng continued analyses of DNA sequences and morphological characters of populations of a taxon ofSidalcea(Malvaceae) from serpentine soils in the North Coast range in California whose identity is uncertain. These plants are potentially assignable, based on morphology, to the federally endangered speciesS. keckii, otherwise known only from a few populations in the southern Sierra Nevada foothills, but they also show varying degrees of intergradation with the more widespread speciesS. diploscypha, suggesting that they might represent hybrids or a new species. Chenjiao' s data to date suggest that the latter is most likely, but further study is needed and in progress. In the course of these analyses, Chenjiao also discovered that some populations from San Mateo County that had been assigned toS. diploscyphaseem to represent a distinct genetic lineage. These populations occur on land owned by the San Francisco Public Utilities Commission, who have provided funding to support adding analysis of highly variable microsatellite markers to the study, and Chenjiao has begun this phase of the project. The work has important conservation implications. 4. Continued contributions to understanding of the diversification and diversity of the stone-fruit genus,Prunus, especially the tropical members of the polyploid subgeneraLaurocerasusandPadus, with Jun Wen, Liz Zimmer, and Richard Hodel, all at the Smithsonian Institution. They are using a phylogenomic approach - generating phylogenies based on sequences of hundreds of nuclear loci obtained using the HybSeq methods -to improve understanding of phylogenetic relationships across the genus, which to date have been based on sequences from a few nuclear and chloroplast gene sequences. Theyhave invited me to collaborate by providing material of some species and contributing to data analysis and interpretation. To date, I have sent them material of twoPrunusspecies and multiple outgroupspecies representing other tribes in Rosaceae. As an additional component of this collaboration, I collected material of four species ofPrunusrepresenting (based on already published phylogenies) four different lineages within theLaurocerasus-Padusgroup, which were submitted to the UC Davis genome center for complete genome sequencing; the data are currently being analyzed by Hodel. Together, all of these data should provide powerful tools to test current ideas about the evolution and classification of this large, economically important genus, in particular the hypothesis, presented in previous collaborative publications by Jun Wen, myself, and others, of multiple allopolyploid hybrid origins of theLaurocerasus-Padusgroup. 5. Transcriptome data from young developing leaves of several genera of Rosaceae tribe Spiraeeae (Aruncus,Petrophytum, Spiraea) with diverse leaf morphologies, from material we collected in 2019, were generated by the UC Davis Genome Center. In order to facilitate reference genome assembly because no published genome exists for any species in any of these genera, the Genome Center's bioinformatics expert recommended additional sequencing of these samples, which was completed this fall; data are currently being analyzed. 6. We obtained funding from the California Conservation Genomics Project and from the Redbud and Eldorado chapters of the California Native Plant Society to support genomic and genetic studies of the three shrub species that comprise the genusFremontodendron(Malvaceae), commonly known as flannelbush. We will analyze genomic variation within and between all three species, which includeF. californicum,widely distributed in California and neighboring states and highly morphologically variable, and twospecies with highly restricted distributions that are listed at the state (rare) and federal (endangered) levels:F. mexicanumDavidson, known from only two natural occurrences in San Diego County and Baja California, andF. decumbens, known only from a few populations in El Dorado County. We will also sample individuals from some populations of uncertain taxonomic status in Nevada and Yuba Counties. Our goals are to understand how genomic variation in these plants is related to morphological variation, taxonomic identity, and status as rare,with important management implications for the listed species. 7. In my role as director of the UC Davis herbarium, I am localPI of a multi-institutional project, funded by NSF and led by Cal Poly - San Luis Obispo, which is digitizing and making publicly availableimages, label data, and phenological information (scored during this project) for nearly 1 million herbarium specimens (50,000 at UC Davis) of native California in selected ecologically important families, which will provide tremendously valuable resources for research on the California flora, in particular how climate change affects diversity and phenology (flowering and fruiting times) in the flora of a biodiversity hotspot. An articledescribing the project was published during the review period.

Publications

• Type: Journal Articles Status: Published Year Published: 2019 Citation: Hussain, A., Potter, D., Kim, S., Hayat, M. and Bokhari, S. 2019. Molecular phylogeny of Artemisia (Asteraceae-Anthemideae) with emphasis on undescribed taxa from Gilgit-Baltistan (Pakistan) based on nrDNA (ITS and ETS) and cpDNA (psbA-trnH) sequences. Plant Ecology and Evolution, 152: 507520.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Hussain, A., Potter, D., Hayat, M., Sahreen, S., and Bokhari, S. A. 2019. Pollen morphology and its systematic implication on some species of Artemisia L. from Gilgit-Baltistan Pakistan. Bangladesh Journal of Plant Taxonomy 26: 157168.
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Li, Q-j., Su, N., Zhang, L., Tong, R-c., Zhang, X-h., Wang, J-r., Chang, Z-y., Zhao, L., and Potter, D. 2020. Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae). Scientific Reports 10: 112. https://www.nature.com/articles/s41598-020-76699-7
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Ragosta, S., Potter, D., and Bartosh, H. 2020. Broadening student perceptions of science through participatory data collection & research-education partnerships: a case study in Californias Central Valley. The American Biology Teacher 82: 515521. https://doi.org/10.1525/abt.2020.82.8.515
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Guo, W., Fan, Q., Zhang, X-z., Liao, W-b., Wang, L-y., Wu, W., and Potter, D. 2020. Molecular reappraisal of relationships between Photinia, Stranvaesia and Heteromeles (Rosaceae, Maleae). Phytotaxa, 447: 103115. https://doi.org/10.11646/phytotaxa.447.2.3
• Type: Journal Articles Status: Published Year Published: 2020 Citation: Yost, J. M., Pearson, K. D., Alexander, J., Gilbert, E., Hains, L. A., Barry, T., Bencie, R., Bowler, P., Carter, B., Crowe, R. E., Dean, E., Der, J., Fisher, A., Fisher, K., Flores-Renteria, L., Guilliams, C. M., Hatfield, C., Hendrickson, L., Huggins, T., Janeway, L., Lay, C., Litt, A., Markos, S., Mazer, S. J., McCamish, D., McDade, L., Mesler, M., Mishler, B., Nazaire, J., Rebman, J., Rosengreen, L., Rundel, P. W., Potter, D., Sanders, A., Seltmann, K. C., Simpson, M. G., Wahlert, G. A., Waselkov, K., Williams, K., and Wilson, P. S. 2020. The California phenology collections network: using digital images to investigate phenological change in a biodiversity hotspot. Madro�o 66: 130141. https://doi.org/10.3120/0024-9637-66.4.130

Progress 10/01/18 to 09/30/19

Outputs
Target Audience:The target audiences for the project during this period 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 international collaborators including faculty and students from universities in various countries, several of whom have visited UC Davis for periods of several months during the review period. In addition, some of our work is focused specifically on the California flora, especially taxonomic identity and conservation status of selected species; this work is of particular interest to professional botanists associated with the California Native Plant Society, the California Department of Fish and Wildlife, county governments, and consulting firms, as well as to amateur botanists and landowners throughout the state. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?During the review period, I have served as major professor for the following graduate students: Christopher Adlam Ph.D. in progress Oscar Hinojosa Ph.D. in progress Deniss Martinez, Ph.D. in progress Rachel Spaeth, Ph.D. in progress Mark Uleh, Ph.D. in progress Chenjiao Deng, M.S. in progress Abbey Hart, M.S. in progress Angelica Saucedo, M.S. in progress The following visiting international scholars have worked with me at UC Davis in association with the project during the review period: Dr. Sheikh Saeed Ahmad, Pakistan Monica Jimenez-Rojas, Mexico Tahir Madiha, Pakistan How have the results been disseminated to communities of interest?During this review period, results have been disseminated formally through journal publications,an invited lecture at Instituto Tecnologico de Conkal, Yucatan, Merida, Mexico, presentations to students from St. Patrick - St. Vincent Catholic High School on a field trip in Vacaville and during their visits to the herbarium at UC Davis, and informally through email exchanges and telephone and in-person conversations. . What do you plan to do during the next reporting period to accomplish the goals?1) To continue to investigate species delimitations, phylogenetic relationships, and patterns of character evolution and historical biogeography in major horticultural crop plants and their wild relatives, as exemplified by our work on Rosaceae, especially Prunus. 2) To continue to investigate domestication status, genetic diversity, and geographic and phylogenetic origins of locally important tropical edible fruit crops, as exemplified by our work on Melicoccus (Sapindaceae). 3) To continue to investigate the conservation status, geographic distributions, levels of genetic diversity, and potential for hybridization with other species, of selected plant taxa native to the California Floristic Province, especially taxa considered rare, as exemplified by our past work on Juglans hindsii and current work on Sidalcea (Malvaceae). Plans for a study of the rare species Lupinus milo-bakeri, with funding from the California Department of Fish and Wildlife, are under development. We also hope to extend our study of California native walnut species to include the southern California black walnut, Juglans californica. 4) To undertake floristic surveys within California with employees and volunteers at the UC Davis Center for Plant Diversity (herbarium), in consultation and collaboration with botanists from California State Parks and the California Department of Fish and Wildlife. 5) To continue collaborative research with international visiting scholars from various countries. For example, a visiting Ph.D. student from China, Jinliang Huang, recently arrived for a 2-year stay and will be working on taxonomic and phylogenetic studies of Populus, while a postdoc. from Pakistan plans to come later this year to work on studies of Pyrus.

Impacts
What was accomplished under these goals? Research accomplishments during the review period include the following: 1. Continued contributions to understanding of the diversification and diversity of the stone-fruit genus, Prunus, especially the tropical members of subgenera Laurocerasus and Padus. A paper on the phylogeny and spatio-temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum in the Malesian region (Southeast Asia),with collaborators Jun Wen (Smithsonian Institution), Liang Zhao (Northwest A&F University, China) and several others, was published during the review period. 2. Continued study of the domestication status of the locally important crop plant `huaya India' (Melicoccus oliviformis, Sapindaceae) on the Yucatán Peninsula, a collaboration with Dr. Jaime Martinez Castíllo and others at Centro de Investigación Científica de Yucatán (CICY), Mexico, 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. Two papers on this research were published during the review period. The first one documents the morphological diversity of fruits of the species from cultivated populations in several areas of the Yucatan Peninsula. The second one incorporates ethnobotanical data on management and perceptions of the species by people in communities where it is cultivated, as well as morphological and chemical (sugars) measurements of both wild and cultivated fruits, to demonstrate that there are minimal differences in the latter, likely due to unconscious management by local people. Analyses of variation at 30 microsatellite loci are in progress in order to determine the relative extents to which the observed differences are due to environmental effects or genetic differences caused by human selection. 3. MS student Chenjiao Deng conducted analyses of DNA sequences and morphological characters of populations of a taxon of Sidalcea (Malvaceae) from serpentine soils in the North Coast range in California whose identity is uncertain. These plants are potentially assignable, based on morphology, to the federally endangered species S. keckii, otherwise known only from a few populations in the southern Sierra Nevada foothills, but they also show varying degrees of intergradation with the more widespread species S. diploscypha, suggesting that they might represent hybrids or a new species. Chenjiao's data to date suggest that the latter is most likely, but further study is needed and in progress. The work has important conservation implications. 4. A partnership with with Dr. Summer Ragosta, a botanist and environmental science teacher and Heath Bartosh, lead botanist of the Solano County Flora Project, with funding from the Toomey Foundation, in which students in Dr. Ragosta's classes at the ethnically diverse St. Patrick - St. Vincent Catholic High School in Vallejo conducted floristic surveys and plant collections in an open space area in Vacaville. A paper describing the project and its educational impact and botanical significance is in press in the journal American Biology Teacher. 5. Visiting scholar Tahir Madiha (Pakistan) conducted studies of genetic diversity of mango (Mangifera indica) varieties using microsatellite markers; data analyses are in progress. 6. Field work was conducted to collect young developing leaves of several genera of Rosaceae tribe Spiraeeae (Aruncus, Holodiscus, Kelseya, Luetkea, Petrophytum, Spiraea) with diverse leaf morphologies to be subjected to comparative transcriptomic analysis in order to investigate the genetic basis for this morphological diversity in close relatives; data generation is in progress. 7. Publication of papers resulting from past and ongoing international collaborations, especially with previous visiting scholars in the Potter lab. These include taxonomic studies of Prunus and phylogenetic studies of Artemisia (Asteraceae), Ornithogaloideae (Hyacinthaceae), and Pulsatilla (Ranunculaceae).

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhao, L., Potter, D., Xu, Y., Liu, P., Johnson, G., Chang, Z.-Y., and Wen, J. 2018. Phylogeny and spatio-temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region. Journal of Systematics and Evolution. 56: 637-651.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Hussain, A., Potter, D., Kim, S., Hayat, M. Q., and Bokhari, S. A. 2019. Molecular phylogeny of Artemisia (Asteraceae-Anthemideae) with emphasis on undescribed taxa from Gilgit-Baltistan (Pakistan) based on nrDNA (ITS and ETS) and cpDNA (psbA-trnH) sequences. Plant Ecology and Evolution 152: 507-520. https://doi.org/10.5091/plecevo.2019.1583
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Jim�nez-Rojas. M. I., Mart�nez-Castillo, J., Potter, D., Dzib, G. R., Ballina-G�mez, H. S., Latournerie-Moreno, L., and Andueza-Noh, R. H. 2019. Morphological diversity of Huaya India fruits (Melicoccus oliviformis Kunth) in the Maya Lowlands. Genetic Resources and Crop Evolution. 66: 513-522. https://doi.org/10.1007/s10722-018-00731-z..
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Wu, B., Liu, C., Potter, D., and Cui, D. 2019.Taxonomic reconsideration of Prunus veitchii. PhytoKeys, 115: 59-71. https://doi.org/10.3897/phytokeys.115.29219
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Wu, B., Potter, D., and Cui, D. 2019. The identity of Prunus dielsiana (Rosaceae). PhytoKeys. 126: 71-77. https://doi.org/10.3897/phytokeys.126.35305.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Jim�nez-Rojas. M. I., Andueza-Noh, R. H.,Mart�nez-Castillo, J., and Potter, D. 2019.Management and Cultivation of the Huaya India (Melicoccus oliviformis Kunth) on the Yucatan Peninsula. Economic Botany. https://doi.org/10.1007/s12231-019-09470-3.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Li, Q-J., Wang, X., Wang, J-R., Su, N. Zhang, L., Ma, Y., Chang, Z-Y., Zhao, L., and Potter, D. 2019. Efficient identification of Pulsatilla (Ranunculaceae) using DNA barcodes and micro-morphological characters. Frontiers in Plant Science, 10: 1196.
• Type: Journal Articles Status: Published Year Published: 2019 Citation: Riahi Rad, K., Babaei, A., Mozaffarian, V., and Potter, D. 2019. Phylogenetic affinities of wild and cultivated Ornithogaloideae based on ITS and trnL -F DNA sequences by extended sampling from Iran. Journal of Agricultural Science and Technology. 21: 1005-1021.

Progress 10/01/17 to 09/30/18

Outputs
Target Audience:The target audiences for the project during this period 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 international collaborators including faculty and students from universities in various countries, several of whom have visited UC Davis for periods of several months during the review period. In addition, our work on the conservation status of northern California black walnut (Juglans hindsii) is of particular interest to 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 review period, I have served as major professor for the following graduate students: Christopher Adlam Ph.D. in progress Oscar Hinojosa Ph.D. in progress Deniss Martinez, Ph.D. in progress Rachel Spaeth, Ph.D. in progress Mark Uleh, Ph.D. in progress Chenjiao Deng, M.S. in progress Angelica Saucedo, M.S. in progress The following visiting international scholars have worked with me at UC Davis in association with the project during the review period: Naeem Akhtar, Pakistan Adil Hussain, Pakistan Monica Jimenez-Rojas, Mexico Blandine Nacoulma, Burkina Faso Maryam Saffariha, Iran How have the results been disseminated to communities of interest?During this review period, results have been disseminated formally through publications and informally through email exchanges, telephone conversations, and discussions at research group meetings (e.g., annual the USDA Juglans Crop Germplasm Committee meetings). What do you plan to do during the next reporting period to accomplish the goals?1) To continue to investigate species delimitations, phylogenetic relationships, and patterns of character evolution and historical biogeography in major horticultural crop plants and their wild relatives, as exemplified by our work on Rosaceae, especially Prunus. 2) To continue to investigate domestication status, genetic diversity, and geographic and phylogenetic origins of locally important tropical edible fruit crops, as exemplified by our work on Melicoccus (Sapindaceae). 3) To continue to investigate the conservation status, geographic distributions, levels of genetic diversity, and potential for hybridization with other species, of selected plant taxa native to the California Floristic Province, especially taxa considered rare, as exemplified by our work on Juglans hindsii. 4) To continue to investigate the taxonomic circumscriptions, geographic distributions, and levels of genetic diversity of selected plant taxa native to the California Floristic Province, e. g., Holodiscus (Rosaceae) and Sidalcea (Malvaceae). 5) To continue collaborative research with international visiting scholars from various countries.

Impacts
What was accomplished under these goals? Research accomplishments during the review period include the following: 1. Continued contributions to understanding of the diversification and diversity of the stone-fruit genus, Prunus, especially the tropical members of subgenera Laurocerasus and Padus. Studies of genetic differentiation among four subspecies of black cherry (Prunus serotina) using microsatellite markers, conducted in collaboration with Félix Guzmán and Sergio Segura (Universidad Autónoma Chapingo, Mexico) and Malli Aradhya (USDA National Clonal Germplasm Repository, Davis) detected six clusters that did not correspond to the four named subspecies. Instead, the composition of the clusters reflected geographic structuring, suggesting gene flow between populations with geographical proximity. (Guzmán et al., 2018). A paper on the phylogeny and spatio-temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum in the Malesian region (Southeast Asia),with collaborators Jun Wen (Smithsonian Institution), Liang Zhao (Northwest A&F University, China) and several others, was submitted to the Journal of Systematics and Evolution. 2. 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 71.5% 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. Proposed revisions to conservation assessments for the species are being prepared. 3. Incipient domestication in the locally important crop plant `huaya India' (Melicoccus oliviformis, Sapindaceae) on the Yucatán Peninsula, a collaboration with Dr. Jaime Martinez Castíllo and others at Centro de Investigación Científica de Yucatán (CICY), Mexico, 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. Additional projects with UC Davis graduate students and campus colleagues, including the work of Kai Battenberg (Ph.D. 2017), co-advised with Alison Berry, who 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 (Battenberg et al., 2018).

Publications

• Type: Journal Articles Status: Published Year Published: 2018 Citation: Guzm�n , F. A., Segura, S., Aradhya, M., and Potter D. 2018. Evaluation of the genetic structure present in natural populations of four subspecies of black cherry (Prunus serotina Ehrh.) from North America using SSR markers. Scientia Horticulturae 232: 206-215.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Potter, D., Bartosh, H., Dangl, G., Yang, J., Bittman, R., and Preece, J. 2018.�Clarifying the conservation status of the northern California black walnut (Juglans hindsii) using microsatellite markers.�Madro�o 65: 131-140.
• Type: Journal Articles Status: Published Year Published: 2018 Citation: Battenberg, K., Potter, D., Chiu, J. C., and Berry, A. M. 2018.�Comparative transcriptomic analysis of two actinorhizal plants and the legume Medicago truncatula supports the homology of root nodule symbioses and is congruent with a two-step process of evolution in the nitrogen-fixing clade of angiosperms.�Frontiers in Plant Science. 9: 1256.